diff --git a/cli/cmd/workspace.go b/cli/cmd/workspace.go
index bacde5d..4733535 100644
--- a/cli/cmd/workspace.go
+++ b/cli/cmd/workspace.go
@@ -6,6 +6,7 @@ import (
 	"fmt"
 	"os"
 	"strings"
+	"time"
 
 	"github.com/anthropics/code-index/cli/internal/client"
 	"github.com/spf13/cobra"
@@ -140,17 +141,17 @@ func cmdListWorkspaces(cli *client.Client) error {
 		}
 		fmt.Println(line)
 		if wsVerbose {
-			// In verbose mode we follow each workspace with its repo
+			// In verbose mode we follow each workspace with its project
 			// count + indexed status. Two extra HTTP calls per
 			// workspace; acceptable at typical scale (<10 workspaces).
-			if reposResp, rerr := cli.ListWorkspaceRepos(w.ID); rerr == nil {
+			if pr, perr := cli.ListWorkspaceProjects(w.ID); perr == nil {
 				indexed := 0
-				for _, r := range reposResp.Repos {
-					if r.Status == "indexed" {
+				for _, wp := range pr.Projects {
+					if wp.Project.Status == "indexed" {
 						indexed++
 					}
 				}
-				fmt.Printf("       %d repos (%d indexed)\n", reposResp.Total, indexed)
+				fmt.Printf("       %d projects (%d indexed)\n", pr.Total, indexed)
 			}
 		}
 	}
@@ -166,7 +167,7 @@ func cmdListRepos(cli *client.Client, identifier string) error {
 	if err != nil {
 		return err
 	}
-	resp, err := cli.ListWorkspaceRepos(id)
+	resp, err := cli.ListWorkspaceProjects(id)
 	if err != nil {
 		return err
 	}
@@ -174,28 +175,21 @@ func cmdListRepos(cli *client.Client, identifier string) error {
 		return emitJSON(resp)
 	}
 	if resp.Total == 0 {
-		fmt.Fprintln(os.Stderr, "no repos attached — add one at /dashboard/workspaces")
+		fmt.Fprintln(os.Stderr, "no projects linked — add one at /dashboard/workspaces")
 		return nil
 	}
-	for _, r := range resp.Repos {
-		statusBadge := r.Status
-		switch r.Status {
-		case "indexed":
-			statusBadge = "✓ indexed"
-		case "failed":
-			statusBadge = "✗ failed"
-		case "cloning", "indexing", "pending":
-			statusBadge = "… " + r.Status
-		}
-		fmt.Printf("%s  %s@%s\n", statusBadge, r.GitHubURL, r.Branch)
+	for _, wp := range resp.Projects {
+		p := wp.Project
+		fmt.Printf("%s  %s\n", projectStatusBadge(p.Status), p.HostPath)
 		if wsVerbose {
-			fmt.Printf("       project: %s\n", r.ProjectPath)
-			if r.LastIndexedAt != nil {
-				fmt.Printf("       last indexed: %s\n", *r.LastIndexedAt)
+			fmt.Printf("       path_hash: %s\n", p.PathHash)
+			if p.LastIndexedAt != nil {
+				fmt.Printf("       last indexed: %s\n", p.LastIndexedAt.Format(time.RFC3339))
 			}
-			if r.LastError != nil && *r.LastError != "" {
-				fmt.Printf("       last error: %s\n", *r.LastError)
+			if len(p.Languages) > 0 {
+				fmt.Printf("       languages: %s\n", strings.Join(p.Languages, ", "))
 			}
+			fmt.Printf("       linked: %s\n", wp.AddedAt.Format(time.RFC3339))
 		}
 	}
 	return nil
@@ -221,7 +215,7 @@ func cmdDescribeWorkspace(cli *client.Client, identifier string) error {
 	if ws == nil {
 		return fmt.Errorf("workspace %q not found (run `cix ws list`)", identifier)
 	}
-	reposResp, err := cli.ListWorkspaceRepos(ws.ID)
+	projResp, err := cli.ListWorkspaceProjects(ws.ID)
 	if err != nil {
 		return err
 	}
@@ -229,8 +223,8 @@ func cmdDescribeWorkspace(cli *client.Client, identifier string) error {
 	if wsJSON {
 		return emitJSON(map[string]any{
 			"workspace": ws,
-			"repos":     reposResp.Repos,
-			"total":     reposResp.Total,
+			"projects":  projResp.Projects,
+			"total":     projResp.Total,
 		})
 	}
 
@@ -240,39 +234,62 @@ func cmdDescribeWorkspace(cli *client.Client, identifier string) error {
 		fmt.Printf("  description: %s\n", ws.Description)
 	}
 	indexed := 0
-	for _, r := range reposResp.Repos {
-		if r.Status == "indexed" {
+	for _, wp := range projResp.Projects {
+		if wp.Project.Status == "indexed" {
 			indexed++
 		}
 	}
-	fmt.Printf("  repos: %d (%d indexed)\n", reposResp.Total, indexed)
-	if reposResp.Total == 0 {
-		fmt.Fprintln(os.Stderr, "\n  (no repos attached — add at /dashboard/workspaces)")
+	fmt.Printf("  projects: %d (%d indexed)\n", projResp.Total, indexed)
+	if projResp.Total == 0 {
+		fmt.Fprintln(os.Stderr, "\n  (no projects linked — add at /dashboard/workspaces)")
 		return nil
 	}
 	fmt.Println()
-	for _, r := range reposResp.Repos {
-		statusBadge := r.Status
-		switch r.Status {
-		case "indexed":
-			statusBadge = "✓"
-		case "failed":
-			statusBadge = "✗"
-		default:
-			statusBadge = "…"
-		}
-		fmt.Printf("  %s  %s@%s\n", statusBadge, r.GitHubURL, r.Branch)
-		fmt.Printf("     project: %s\n", r.ProjectPath)
-		if r.LastIndexedAt != nil {
-			fmt.Printf("     last indexed: %s\n", *r.LastIndexedAt)
-		}
-		if r.LastError != nil && *r.LastError != "" {
-			fmt.Printf("     last error: %s\n", *r.LastError)
+	for _, wp := range projResp.Projects {
+		p := wp.Project
+		fmt.Printf("  %s  %s\n", projectStatusBadgeShort(p.Status), p.HostPath)
+		fmt.Printf("     path_hash: %s\n", p.PathHash)
+		if p.LastIndexedAt != nil {
+			fmt.Printf("     last indexed: %s\n", p.LastIndexedAt.Format(time.RFC3339))
 		}
+		fmt.Printf("     linked: %s\n", wp.AddedAt.Format(time.RFC3339))
 	}
 	return nil
 }
 
+// projectStatusBadge renders the long status form used by
+// `cix ws <name> list`. The new wire enum (post-split) is:
+//
+//	created | indexing | indexed | error
+//
+// Unknown values fall through to the literal string so future enum
+// additions render readably without crashing the CLI.
+func projectStatusBadge(status string) string {
+	switch status {
+	case "indexed":
+		return "✓ indexed"
+	case "error":
+		return "✗ error"
+	case "indexing", "created":
+		return "… " + status
+	default:
+		return status
+	}
+}
+
+// projectStatusBadgeShort renders the single-glyph badge used by the
+// describe view's per-project bullet list.
+func projectStatusBadgeShort(status string) string {
+	switch status {
+	case "indexed":
+		return "✓"
+	case "error":
+		return "✗"
+	default:
+		return "…"
+	}
+}
+
 // ---------------------------------------------------------------------------
 // `cix ws <name> search <query>`
 // ---------------------------------------------------------------------------
diff --git a/cli/cmd/workspace_test.go b/cli/cmd/workspace_test.go
new file mode 100644
index 0000000..ea0c979
--- /dev/null
+++ b/cli/cmd/workspace_test.go
@@ -0,0 +1,348 @@
+package cmd
+
+import (
+	"net/http"
+	"strings"
+	"testing"
+)
+
+// TestListWorkspaceProjects_DecodesPayload locks the acceptance from
+// docs/code-review-workspaces-link-local-projects.md (Fix #1, line 284):
+// after the rewrite, `cix ws <name> list` must return 200 and render a
+// readable list with status badges. We also assert the absence of the
+// literal "@undefined" — the regression that broke the dashboard side
+// of this contract per Fix #2.
+func TestListWorkspaceProjects_DecodesPayload(t *testing.T) {
+	srv := mockServer(t, defaultWorkspaceHandler())
+	useAPI(t, srv)
+
+	cli, err := getClient()
+	if err != nil {
+		t.Fatalf("getClient: %v", err)
+	}
+
+	prevVerbose := wsVerbose
+	wsVerbose = true
+	t.Cleanup(func() { wsVerbose = prevVerbose })
+
+	out, err := captureOutput(func() error { return cmdListRepos(cli, "platform") })
+	if err != nil {
+		t.Fatalf("cmdListRepos: %v", err)
+	}
+
+	// Status badges per the new enum.
+	if !strings.Contains(out, "✓ indexed") {
+		t.Errorf("expected '✓ indexed' badge, got:\n%s", out)
+	}
+	if !strings.Contains(out, "… indexing") {
+		t.Errorf("expected '… indexing' badge, got:\n%s", out)
+	}
+
+	// Host-paths render directly — github form already carries @branch.
+	if !strings.Contains(out, "github.com/owner/repo@main") {
+		t.Errorf("expected github host_path with @branch, got:\n%s", out)
+	}
+	if !strings.Contains(out, "/Users/me/local-proj") {
+		t.Errorf("expected local host_path, got:\n%s", out)
+	}
+
+	// Verbose extras for the indexed row.
+	if !strings.Contains(out, "path_hash: a1b2c3d4e5f60718") {
+		t.Errorf("expected path_hash in verbose output, got:\n%s", out)
+	}
+	if !strings.Contains(out, "last indexed: 2026-05-14T12:30:45Z") {
+		t.Errorf("expected RFC3339 last_indexed in verbose output, got:\n%s", out)
+	}
+	if !strings.Contains(out, "languages: go, typescript") {
+		t.Errorf("expected languages line for indexed row, got:\n%s", out)
+	}
+
+	// Regression canary — Fix #2 dashboard bug rendered the literal
+	// "@undefined" because branch came from a missing field. The CLI
+	// equivalent must never print that.
+	if strings.Contains(out, "@undefined") || strings.Contains(out, "undefined") {
+		t.Errorf("unexpected 'undefined' in output:\n%s", out)
+	}
+}
+
+// TestListWorkspaces_VerboseProjectCount covers the silent-fail path
+// that broke `cix ws list -v` — it used to swallow 404s from the deleted
+// /repos endpoint and just omit the count row. After the fix the verbose
+// row must reappear with the new "projects" terminology.
+func TestListWorkspaces_VerboseProjectCount(t *testing.T) {
+	srv := mockServer(t, defaultWorkspaceHandler())
+	useAPI(t, srv)
+
+	cli, err := getClient()
+	if err != nil {
+		t.Fatalf("getClient: %v", err)
+	}
+
+	prevVerbose := wsVerbose
+	wsVerbose = true
+	t.Cleanup(func() { wsVerbose = prevVerbose })
+
+	out, err := captureOutput(func() error { return cmdListWorkspaces(cli) })
+	if err != nil {
+		t.Fatalf("cmdListWorkspaces: %v", err)
+	}
+
+	if !strings.Contains(out, "2 projects (1 indexed)") {
+		t.Errorf("expected '2 projects (1 indexed)' verbose count, got:\n%s", out)
+	}
+	// Sanity: the old wording must not leak back.
+	if strings.Contains(out, "repos (") {
+		t.Errorf("unexpected old 'repos (...)' wording in output:\n%s", out)
+	}
+}
+
+// TestListWorkspaceProjects_ServiceUnavailable locks in the
+// CIX_WORKSPACES_ENABLED=false → 503 path. The CLI must surface a
+// helpful error rather than crash or hang.
+func TestListWorkspaceProjects_ServiceUnavailable(t *testing.T) {
+	srv := mockServer(t, func(w http.ResponseWriter, r *http.Request) {
+		switch r.URL.Path {
+		case "/api/v1/workspaces":
+			writeJSON(w, 200, map[string]any{
+				"workspaces": []map[string]any{{"id": "ws_1", "name": "platform"}},
+				"total":      1,
+			})
+		case "/api/v1/workspaces/ws_1/projects":
+			apiError(w, http.StatusServiceUnavailable,
+				"workspaces feature is disabled (set CIX_WORKSPACES_ENABLED=true and restart)")
+		default:
+			http.NotFound(w, r)
+		}
+	})
+	useAPI(t, srv)
+
+	cli, err := getClient()
+	if err != nil {
+		t.Fatalf("getClient: %v", err)
+	}
+
+	_, err = captureOutput(func() error { return cmdListRepos(cli, "platform") })
+	if err == nil {
+		t.Fatal("expected error on 503, got nil")
+	}
+	if !strings.Contains(err.Error(), "503") || !strings.Contains(err.Error(), "disabled") {
+		t.Errorf("expected error to mention 503 + 'disabled', got: %v", err)
+	}
+}
+
+// TestDescribeWorkspace_ByCaseInsensitiveName exercises the
+// describe path that lives separately from `resolveWorkspaceID` (it has
+// its own inline name-match loop) and confirms mixed-case lookup works.
+func TestDescribeWorkspace_ByCaseInsensitiveName(t *testing.T) {
+	srv := mockServer(t, defaultWorkspaceHandler())
+	useAPI(t, srv)
+
+	cli, err := getClient()
+	if err != nil {
+		t.Fatalf("getClient: %v", err)
+	}
+
+	out, err := captureOutput(func() error { return cmdDescribeWorkspace(cli, "PLATFORM") })
+	if err != nil {
+		t.Fatalf("cmdDescribeWorkspace: %v", err)
+	}
+
+	if !strings.Contains(out, "Workspace: platform") {
+		t.Errorf("expected workspace header, got:\n%s", out)
+	}
+	if !strings.Contains(out, "projects: 2 (1 indexed)") {
+		t.Errorf("expected per-workspace project count line, got:\n%s", out)
+	}
+	if !strings.Contains(out, "github.com/owner/repo@main") {
+		t.Errorf("expected indexed project's host_path in describe output, got:\n%s", out)
+	}
+	if !strings.Contains(out, "path_hash: a1b2c3d4e5f60718") {
+		t.Errorf("expected path_hash in describe output, got:\n%s", out)
+	}
+}
+
+// TestListWorkspaces_ParsesEmpty pins the empty-server response path —
+// the CLI must handle `{"workspaces": [], "total": 0}` cleanly: no
+// error, no spurious lines on stdout, and (silently here, on stderr in
+// real use) an operator-friendly hint pointing at the dashboard. Fix #17
+// minimum #1.
+func TestListWorkspaces_ParsesEmpty(t *testing.T) {
+	srv := mockServer(t, func(w http.ResponseWriter, r *http.Request) {
+		if r.URL.Path == "/api/v1/workspaces" {
+			writeJSON(w, 200, map[string]any{
+				"workspaces": []map[string]any{},
+				"total":      0,
+			})
+			return
+		}
+		http.NotFound(w, r)
+	})
+	useAPI(t, srv)
+
+	cli, err := getClient()
+	if err != nil {
+		t.Fatalf("getClient: %v", err)
+	}
+
+	out, err := captureOutput(func() error { return cmdListWorkspaces(cli) })
+	if err != nil {
+		t.Fatalf("cmdListWorkspaces on empty list: %v", err)
+	}
+	// captureOutput only watches stdout; the "no workspaces — create one
+	// at …" hint goes to stderr in the real binary. Stdout must be empty
+	// so a future regression that accidentally prints a header row (or a
+	// stray "0 workspaces" line) trips this assertion.
+	if out != "" {
+		t.Errorf("expected empty stdout for 0 workspaces, got: %q", out)
+	}
+}
+
+// TestProjectStatusBadge — exhaustive per-status formatting check for
+// the two badge helpers. Fix #17 minimum #2: a future renumber of the
+// status enum (e.g. dropping 'created' or adding 'archived') must trip
+// at least one of these table rows. Direct unit test bypasses the HTTP
+// harness — the two functions are pure mappings.
+func TestProjectStatusBadge(t *testing.T) {
+	cases := []struct {
+		in    string
+		long  string
+		short string
+	}{
+		{"indexed", "✓ indexed", "✓"},
+		{"indexing", "… indexing", "…"},
+		{"created", "… created", "…"},
+		{"error", "✗ error", "✗"},
+		// Default-arm coverage: unknown future statuses must surface
+		// verbatim (long) and degrade to the "still working" glyph
+		// (short) rather than crash or panic. This protects forward
+		// compatibility — the CLI should render whatever the server
+		// returns, not gate on the enum.
+		{"archived", "archived", "…"},
+	}
+	for _, c := range cases {
+		if got := projectStatusBadge(c.in); got != c.long {
+			t.Errorf("projectStatusBadge(%q) = %q, want %q", c.in, got, c.long)
+		}
+		if got := projectStatusBadgeShort(c.in); got != c.short {
+			t.Errorf("projectStatusBadgeShort(%q) = %q, want %q", c.in, got, c.short)
+		}
+	}
+}
+
+// TestResolveWorkspaceID_ByName covers Fix #17 minimum #3. The shared
+// resolver supports three ways to address a workspace: exact ID, exact
+// name (case-sensitive), and case-insensitive name match. Unknown
+// identifiers must return an error mentioning the input so the user
+// can correct the typo. Distinct from
+// TestDescribeWorkspace_ByCaseInsensitiveName, which exercises the
+// describe-command's inline name-match loop — this one hits the
+// resolveWorkspaceID function used by `cix ws <name> list/repos`.
+func TestResolveWorkspaceID_ByName(t *testing.T) {
+	srv := mockServer(t, func(w http.ResponseWriter, r *http.Request) {
+		if r.URL.Path == "/api/v1/workspaces" {
+			writeJSON(w, 200, map[string]any{
+				"workspaces": []map[string]any{
+					{"id": "ws_alpha", "name": "platform"},
+					{"id": "ws_beta", "name": "ML-Pipeline"},
+				},
+				"total": 2,
+			})
+			return
+		}
+		http.NotFound(w, r)
+	})
+	useAPI(t, srv)
+	cli, err := getClient()
+	if err != nil {
+		t.Fatalf("getClient: %v", err)
+	}
+
+	cases := []struct {
+		in      string
+		wantID  string
+		wantErr bool
+	}{
+		{"platform", "ws_alpha", false},   // exact name match
+		{"PLATFORM", "ws_alpha", false},   // upper-case name match
+		{"PlatForm", "ws_alpha", false},   // mixed-case name match
+		{"ml-pipeline", "ws_beta", false}, // case-insensitive on hyphenated name
+		{"ML-PIPELINE", "ws_beta", false}, // upper-case variant
+		{"ws_alpha", "ws_alpha", false},   // exact ID match
+		{"nonexistent", "", true},         // not found → error
+	}
+	for _, c := range cases {
+		got, err := resolveWorkspaceID(cli, c.in)
+		if c.wantErr {
+			if err == nil {
+				t.Errorf("resolveWorkspaceID(%q): expected error, got id=%q", c.in, got)
+				continue
+			}
+			if !strings.Contains(err.Error(), c.in) {
+				t.Errorf("resolveWorkspaceID(%q): error should mention input, got: %v", c.in, err)
+			}
+			continue
+		}
+		if err != nil {
+			t.Errorf("resolveWorkspaceID(%q): unexpected error: %v", c.in, err)
+			continue
+		}
+		if got != c.wantID {
+			t.Errorf("resolveWorkspaceID(%q) = %q, want %q", c.in, got, c.wantID)
+		}
+	}
+}
+
+// defaultWorkspaceHandler returns the standard 2-project fixture used
+// by every test in this file. Factored out to avoid copy-pasting the
+// JSON literal across handlers.
+func defaultWorkspaceHandler() http.HandlerFunc {
+	return func(w http.ResponseWriter, r *http.Request) {
+		switch r.URL.Path {
+		case "/api/v1/workspaces":
+			writeJSON(w, 200, map[string]any{
+				"workspaces": []map[string]any{
+					{"id": "ws_1", "name": "platform", "description": "core platform repos"},
+				},
+				"total": 1,
+			})
+		case "/api/v1/workspaces/ws_1/projects":
+			writeJSON(w, 200, map[string]any{
+				"projects": []map[string]any{
+					{
+						"added_at": "2026-05-10T08:15:00Z",
+						"project": map[string]any{
+							"path_hash":       "a1b2c3d4e5f60718",
+							"host_path":       "github.com/owner/repo@main",
+							"container_path":  "/code/owner/repo",
+							"languages":       []string{"go", "typescript"},
+							"settings":        map[string]any{"exclude_patterns": []string{}, "max_file_size": 524288},
+							"stats":           map[string]any{"total_files": 50, "indexed_files": 50, "total_chunks": 200, "total_symbols": 30},
+							"status":          "indexed",
+							"created_at":      "2026-05-01T00:00:00Z",
+							"updated_at":      "2026-05-14T12:30:45Z",
+							"last_indexed_at": "2026-05-14T12:30:45Z",
+						},
+					},
+					{
+						"added_at": "2026-05-11T09:00:00Z",
+						"project": map[string]any{
+							"path_hash":       "7f3e2c1a0d4b5e69",
+							"host_path":       "/Users/me/local-proj",
+							"container_path":  "/Users/me/local-proj",
+							"languages":       []string{},
+							"settings":        map[string]any{"exclude_patterns": []string{}, "max_file_size": 524288},
+							"stats":           map[string]any{"total_files": 0, "indexed_files": 0, "total_chunks": 0, "total_symbols": 0},
+							"status":          "indexing",
+							"created_at":      "2026-05-11T08:55:00Z",
+							"updated_at":      "2026-05-11T09:00:00Z",
+							"last_indexed_at": nil,
+						},
+					},
+				},
+				"total": 2,
+			})
+		default:
+			http.NotFound(w, r)
+		}
+	}
+}
diff --git a/cli/internal/client/projects.go b/cli/internal/client/projects.go
index af70475..1278236 100644
--- a/cli/internal/client/projects.go
+++ b/cli/internal/client/projects.go
@@ -7,15 +7,21 @@ import (
 
 // Project represents a code project
 type Project struct {
-	HostPath      string            `json:"host_path"`
-	ContainerPath string            `json:"container_path"`
-	Languages     []string          `json:"languages"`
-	Settings      ProjectSettings   `json:"settings"`
-	Stats         ProjectStats      `json:"stats"`
-	Status        string            `json:"status"` // created, indexing, indexed, error
-	CreatedAt     time.Time         `json:"created_at"`
-	UpdatedAt     time.Time         `json:"updated_at"`
-	LastIndexedAt *time.Time        `json:"last_indexed_at"`
+	PathHash         string          `json:"path_hash"`
+	HostPath         string          `json:"host_path"`
+	ContainerPath    string          `json:"container_path"`
+	Languages        []string        `json:"languages"`
+	Settings         ProjectSettings `json:"settings"`
+	Stats            ProjectStats    `json:"stats"`
+	Status           string          `json:"status"` // created, indexing, indexed, error
+	CreatedAt        time.Time       `json:"created_at"`
+	UpdatedAt        time.Time       `json:"updated_at"`
+	LastIndexedAt    *time.Time      `json:"last_indexed_at"`
+	IndexedWithModel *string         `json:"indexed_with_model,omitempty"`
+	SqlitePath       *string         `json:"sqlite_path,omitempty"`
+	SqliteSizeBytes  *int64          `json:"sqlite_size_bytes,omitempty"`
+	ChromaPath       *string         `json:"chroma_path,omitempty"`
+	ChromaSizeBytes  *int64          `json:"chroma_size_bytes,omitempty"`
 }
 
 type ProjectSettings struct {
diff --git a/cli/internal/client/workspace.go b/cli/internal/client/workspace.go
index a3be475..1d979ec 100644
--- a/cli/internal/client/workspace.go
+++ b/cli/internal/client/workspace.go
@@ -3,6 +3,7 @@ package client
 import (
 	"fmt"
 	"net/url"
+	"time"
 )
 
 // WorkspaceSearchProject mirrors the OpenAPI WorkspaceSearchProject
@@ -57,28 +58,18 @@ type WorkspaceListResponse struct {
 	Total      int         `json:"total"`
 }
 
-// WorkspaceRepo mirrors the server's WorkspaceRepo payload — every
-// field the dashboard or `cix ws <name> list` would display.
-type WorkspaceRepo struct {
-	ID            string  `json:"id"`
-	WorkspaceID   string  `json:"workspace_id"`
-	GitHubURL     string  `json:"github_url"`
-	Branch        string  `json:"branch"`
-	ProjectPath   string  `json:"project_path"`
-	TokenID       *string `json:"token_id,omitempty"`
-	AutoWebhook   bool    `json:"auto_webhook"`
-	Status        string  `json:"status"`
-	LastSHA       *string `json:"last_sha,omitempty"`
-	LastError     *string `json:"last_error,omitempty"`
-	LastIndexedAt *string `json:"last_indexed_at,omitempty"`
-	CreatedAt     string  `json:"created_at"`
-	UpdatedAt     string  `json:"updated_at"`
+// WorkspaceProject mirrors the server's WorkspaceProject — the embedded
+// project (full Project shape, defined in projects.go) plus the
+// membership-added timestamp.
+type WorkspaceProject struct {
+	AddedAt time.Time `json:"added_at"`
+	Project Project   `json:"project"`
 }
 
-// WorkspaceRepoListResponse is the GET /workspaces/{id}/repos shape.
-type WorkspaceRepoListResponse struct {
-	Repos []WorkspaceRepo `json:"repos"`
-	Total int             `json:"total"`
+// WorkspaceProjectListResponse is the GET /workspaces/{id}/projects shape.
+type WorkspaceProjectListResponse struct {
+	Projects []WorkspaceProject `json:"projects"`
+	Total    int                `json:"total"`
 }
 
 // ListWorkspaces — GET /api/v1/workspaces. Returns
@@ -96,16 +87,17 @@ func (c *Client) ListWorkspaces() (*WorkspaceListResponse, error) {
 	return &out, nil
 }
 
-// ListWorkspaceRepos — GET /api/v1/workspaces/{id}/repos. Returns
-// every attached repo with its current status (pending / cloning /
-// indexing / indexed / failed) so the CLI can render a readable
-// per-repo summary.
-func (c *Client) ListWorkspaceRepos(workspaceID string) (*WorkspaceRepoListResponse, error) {
-	resp, err := c.do("GET", "/api/v1/workspaces/"+url.PathEscape(workspaceID)+"/repos", nil)
+// ListWorkspaceProjects — GET /api/v1/workspaces/{id}/projects. Returns
+// every linked project with its current status (created / indexing /
+// indexed / error), host path, path hash, and membership timestamp so
+// the CLI can render a readable per-project summary without a second
+// round-trip.
+func (c *Client) ListWorkspaceProjects(workspaceID string) (*WorkspaceProjectListResponse, error) {
+	resp, err := c.do("GET", "/api/v1/workspaces/"+url.PathEscape(workspaceID)+"/projects", nil)
 	if err != nil {
 		return nil, err
 	}
-	var out WorkspaceRepoListResponse
+	var out WorkspaceProjectListResponse
 	if err := parseResponse(resp, &out); err != nil {
 		return nil, err
 	}
diff --git a/doc/WORKSPACES.md b/doc/WORKSPACES.md
index 1ae0131..72e21a9 100644
--- a/doc/WORKSPACES.md
+++ b/doc/WORKSPACES.md
@@ -28,9 +28,9 @@ and troubleshoot the feature in production.
    branch, optional token, and choose **Auto-register webhook** if
    your PAT carries `admin:repo_hook`. Otherwise check **I'll set it
    up myself** and copy the displayed URL + secret into GitHub.
-6. The server clones the repo into `<CIX_WORKSPACES_DATA_DIR>/<repo_id>/`
+6. The server clones the repo into `<CIX_WORKSPACES_DATA_DIR>/<path_hash>/`
    and runs the existing indexer pipeline against it. Status transitions
-   visible on the workspace detail page: `pending → cloning → indexing → indexed`.
+   visible on the workspace detail page: `created → indexing → indexed`.
 
 ## Environment variables
 
@@ -62,11 +62,11 @@ convenience for dev.
 
 ## Webhooks
 
-GitHub deliveries hit `POST /api/v1/webhooks/github/<workspace_repo_id>`.
+GitHub deliveries hit `POST /api/v1/webhooks/github/<path_hash>`.
 The endpoint is **public** in the auth sense (no Bearer/session check)
 but every delivery is HMAC-SHA256-validated against the per-row
-`webhook_secret`. The secret is shown exactly once on add-repo and on
-**Workspaces → Repo → Webhook info**.
+`webhook_secret` stored on the matching `git_repos` row. The secret is
+shown exactly once on add-repo and on **Project → Webhook info**.
 
 Supported events:
 
@@ -115,7 +115,7 @@ production but perfect for the first end-to-end smoke test.
 
 ### Manual webhook setup
 
-If `auto_webhook=false` (default) the dashboard surfaces the URL + secret
+If `webhook_mode=manual` (default) the dashboard surfaces the URL + secret
 after add-repo. Paste them into GitHub:
 
 1. Repo → **Settings → Webhooks → Add webhook**
@@ -130,12 +130,12 @@ GitHub's webhook page will mark the delivery green.
 
 ### Auto-register
 
-When the PAT carries `admin:repo_hook` scope and `auto_webhook=true`,
-the server calls `POST /repos/{owner}/{repo}/hooks` on your behalf
-during add-repo and persists the resulting hook id (used to
-de-register on delete). Failure is non-fatal — the response includes
-`auto_registered: false` and an operator-facing note explaining the
-specific reason (missing scope, network error, etc.).
+When the PAT carries `admin:repo_hook` scope and `webhook_mode=auto`,
+the server uses GitHub's hooks API on your behalf during add-repo and
+persists the resulting hook id (used to de-register on delete). Failure
+is non-fatal — the response includes `auto_registered: false` and an
+operator-facing note explaining the specific reason (missing scope,
+network error, etc.).
 
 ## Background workers
 
@@ -157,17 +157,17 @@ Future PRs add `build_call_graph` and `compute_workspace_communities`.
 
 ## Troubleshooting
 
-- **Status stuck at `cloning`** — check `GET /jobs?status=running` and
+- **Status stuck at `indexing`** — check `GET /jobs?status=running` and
   the cix-server logs. Most common cause: PAT missing `repo` scope on
   a private repo, or network not reaching github.com.
-- **Status stuck at `failed`** with `last_error` set — the message
-  comes directly from go-git or the indexer. Common fixes: rotate the
-  PAT, confirm the branch name, verify the runtime model is loaded
+- **Status stuck at `error`** — the underlying job's error message is
+  surfaced on the project detail page. Common fixes: rotate the PAT,
+  confirm the branch name, verify the runtime model is loaded
   (`GET /api/v1/admin/sidecar/status`).
 - **Webhook deliveries returning 401** — the secret in GitHub doesn't
   match what cix stored. Click **Webhook info** in the dashboard to
   see the canonical value, paste again. Secrets rotate when the
-  workspace_repo is recreated.
+  git_repos row is recreated.
 - **Encryption key mismatch on startup** — operator-readable error in
   the boot log. Recover the prior `CIX_SECRET_KEY` from your secrets
   manager or wipe `github_tokens` manually before retrying.
diff --git a/doc/openapi.yaml b/doc/openapi.yaml
index 4990567..c4585e1 100644
--- a/doc/openapi.yaml
+++ b/doc/openapi.yaml
@@ -733,8 +733,8 @@ paths:
         the user can click to jump to the workspace detail page.
 
         Empty list when the project isn't part of any workspace yet —
-        either it was indexed directly via /projects rather than via a
-        workspace_repo, or all its memberships have been detached.
+        either it was indexed directly via /projects without ever being
+        linked, or all its memberships have been detached.
       responses:
         "200":
           description: Memberships
@@ -1237,9 +1237,11 @@ paths:
       tags: [workspaces]
       summary: Delete a workspace
       description: |
-        Removes the workspace row. PR1 has nothing else to cascade
-        (workspace_repos lands in PR2); future PRs will cascade repos,
-        communities, and the centroid Chroma collection.
+        Removes the workspace row. workspace_projects memberships
+        referencing this workspace are removed via ON DELETE CASCADE;
+        the underlying projects, git_repos peers, and on-disk clones
+        are preserved (delete those explicitly via /projects/{path}
+        when desired).
       responses:
         "204":
           description: Deleted
@@ -1250,66 +1252,38 @@ paths:
         "503":
           $ref: "#/components/responses/WorkspacesDisabled"
 
-  /api/v1/workspaces/{id}/repos:
-    parameters:
-      - name: id
-        in: path
-        required: true
-        schema:
-          type: string
-        description: Workspace ID.
-    get:
-      operationId: listWorkspaceRepos
-      tags: [workspaces]
-      summary: List repositories attached to a workspace
-      responses:
-        "200":
-          description: Repo list
-          content:
-            application/json:
-              schema:
-                $ref: "#/components/schemas/WorkspaceRepoListResponse"
-        "401":
-          $ref: "#/components/responses/Unauthorized"
-        "404":
-          $ref: "#/components/responses/NotFound"
-        "503":
-          $ref: "#/components/responses/WorkspacesDisabled"
+  /api/v1/git-repos:
     post:
-      operationId: addWorkspaceRepo
-      tags: [workspaces]
-      summary: Attach a GitHub repository to a workspace
+      operationId: addGitRepo
+      tags: [projects]
+      summary: Clone + index a GitHub repository as a standalone project
       description: |
-        Inserts a workspace_repos row in status `pending` and enqueues a
-        `clone_repo` background job. The clone job is followed by an
-        `index_repo` job on success; the dashboard polls
-        `/api/v1/workspaces/{id}/repos` to surface status transitions.
-
-        Provide `token_id` to clone a private repository. The
-        `auto_webhook` flag is accepted in PR2 but not yet acted upon —
-        PR3 wires the auto-register path against the GitHub API.
-
-        The response includes a one-shot `webhook_url` + `webhook_secret`
-        so an operator can manually register the webhook in GitHub if
-        `auto_webhook` is false. The secret is also returned by the
-        webhook-info endpoint added in PR3.
+        Inserts a projects row (status=pending), a matching git_repos
+        row, and enqueues a `clone_repo` background job that is chained
+        to an `index_repo` job on success. The resulting project lives
+        in `/api/v1/projects` and is initially attached to no
+        workspaces — link it into specific workspaces via
+        `/api/v1/workspaces/{id}/projects` if desired.
+
+        `token_id` is required for private repos; `webhook_mode`
+        defaults to `manual`. The response carries a one-shot
+        `webhook_url` + `webhook_secret` so the operator can register
+        the webhook in GitHub by hand (`auto` mode does it for them).
       requestBody:
         required: true
         content:
           application/json:
             schema:
-              $ref: "#/components/schemas/AddWorkspaceRepoRequest"
+              $ref: "#/components/schemas/AddGitRepoRequest"
       responses:
         "201":
-          description: Repo attached + clone enqueued
+          description: Project created + clone enqueued
           content:
             application/json:
               schema:
-                $ref: "#/components/schemas/WorkspaceRepoCreated"
+                $ref: "#/components/schemas/GitRepoCreated"
         "401":
           $ref: "#/components/responses/Unauthorized"
-        "404":
-          $ref: "#/components/responses/NotFound"
         "409":
           $ref: "#/components/responses/Conflict"
         "422":
@@ -1317,47 +1291,53 @@ paths:
         "503":
           $ref: "#/components/responses/WorkspacesDisabled"
 
-  /api/v1/workspaces/{id}/repos/link:
+  /api/v1/workspaces/{id}/projects:
     parameters:
       - name: id
         in: path
         required: true
         schema:
           type: string
+        description: Workspace ID.
+    get:
+      operationId: listWorkspaceProjects
+      tags: [workspaces]
+      summary: List projects currently linked to a workspace
+      responses:
+        "200":
+          description: Workspace project list
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/WorkspaceProjectListResponse"
+        "401":
+          $ref: "#/components/responses/Unauthorized"
+        "404":
+          $ref: "#/components/responses/NotFound"
+        "503":
+          $ref: "#/components/responses/WorkspacesDisabled"
     post:
-      operationId: linkExistingProject
+      operationId: linkProjectToWorkspace
       tags: [workspaces]
-      summary: Attach an already-indexed project to a workspace
+      summary: Link an existing project into this workspace
       description: |
-        Inserts a workspace_repos row marked `is_linked=true` pointing at
-        an existing indexed project. No clone happens, no index job is
-        enqueued, no GitHub webhook is registered — the row is a
-        lightweight membership pointer so workspace-level features
-        (search, communities, the repo list) include the project.
-
-        The project's `host_path` must be of the form
-        "github.com/owner/repo@branch" (i.e. created from a GitHub
-        source) and the project must be in `status='indexed'`. Per-
-        workspace uniqueness is enforced via the same composite UNIQUE
-        as the regular Add Repo flow — a project already in this
-        workspace (owned or linked) returns 409.
-
-        Use this when the user wants to bring an existing repo from
-        workspace A into workspace B without paying the clone+index
-        cost twice.
+        Inserts a (workspace_id, project_path) row into
+        `workspace_projects`. The project must already exist and be in
+        `status='indexed'`. Duplicates return 409. The project itself
+        is untouched — workspaces are pure membership collections.
       requestBody:
         required: true
         content:
           application/json:
             schema:
-              $ref: "#/components/schemas/LinkExistingProjectRequest"
+              $ref: "#/components/schemas/LinkProjectRequest"
       responses:
         "201":
           description: Linked
           content:
             application/json:
               schema:
-                $ref: "#/components/schemas/WorkspaceRepoCreated"
+                $ref: "#/components/schemas/WorkspaceProjectMembership"
         "401":
           $ref: "#/components/responses/Unauthorized"
         "404":
@@ -1369,30 +1349,30 @@ paths:
         "503":
           $ref: "#/components/responses/WorkspacesDisabled"
 
-  /api/v1/workspaces/{id}/repos/{repo_id}:
+  /api/v1/workspaces/{id}/projects/{hash}:
     parameters:
       - name: id
         in: path
         required: true
         schema:
           type: string
-      - name: repo_id
+      - name: hash
         in: path
         required: true
         schema:
           type: string
+        description: Project's path_hash.
     delete:
-      operationId: deleteWorkspaceRepo
+      operationId: unlinkProjectFromWorkspace
       tags: [workspaces]
-      summary: Detach a repository from a workspace
+      summary: Remove a project from this workspace (does not delete the project)
       description: |
-        Removes the workspace_repos row. The cloned directory on disk and
-        the indexed project rows remain — a follow-up cleanup job lands
-        in a later release. PR3 will also de-register the GitHub webhook
-        when auto_webhook=true.
+        Drops the (workspace_id, project_path) row. The project itself,
+        its clone on disk, its indexed content, and its memberships in
+        other workspaces are all untouched.
       responses:
         "204":
-          description: Detached
+          description: Unlinked
         "401":
           $ref: "#/components/responses/Unauthorized"
         "404":
@@ -1487,27 +1467,58 @@ paths:
         "503":
           $ref: "#/components/responses/WorkspacesDisabled"
 
-  /api/v1/workspaces/{id}/repos/{repo_id}/webhook-info:
+  /api/v1/projects/{hash}/git-repo:
     parameters:
-      - name: id
+      - name: hash
         in: path
         required: true
         schema:
           type: string
-      - name: repo_id
+    get:
+      operationId: getProjectGitRepo
+      tags: [projects]
+      summary: Read the git_repos metadata for an external project
+      description: |
+        Returns clone + webhook metadata. 404 when the project is local
+        (has no git_repos row). The webhook_secret is included so the
+        operator can paste it into GitHub Settings → Webhooks.
+      responses:
+        "200":
+          description: git_repos row
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/GitRepo"
+        "401":
+          $ref: "#/components/responses/Unauthorized"
+        "404":
+          $ref: "#/components/responses/NotFound"
+        "503":
+          $ref: "#/components/responses/WorkspacesDisabled"
+
+  /api/v1/projects/{hash}/webhook-info:
+    parameters:
+      - name: hash
         in: path
         required: true
         schema:
           type: string
     get:
-      operationId: getWorkspaceRepoWebhookInfo
-      tags: [workspaces]
-      summary: Get the webhook URL + secret for manual GitHub setup
+      operationId: getProjectWebhookInfo
+      tags: [projects]
+      summary: Webhook URL + secret for manual GitHub setup
       description: |
-        Returns the publicly-reachable webhook URL and the HMAC secret.
-        Pair this with GitHub Settings → Webhooks when `auto_webhook` is
-        false. The secret rotates if the workspace_repo is deleted and
-        re-attached.
+        Returns the publicly-reachable webhook URL and the HMAC secret
+        for an external (GitHub-cloned) project. Only projects with a
+        `git_repos` peer participate in webhook delivery — local-path
+        projects have no clone lifecycle and no webhook.
+
+        The handler returns 404 in two distinct cases, indistinguishable
+        on the wire: (a) the `path_hash` doesn't resolve to any project
+        at all, and (b) the project exists but is local. Callers that
+        need to disambiguate must query `GET /projects/{hash}` first to
+        confirm existence, then treat a subsequent webhook-info 404 as
+        "local project, no webhook to configure".
       responses:
         "200":
           description: Webhook coordinates
@@ -1517,33 +1528,72 @@ paths:
                 $ref: "#/components/schemas/WebhookInfoResponse"
         "401":
           $ref: "#/components/responses/Unauthorized"
+        "404":
+          description: |
+            Either the project does not exist, OR the project exists but
+            is local (no `git_repos` row, no webhook to surface).
+            Disambiguate by checking `GET /projects/{hash}` first.
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/Error"
+        "503":
+          $ref: "#/components/responses/WorkspacesDisabled"
+
+  /api/v1/projects/{hash}/reindex:
+    parameters:
+      - name: hash
+        in: path
+        required: true
+        schema:
+          type: string
+    post:
+      operationId: reindexProject
+      tags: [projects]
+      summary: Manually re-trigger the clone + index pipeline
+      description: |
+        Enqueues a fresh `clone_repo` job for the matching git_repos
+        row. 422 when the project is local (no clone pipeline — local
+        projects reindex via the CLI). Dedupe collapses repeated
+        triggers into the existing in-flight job.
+      responses:
+        "202":
+          description: Reindex enqueued (or already running — dedupe)
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/ReindexEnqueuedResponse"
+        "401":
+          $ref: "#/components/responses/Unauthorized"
         "404":
           $ref: "#/components/responses/NotFound"
+        "422":
+          $ref: "#/components/responses/Unprocessable"
         "503":
           $ref: "#/components/responses/WorkspacesDisabled"
 
-  /api/v1/webhooks/github/{repo_id}:
+  /api/v1/webhooks/github/{hash}:
     parameters:
-      - name: repo_id
+      - name: hash
         in: path
         required: true
         schema:
           type: string
+        description: Project's path_hash (16 hex chars).
     post:
       operationId: receiveGithubWebhook
-      tags: [workspaces]
+      tags: [projects]
       summary: Receive a GitHub webhook delivery (public, HMAC-authenticated)
       description: |
-        Public endpoint — `requireAuth` is bypassed. Authentication is
-        per-row via the `X-Hub-Signature-256` header which must be
-        HMAC-SHA256 of the request body keyed by the workspace_repo's
-        `webhook_secret`. Mismatched signatures return 401; unknown
-        `repo_id` returns 404. On a valid `push` for the tracked branch
-        the server enqueues a `fetch_repo` job (dedupe collapses burst
-        deliveries).
-
-        GitHub `ping` deliveries return 200 with no side effects so the
-        setup confirmation flow works.
+        Public endpoint — auth is bypassed. The `X-Hub-Signature-256`
+        header must be HMAC-SHA256 of the request body keyed by the
+        project's `git_repos.webhook_secret`. Mismatched signatures
+        return 401; an unknown `hash` returns 404. On a valid `push`
+        for the tracked branch the server enqueues a `clone_repo` job
+        (dedupe collapses burst deliveries).
+
+        GitHub `ping` deliveries return 200 with no side effects so
+        the setup confirmation flow works.
       security: []
       parameters:
         - name: X-Hub-Signature-256
@@ -1584,7 +1634,7 @@ paths:
               schema:
                 $ref: "#/components/schemas/Error"
         "404":
-          description: Unknown workspace_repo id
+          description: Unknown project hash
           content:
             application/json:
               schema:
@@ -1592,40 +1642,6 @@ paths:
         "503":
           $ref: "#/components/responses/WorkspacesDisabled"
 
-  /api/v1/workspaces/{id}/repos/{repo_id}/reindex:
-    parameters:
-      - name: id
-        in: path
-        required: true
-        schema:
-          type: string
-      - name: repo_id
-        in: path
-        required: true
-        schema:
-          type: string
-    post:
-      operationId: reindexWorkspaceRepo
-      tags: [workspaces]
-      summary: Manually re-trigger the clone + index pipeline
-      description: |
-        Enqueues a fresh `clone_repo` job for the repo. Dedupe collapses
-        repeated triggers into the existing in-flight job — only one
-        clone is ever active per repo at a time.
-      responses:
-        "202":
-          description: Reindex enqueued (or already running — dedupe)
-          content:
-            application/json:
-              schema:
-                $ref: "#/components/schemas/ReindexEnqueuedResponse"
-        "401":
-          $ref: "#/components/responses/Unauthorized"
-        "404":
-          $ref: "#/components/responses/NotFound"
-        "503":
-          $ref: "#/components/responses/WorkspacesDisabled"
-
   /api/v1/jobs:
     get:
       operationId: listJobs
@@ -1729,9 +1745,11 @@ paths:
       summary: Delete a stored GitHub PAT
       description: |
         Permanently removes the encrypted blob. Subsequent workspaces
-        operations that reference this token id will fail. PR1 does not
-        block deletion when the token is referenced — workspace_repos
-        landing in PR2 will introduce that FK.
+        operations that reference this token id will fail. The
+        git_repos.token_id FK uses ON DELETE SET NULL, so existing
+        rows survive token revocation but their re-clone / webhook
+        flows that need GitHub auth will fail until a token is
+        re-attached.
       responses:
         "204":
           description: Deleted
@@ -3212,79 +3230,49 @@ components:
             consulted. Kept for backwards compatibility with older
             clients that still send it.
 
-    WorkspaceRepo:
+    GitRepo:
       type: object
       required:
-        - id
-        - workspace_id
+        - project_path
+        - path_hash
         - github_url
         - branch
-        - project_path
-        - status
         - auto_webhook
         - webhook_mode
-        - is_linked
         - created_at
         - updated_at
+      description: |
+        Clone + webhook metadata for an external (git-cloned) project.
+        Exactly 1:1 with the matching projects row; local projects have
+        no GitRepo row.
       properties:
-        id:
+        project_path:
           type: string
-        workspace_id:
+          description: |
+            Matches projects.host_path — canonical
+            "github.com/owner/repo@branch" string.
+        path_hash:
           type: string
+          description: 16-hex SHA1 prefix of project_path, used in URLs.
         github_url:
           type: string
-          description: Canonical https://github.com/owner/repo URL.
         branch:
           type: string
-        project_path:
-          type: string
-          description: |
-            Indexed project's host_path — "github.com/owner/repo@branch".
-            Use this with the existing /api/v1/projects/{path}/* endpoints
-            (path = first 16 hex chars of SHA1).
         token_id:
           type: string
           nullable: true
-          description: |
-            GitHub token used for clone+webhook calls. Null when the
-            repo is public.
         auto_webhook:
           type: boolean
-          description: |
-            Legacy alias for `webhook_mode == "auto"`. Always present so
-            old clients keep working; new clients should consult
-            `webhook_mode` instead.
+          description: Legacy alias for `webhook_mode == "auto"`.
         webhook_mode:
           type: string
           enum: [manual, auto, disabled]
-          description: |
-            Operator's intent for how this repo gets kept fresh. `auto`
-            asks the server to register the GitHub webhook; `manual`
-            means the operator pastes the URL+secret into GitHub
-            themselves; `disabled` skips auto-sync entirely — reindex
-            via the dashboard button only.
-        status:
-          type: string
-          enum: [pending, cloning, indexing, indexed, failed]
         last_sha:
           type: string
           nullable: true
-          description: HEAD SHA at last successful clone.
         last_error:
           type: string
           nullable: true
-        last_indexed_at:
-          type: string
-          format: date-time
-          nullable: true
-        is_linked:
-          type: boolean
-          description: |
-            True when this row is a lightweight pointer to a project
-            already owned by another workspace_repo — added via the
-            "Add Existing Project" flow. Linked rows have no clone on
-            disk, no webhook, and no token; reindex is a no-op (must
-            be triggered from the canonical owning row).
         created_at:
           type: string
           format: date-time
@@ -3292,18 +3280,7 @@ components:
           type: string
           format: date-time
 
-    WorkspaceRepoListResponse:
-      type: object
-      required: [repos, total]
-      properties:
-        repos:
-          type: array
-          items:
-            $ref: "#/components/schemas/WorkspaceRepo"
-        total:
-          type: integer
-
-    AddWorkspaceRepoRequest:
+    AddGitRepoRequest:
       type: object
       required: [github_url, branch]
       properties:
@@ -3315,28 +3292,11 @@ components:
           minLength: 1
         token_id:
           type: string
-          description: |
-            Optional id of a stored GitHub PAT. Required for private repos.
-        auto_webhook:
-          type: boolean
-          default: false
-          deprecated: true
-          description: |
-            Legacy field. New clients should send `webhook_mode` instead.
-            When both are provided, `webhook_mode` wins; when only the
-            bool is set, `true` is mapped to `webhook_mode = "auto"`.
+          description: Optional id of a stored GitHub PAT (required for private repos).
         webhook_mode:
           type: string
           enum: [manual, auto, disabled]
           default: manual
-          description: |
-            How the server should keep this repo fresh:
-            - `auto` — server registers the webhook in GitHub on your
-              behalf (requires admin:repo_hook on the PAT).
-            - `manual` — server stores a webhook_secret and returns it
-              once; you paste the URL + secret into GitHub yourself.
-            - `disabled` — no auto-sync at all; reindex via the
-              dashboard button only.
 
     GithubRepo:
       type: object
@@ -3379,27 +3339,72 @@ components:
         avatar_url:
           type: string
 
-    WorkspaceRepoCreated:
+    GitRepoCreated:
       type: object
-      required: [repo, webhook_url, webhook_secret]
+      required: [project, git_repo, webhook_url, webhook_secret]
       properties:
-        repo:
-          $ref: "#/components/schemas/WorkspaceRepo"
+        project:
+          $ref: "#/components/schemas/Project"
+        git_repo:
+          $ref: "#/components/schemas/GitRepo"
         webhook_url:
           type: string
           description: |
             Publicly-reachable POST endpoint to register in GitHub when
-            doing the webhook setup manually. Includes the workspace_repo
-            id segment. Empty string for linked rows (no webhook).
+            doing webhook setup manually.
         webhook_secret:
           type: string
           description: |
             HMAC secret. **Returned once on create + once via
-            webhook-info.** Use as the "Secret" field in GitHub's webhook
-            UI; deliveries are validated by HMAC-SHA256 over the body.
-            Empty string for linked rows (no webhook).
+            /projects/{hash}/webhook-info.**
+        auto_registered:
+          type: boolean
+          description: |
+            True when webhook_mode was 'auto' AND the server
+            successfully registered the hook with GitHub.
+        auto_register_note:
+          type: string
+          description: Human-readable reason when auto_registered is false.
+
+    WorkspaceProjectMembership:
+      type: object
+      required: [workspace_id, project_path, added_at]
+      properties:
+        workspace_id:
+          type: string
+        project_path:
+          type: string
+        added_at:
+          type: string
+          format: date-time
+
+    WorkspaceProject:
+      type: object
+      required: [project, added_at]
+      description: |
+        A project listed under a workspace, decorated with the membership
+        timestamp. The embedded Project carries the full project info
+        (status, languages, last_indexed_at) so the dashboard doesn't
+        need a second roundtrip.
+      properties:
+        project:
+          $ref: "#/components/schemas/Project"
+        added_at:
+          type: string
+          format: date-time
+
+    WorkspaceProjectListResponse:
+      type: object
+      required: [projects, total]
+      properties:
+        projects:
+          type: array
+          items:
+            $ref: "#/components/schemas/WorkspaceProject"
+        total:
+          type: integer
 
-    LinkExistingProjectRequest:
+    LinkProjectRequest:
       type: object
       required: [project_hash]
       properties:
@@ -3408,11 +3413,9 @@ components:
           minLength: 16
           maxLength: 16
           description: |
-            The 16-hex `path_hash` of an indexed project — the same value
-            used in /api/v1/projects/{path}. The server resolves it to
-            the canonical `host_path` and inserts a linked workspace_repo
-            row. The project must already be in status='indexed' and have
-            a host_path of the form "github.com/owner/repo@branch".
+            The 16-hex `path_hash` of an indexed project. The server
+            resolves it to host_path and inserts the (workspace_id,
+            project_path) row. The project must be in status='indexed'.
 
     ProjectWorkspaceList:
       type: object
@@ -3425,22 +3428,15 @@ components:
 
     ProjectWorkspaceEntry:
       type: object
-      required: [workspace_id, workspace_name, repo_id, branch, status, is_linked]
+      required: [workspace_id, workspace_name, added_at]
       properties:
         workspace_id:
           type: string
         workspace_name:
           type: string
-        repo_id:
-          type: string
-          description: workspace_repos.id — same value used in /repos endpoints.
-        branch:
-          type: string
-        status:
+        added_at:
           type: string
-          enum: [pending, cloning, indexing, indexed, failed]
-        is_linked:
-          type: boolean
+          format: date-time
 
     ReindexEnqueuedResponse:
       type: object
@@ -3449,8 +3445,8 @@ components:
         status:
           type: string
           enum: [enqueued, already_running]
-        repo:
-          $ref: "#/components/schemas/WorkspaceRepo"
+        project:
+          $ref: "#/components/schemas/Project"
 
     Job:
       type: object
@@ -3608,9 +3604,8 @@ components:
           type: string
           enum: [pending, cloning, indexing, failed]
           description: |
-            Current row state in `workspace_repos.status`. Anything
-            other than `indexed` means the repo hasn't contributed to
-            this response.
+            Current per-project status. Anything other than `indexed`
+            means the project hasn't contributed to this response.
 
     WorkspaceSearchFailedRepo:
       type: object
diff --git a/plugins/cix/scripts/sync-skills.sh b/plugins/cix/scripts/sync-skills.sh
new file mode 100755
index 0000000..1a520d6
--- /dev/null
+++ b/plugins/cix/scripts/sync-skills.sh
@@ -0,0 +1,93 @@
+#!/usr/bin/env bash
+# sync-skills.sh — keep plugin-bundled skill files byte-identical with
+# the canonical sources under skills/.
+#
+# Fix #19 acceptance: the plugin ships byte-identical copies of files
+# that have a single source of truth elsewhere in the repo. Without
+# this script, contributors edit one file and forget the mirror; the
+# two diverge silently until someone runs cix-workspace via the plugin
+# and gets a stale workflow.
+#
+# Files in scope (canonical source → plugin bundle destination):
+#
+#   skills/cix-workspace/SKILL.md
+#     → plugins/cix/skills/cix-workspace/SKILL.md
+#
+#   skills/cix-workspace/agents/cix-workspace-investigator.md
+#     → plugins/cix/agents/cix-workspace-investigator.md
+#
+# Out of scope: skills/cix/SKILL.md vs plugins/cix/skills/cix/SKILL.md —
+# those are INTENTIONALLY different. The plugin version carries extra
+# frontmatter (description, when_to_use, allowed-tools) the standalone
+# skill loader doesn't need; treating them as drift would be wrong.
+#
+# Usage:
+#   sync-skills.sh           # copy source → plugin, print what changed
+#   sync-skills.sh --check   # diff only, exit 1 on drift (for CI / pre-commit)
+
+set -euo pipefail
+
+# Resolve repo root from the script's location so the script works no
+# matter where it's invoked from (CI, IDE task runner, manual cd).
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../../.." && pwd)"
+
+# (source, destination) pairs. Bash 3.2-compatible parallel arrays so
+# this also runs on macOS's default /bin/bash.
+SRC=(
+    "skills/cix-workspace/SKILL.md"
+    "skills/cix-workspace/agents/cix-workspace-investigator.md"
+)
+DST=(
+    "plugins/cix/skills/cix-workspace/SKILL.md"
+    "plugins/cix/agents/cix-workspace-investigator.md"
+)
+
+MODE="copy"
+if [[ "${1:-}" == "--check" ]]; then
+    MODE="check"
+elif [[ "${1:-}" == "-h" || "${1:-}" == "--help" ]]; then
+    sed -n '2,32p' "$0"
+    exit 0
+elif [[ -n "${1:-}" ]]; then
+    echo "sync-skills.sh: unknown argument: $1" >&2
+    echo "Run with --help for usage." >&2
+    exit 2
+fi
+
+drift=0
+for i in "${!SRC[@]}"; do
+    src="$REPO_ROOT/${SRC[$i]}"
+    dst="$REPO_ROOT/${DST[$i]}"
+
+    if [[ ! -f "$src" ]]; then
+        echo "sync-skills.sh: source missing: $src" >&2
+        exit 3
+    fi
+
+    if [[ "$MODE" == "check" ]]; then
+        # Skip the copy; just compare. -q suppresses output, exit code 0
+        # = identical, 1 = differs, 2 = error.
+        if ! diff -q "$src" "$dst" >/dev/null 2>&1; then
+            echo "drift: ${SRC[$i]} != ${DST[$i]}" >&2
+            drift=1
+        fi
+        continue
+    fi
+
+    # Copy mode — only act when the destination differs, so the log
+    # only mentions files that actually changed. cmp -s is the standard
+    # "are these byte-identical" test (returns 0 for identical, 1 for
+    # different, 2 for I/O error).
+    if ! cmp -s "$src" "$dst"; then
+        mkdir -p "$(dirname "$dst")"
+        cp "$src" "$dst"
+        echo "synced: ${SRC[$i]} → ${DST[$i]}"
+    fi
+done
+
+if [[ "$MODE" == "check" && $drift -ne 0 ]]; then
+    echo "" >&2
+    echo "Run plugins/cix/scripts/sync-skills.sh (no args) to fix." >&2
+    exit 1
+fi
diff --git a/plugins/cix/skills/cix-workspace/SKILL.md b/plugins/cix/skills/cix-workspace/SKILL.md
index e7ce03a..276aa95 100644
--- a/plugins/cix/skills/cix-workspace/SKILL.md
+++ b/plugins/cix/skills/cix-workspace/SKILL.md
@@ -492,8 +492,8 @@ fan-out — the same algorithm that produces the false-positive
 failure mode described in the worked example above.
 
 The response includes `stale_fts_repos` listing the affected
-project_paths. Fix: reindex each repo (dashboard → repo card →
-reindex button, or `POST /api/v1/workspaces/{id}/repos/{repo_id}/reindex`).
+project_paths. Fix: reindex each project (dashboard → project card →
+reindex button, or `POST /api/v1/projects/{hash}/reindex`).
 After reindex, BM25 populates incrementally per-file as chunks are
 written.
 
diff --git a/server/.gitignore b/server/.gitignore
index 25d3de5..cdefb84 100644
--- a/server/.gitignore
+++ b/server/.gitignore
@@ -1,5 +1,7 @@
 # Compiled binaries — match only the executable, not the cmd/cix-server/ source directory.
 /cmd/cix-server/cix-server
+# `go build ./cmd/cix-server` run from server/ without -o drops the binary here.
+/cix-server
 /bin/
 /dist/
 
diff --git a/server/cmd/cix-server/main.go b/server/cmd/cix-server/main.go
index 7fe85fd..b4c6661 100644
--- a/server/cmd/cix-server/main.go
+++ b/server/cmd/cix-server/main.go
@@ -21,6 +21,7 @@ import (
 	"github.com/dvcdsys/code-index/server/internal/db"
 	"github.com/dvcdsys/code-index/server/internal/embeddings"
 	"github.com/dvcdsys/code-index/server/internal/githubtokens"
+	"github.com/dvcdsys/code-index/server/internal/gitrepos"
 	"github.com/dvcdsys/code-index/server/internal/httpapi"
 	"github.com/dvcdsys/code-index/server/internal/indexer"
 	"github.com/dvcdsys/code-index/server/internal/jobs"
@@ -31,7 +32,7 @@ import (
 	"github.com/dvcdsys/code-index/server/internal/vectorstore"
 	"github.com/dvcdsys/code-index/server/internal/versioncheck"
 	"github.com/dvcdsys/code-index/server/internal/workspacejobs"
-	"github.com/dvcdsys/code-index/server/internal/workspacerepos"
+	"github.com/dvcdsys/code-index/server/internal/workspaceprojects"
 	"github.com/dvcdsys/code-index/server/internal/workspaces"
 )
 
@@ -94,7 +95,10 @@ func run() error {
 
 	dbPath := cfg.DynamicSQLitePath()
 	logger.Info("opening database", "path", dbPath)
-	database, err := db.Open(dbPath)
+	database, err := db.OpenWith(db.OpenOptions{
+		Path:    dbPath,
+		DataDir: cfg.WorkspacesDataDir,
+	})
 	if err != nil {
 		return fmt.Errorf("open db: %w", err)
 	}
@@ -104,6 +108,12 @@ func run() error {
 		}
 	}()
 
+	// Webhook clean-break notice (Fix #4a): the migration that split
+	// workspace_repos into git_repos + workspace_projects also changed
+	// the webhook URL format. Surface a one-line WARN with row counts
+	// so the operator knows to re-register in GitHub on upgrade.
+	auditWebhookCleanBreak(context.Background(), database, logger)
+
 	// PR-E — overlay dashboard-saved runtime overrides onto the env-loaded
 	// config before any code path reads its fields. The DB row may not
 	// exist yet (fresh install); resolution falls through to env / recommended
@@ -206,7 +216,8 @@ func run() error {
 	var (
 		wsSvc    *workspaces.Service
 		ghSvc    *githubtokens.Service
-		wrSvc    *workspacerepos.Service
+		grSvc    *gitrepos.Service
+		wpSvc    *workspaceprojects.Service
 		jobsSvc  *jobs.Service
 	)
 	if cfg.WorkspacesEnabled {
@@ -249,7 +260,8 @@ func run() error {
 			logger.Info("workspaces: encryption key loaded", "source", secSvc.Source())
 		}
 		wsSvc = workspaces.New(database)
-		wrSvc = workspacerepos.New(database)
+		grSvc = gitrepos.New(database)
+		wpSvc = workspaceprojects.New(database)
 
 		// Persistent job queue + worker pool. Worker concurrency comes
 		// from CIX_WORKER_CONCURRENCY (default 2). Handlers are registered
@@ -259,14 +271,14 @@ func run() error {
 			Logger:      logger,
 		})
 		workspacejobs.Register(workspacejobs.Deps{
-			DB:             database,
-			Jobs:           jobsSvc,
-			WorkspaceRepos: wrSvc,
-			GithubTokens:   ghSvc,
-			Indexer:        idx,
-			VectorStore:    vs,
-			DataDir:        cfg.WorkspacesDataDir,
-			Logger:         logger,
+			DB:           database,
+			Jobs:         jobsSvc,
+			GitRepos:     grSvc,
+			GithubTokens: ghSvc,
+			Indexer:      idx,
+			VectorStore:  vs,
+			DataDir:      cfg.WorkspacesDataDir,
+			Logger:       logger,
 		})
 		jobsSvc.Start(context.Background())
 		// Defer shutdown — stop new claims, drain in-flight work.
@@ -317,7 +329,8 @@ func run() error {
 		WorkspacesEnabled: cfg.WorkspacesEnabled,
 		Workspaces:        wsSvc,
 		GithubTokens:      ghSvc,
-		WorkspaceRepos:    wrSvc,
+		GitRepos:          grSvc,
+		WorkspaceProjects: wpSvc,
 		Jobs:              jobsSvc,
 		PublicBaseURL:     cfg.PublicBaseURL,
 	})
diff --git a/server/cmd/cix-server/webhook_audit.go b/server/cmd/cix-server/webhook_audit.go
new file mode 100644
index 0000000..c0b6045
--- /dev/null
+++ b/server/cmd/cix-server/webhook_audit.go
@@ -0,0 +1,57 @@
+package main
+
+import (
+	"context"
+	"database/sql"
+	"log/slog"
+)
+
+// auditWebhookCleanBreak emits a one-line WARN on startup when git_repos
+// rows still expose webhook URLs that operators must re-register in
+// GitHub. The clean break happened when workspace_repos split into
+// git_repos + workspace_projects: the URL went from
+// /webhooks/github/{workspace_repos.id} (UUID) to
+// /webhooks/github/{path_hash} (16-hex). GitHub will keep POSTing to
+// the OLD URL until the operator updates the webhook config, and the
+// server now returns 404 — deliveries silently fail.
+//
+// We can't detect "already re-registered" from the DB (manual webhooks
+// have no acknowledgement signal), so the warning persists on every
+// startup that still has manual + auto webhooks. That's accepted noise
+// — the alternative is silent breakage. Operators who want to silence
+// it can switch the rows to webhook_mode='disabled' once they've moved
+// off webhook-driven indexing.
+//
+// Counts are surfaced as structured fields so log scrapers can alert
+// on the threshold; the human-readable message points at
+// /api/v1/projects/{hash}/webhook-info as the per-project URL source.
+func auditWebhookCleanBreak(ctx context.Context, db *sql.DB, logger *slog.Logger) {
+	var manualCount, autoCount int
+	if err := db.QueryRowContext(ctx,
+		// COALESCE wraps SUM because SUM() over an empty table returns
+		// NULL — which Scan into *int rejects. Empty table is the
+		// fresh-install case and must scan to (0, 0), not fail.
+		`SELECT
+		     COALESCE(SUM(CASE WHEN webhook_mode = 'manual' THEN 1 ELSE 0 END), 0),
+		     COALESCE(SUM(CASE WHEN webhook_mode = 'auto'   THEN 1 ELSE 0 END), 0)
+		   FROM git_repos`,
+	).Scan(&manualCount, &autoCount); err != nil {
+		// git_repos missing only when called against a non-migrated
+		// DB (pre-Open) — by the time main.go reaches us the schema
+		// is applied, so any error here is a real surprise. Log and
+		// move on; this is not load-bearing for boot.
+		logger.Warn("webhooks: clean-break audit query failed; skipping", "err", err)
+		return
+	}
+	if manualCount == 0 && autoCount == 0 {
+		return
+	}
+	logger.Warn(
+		"webhooks: git_repos rows still point at the OLD webhook URL (workspace_repos UUID). "+
+			"The URL format changed when workspace_repos was split into git_repos + workspace_projects; "+
+			"GitHub deliveries to the old URL will 404. Re-register in GitHub — per-project URLs are at "+
+			"GET /api/v1/projects/{hash}/webhook-info or in the dashboard.",
+		"manual_webhooks", manualCount,
+		"auto_webhooks", autoCount,
+	)
+}
diff --git a/server/cmd/cix-server/webhook_audit_test.go b/server/cmd/cix-server/webhook_audit_test.go
new file mode 100644
index 0000000..93eea70
--- /dev/null
+++ b/server/cmd/cix-server/webhook_audit_test.go
@@ -0,0 +1,122 @@
+package main
+
+import (
+	"bytes"
+	"context"
+	"database/sql"
+	"log/slog"
+	"strings"
+	"testing"
+
+	"github.com/dvcdsys/code-index/server/internal/db"
+)
+
+// capturingLogger returns a slog.Logger that writes text-formatted
+// records into the supplied buffer so the test can inspect them with
+// strings.Contains.
+func capturingLogger(buf *bytes.Buffer) *slog.Logger {
+	return slog.New(slog.NewTextHandler(buf, &slog.HandlerOptions{Level: slog.LevelInfo}))
+}
+
+// seedGitRepo inserts a project + git_repo pair so the audit query has
+// real data to count. project_path is the FK target — git_repos.project_path
+// references projects.host_path.
+func seedGitRepo(t *testing.T, d *sql.DB, hostPath, mode string) {
+	t.Helper()
+	if _, err := d.Exec(`
+		INSERT INTO projects (host_path, container_path, languages, settings, stats,
+			status, created_at, updated_at, path_hash)
+		VALUES (?, ?, '[]', '{}', '{}', 'indexed', '2026-05-14T00:00:00Z', '2026-05-14T00:00:00Z', ?)`,
+		hostPath, hostPath, db.HashHostPath(hostPath),
+	); err != nil {
+		t.Fatalf("seed project %s: %v", hostPath, err)
+	}
+	if _, err := d.Exec(`
+		INSERT INTO git_repos (project_path, github_url, branch, webhook_secret,
+			webhook_mode, created_at, updated_at)
+		VALUES (?, ?, 'main', 'secret-' || ?, ?, '2026-05-14T00:00:00Z', '2026-05-14T00:00:00Z')`,
+		hostPath, "https://"+hostPath, mode, mode,
+	); err != nil {
+		t.Fatalf("seed git_repo %s/%s: %v", hostPath, mode, err)
+	}
+}
+
+// TestAuditWebhookCleanBreak_NoRows — fresh DB with no git_repos rows:
+// the audit must stay silent. A WARN on an empty DB would spam every
+// test run plus every dev boot.
+func TestAuditWebhookCleanBreak_NoRows(t *testing.T) {
+	d, err := db.Open(":memory:")
+	if err != nil {
+		t.Fatalf("open db: %v", err)
+	}
+	defer d.Close()
+
+	buf := &bytes.Buffer{}
+	auditWebhookCleanBreak(context.Background(), d, capturingLogger(buf))
+
+	if buf.Len() != 0 {
+		t.Errorf("expected silent audit on empty DB, got:\n%s", buf.String())
+	}
+}
+
+// TestAuditWebhookCleanBreak_ManualAndAuto — both modes exist + one
+// 'disabled' row that must NOT be counted. Single WARN line, two
+// structured fields with the right counts.
+func TestAuditWebhookCleanBreak_ManualAndAuto(t *testing.T) {
+	d, err := db.Open(":memory:")
+	if err != nil {
+		t.Fatalf("open db: %v", err)
+	}
+	defer d.Close()
+
+	seedGitRepo(t, d, "github.com/x/manual1@main", "manual")
+	seedGitRepo(t, d, "github.com/x/manual2@main", "manual")
+	seedGitRepo(t, d, "github.com/x/manual3@main", "manual")
+	seedGitRepo(t, d, "github.com/x/auto1@main", "auto")
+	seedGitRepo(t, d, "github.com/x/auto2@main", "auto")
+	seedGitRepo(t, d, "github.com/x/disabled1@main", "disabled")
+
+	buf := &bytes.Buffer{}
+	auditWebhookCleanBreak(context.Background(), d, capturingLogger(buf))
+
+	out := buf.String()
+	if !strings.Contains(out, "level=WARN") {
+		t.Errorf("expected WARN level, got:\n%s", out)
+	}
+	if !strings.Contains(out, "manual_webhooks=3") {
+		t.Errorf("expected manual_webhooks=3, got:\n%s", out)
+	}
+	if !strings.Contains(out, "auto_webhooks=2") {
+		t.Errorf("expected auto_webhooks=2, got:\n%s", out)
+	}
+	// Disabled rows must not be counted as either; presence of any
+	// "disabled" mention in the log is fine, but the counts must
+	// match the manual+auto totals exactly.
+	if strings.Count(out, "webhook_mode=") > 0 {
+		t.Errorf("audit log should not surface webhook_mode= field, got:\n%s", out)
+	}
+	if !strings.Contains(out, "/api/v1/projects/{hash}/webhook-info") {
+		t.Errorf("expected pointer to per-project webhook-info endpoint, got:\n%s", out)
+	}
+}
+
+// TestAuditWebhookCleanBreak_OnlyDisabled — webhook_mode='disabled' is
+// the operator opting out of webhook delivery entirely. No
+// re-registration is needed and the audit must stay silent.
+func TestAuditWebhookCleanBreak_OnlyDisabled(t *testing.T) {
+	d, err := db.Open(":memory:")
+	if err != nil {
+		t.Fatalf("open db: %v", err)
+	}
+	defer d.Close()
+
+	seedGitRepo(t, d, "github.com/x/d1@main", "disabled")
+	seedGitRepo(t, d, "github.com/x/d2@main", "disabled")
+
+	buf := &bytes.Buffer{}
+	auditWebhookCleanBreak(context.Background(), d, capturingLogger(buf))
+
+	if buf.Len() != 0 {
+		t.Errorf("expected silent audit on disabled-only rows, got:\n%s", buf.String())
+	}
+}
diff --git a/server/dashboard/.gitignore b/server/dashboard/.gitignore
index fd16421..ac7e93e 100644
--- a/server/dashboard/.gitignore
+++ b/server/dashboard/.gitignore
@@ -3,5 +3,9 @@ node_modules/
 .cache/
 *.log
 
+# TypeScript incremental-build cache — local build artefact, mutates
+# on every `tsc -b` invocation.
+*.tsbuildinfo
+
 # Type-gen output is reproducible — never commit
 src/api/generated.ts
diff --git a/server/dashboard/src/modules/projects/ProjectDetailPage.tsx b/server/dashboard/src/modules/projects/ProjectDetailPage.tsx
index 4b2a604..f18ed4c 100644
--- a/server/dashboard/src/modules/projects/ProjectDetailPage.tsx
+++ b/server/dashboard/src/modules/projects/ProjectDetailPage.tsx
@@ -1,4 +1,4 @@
-import { AlertCircle, AlertTriangle, ArrowLeft, Search } from 'lucide-react';
+import { AlertCircle, AlertTriangle, ArrowLeft, Loader2, Search } from 'lucide-react';
 import { Link, useParams } from 'react-router-dom';
 import { ApiError } from '@/api/client';
 import type { Project } from '@/api/types';
@@ -12,6 +12,7 @@ import { formatDateTime, formatRelative } from '@/lib/formatDate';
 import { useRuntimeModel } from '@/lib/useServerStatus';
 import { DeleteProjectDialog } from './components/DeleteProjectDialog';
 import { ProjectInfoCard } from './components/ProjectInfoCard';
+import { ReindexProjectButton } from './components/ReindexProjectButton';
 import { useProject, useProjectSummary, useProjectWorkspaces } from './hooks';
 
 const STATUS_VARIANT: Record<Project['status'], 'default' | 'secondary' | 'destructive' | 'outline'> = {
@@ -54,6 +55,7 @@ export function ProjectDetailPage() {
   const p = project.data;
   const s = summary.data;
   const drift = !!p.indexed_with_model && !!currentModel && p.indexed_with_model !== currentModel;
+  const isExternal = p.host_path.startsWith('github.com/');
 
   return (
     <div className="space-y-8">
@@ -96,12 +98,26 @@ export function ProjectDetailPage() {
               Search in this project
             </Link>
           </Button>
+          {isExternal ? (
+            <ReindexProjectButton hash={p.path_hash} hostPath={p.host_path} />
+          ) : null}
           {isAdmin ? (
             <DeleteProjectDialog hash={p.path_hash} hostPath={p.host_path} redirectAfter />
           ) : null}
         </div>
       </header>
 
+      {p.status === 'indexing' ? (
+        <Alert>
+          <Loader2 className="h-4 w-4 animate-spin" />
+          <AlertTitle>Indexing in progress</AlertTitle>
+          <AlertDescription>
+            This project is being indexed. Stats and search results will be incomplete
+            until it finishes — this page auto-refreshes when the run completes.
+          </AlertDescription>
+        </Alert>
+      ) : null}
+
       {drift ? (
         <Alert variant="destructive">
           <AlertTriangle className="h-4 w-4" />
@@ -143,27 +159,18 @@ export function ProjectDetailPage() {
           <div className="flex flex-wrap gap-2">
             {workspaces.data.workspaces.map((w) => (
               <Button
-                key={w.repo_id}
+                key={w.workspace_id}
                 asChild
                 variant="outline"
                 size="sm"
                 className="h-auto py-1.5"
-                title={
-                  w.is_linked
-                    ? `Linked into ${w.workspace_name} from another workspace's clone`
-                    : `Owned by ${w.workspace_name} (this is the cloning workspace)`
-                }
+                title={`Linked into ${w.workspace_name} on ${formatDateTime(w.added_at)}`}
               >
                 <Link to={`/workspaces/${w.workspace_id}`}>
                   <span className="font-medium">{w.workspace_name}</span>
-                  <span className="ml-2 font-mono text-xs text-muted-foreground">
-                    @{w.branch}
+                  <span className="ml-2 text-xs text-muted-foreground">
+                    {formatRelative(w.added_at)}
                   </span>
-                  {w.is_linked ? (
-                    <Badge variant="secondary" className="ml-2 text-[10px]">
-                      linked
-                    </Badge>
-                  ) : null}
                 </Link>
               </Button>
             ))}
@@ -226,15 +233,17 @@ export function ProjectDetailPage() {
         </div>
       </section>
 
-      <Alert>
-        <AlertTitle>Reindexing</AlertTitle>
-        <AlertDescription>
-          Indexing reads files from the local filesystem and is driven by the CLI. Run{' '}
-          <code className="rounded bg-muted px-1 py-0.5 text-xs">cix reindex</code> for a one-shot
-          rescan, or keep <code className="rounded bg-muted px-1 py-0.5 text-xs">cix watch</code>{' '}
-          running for automatic updates on file change.
-        </AlertDescription>
-      </Alert>
+      {!isExternal ? (
+        <Alert>
+          <AlertTitle>Reindexing</AlertTitle>
+          <AlertDescription>
+            Indexing reads files from the local filesystem and is driven by the CLI. Run{' '}
+            <code className="rounded bg-muted px-1 py-0.5 text-xs">cix reindex</code> for a one-shot
+            rescan, or keep <code className="rounded bg-muted px-1 py-0.5 text-xs">cix watch</code>{' '}
+            running for automatic updates on file change.
+          </AlertDescription>
+        </Alert>
+      ) : null}
     </div>
   );
 }
diff --git a/server/dashboard/src/modules/projects/ProjectsListPage.tsx b/server/dashboard/src/modules/projects/ProjectsListPage.tsx
index 97bfc5d..cb881f0 100644
--- a/server/dashboard/src/modules/projects/ProjectsListPage.tsx
+++ b/server/dashboard/src/modules/projects/ProjectsListPage.tsx
@@ -2,19 +2,29 @@ import { AlertCircle, FolderPlus } from 'lucide-react';
 import { Alert, AlertDescription, AlertTitle } from '@/ui/alert';
 import { Skeleton } from '@/ui/skeleton';
 import { ApiError } from '@/api/client';
+import { AddRepoDialog } from '@/modules/workspaces/components/AddRepoDialog';
 import { ProjectCard } from './components/ProjectCard';
 import { useProjects } from './hooks';
 
 export function ProjectsListPage() {
-  const { data, error, isLoading } = useProjects();
+  const { data, error, isLoading, refetch } = useProjects();
 
   return (
     <div className="space-y-6">
-      <header>
-        <h1 className="text-2xl font-semibold tracking-tight">Projects</h1>
-        <p className="text-sm text-muted-foreground">
-          {data ? `${data.total} indexed ${data.total === 1 ? 'project' : 'projects'}` : ' '}
-        </p>
+      <header className="flex items-start justify-between gap-4">
+        <div>
+          <h1 className="text-2xl font-semibold tracking-tight">Projects</h1>
+          <p className="text-sm text-muted-foreground">
+            {data
+              ? `${data.total} indexed ${data.total === 1 ? 'project' : 'projects'}`
+              : ' '}
+          </p>
+        </div>
+        {/* Add repo here clones + indexes a GitHub repository as a
+            standalone project. The new project lives in /projects with
+            no workspace attachment — link it into specific workspaces
+            from the workspace detail page if you want. */}
+        <AddRepoDialog onAdded={() => void refetch()} />
       </header>
 
       {isLoading ? (
@@ -51,9 +61,12 @@ function EmptyState() {
       <div className="space-y-1">
         <p className="text-base font-medium">No projects yet</p>
         <p className="max-w-sm text-sm text-muted-foreground">
-          Register a project from the CLI with{' '}
-          <code className="rounded bg-muted px-1 py-0.5 text-xs">cix init &lt;path&gt;</code>.
-          A GitHub source will land here in a future PR.
+          Use <strong>Add repo</strong> above to clone + index a GitHub
+          repository, or register a local project from the CLI with{' '}
+          <code className="rounded bg-muted px-1 py-0.5 text-xs">
+            cix init &lt;path&gt;
+          </code>
+          .
         </p>
       </div>
     </div>
diff --git a/server/dashboard/src/modules/projects/components/ReindexProjectButton.tsx b/server/dashboard/src/modules/projects/components/ReindexProjectButton.tsx
new file mode 100644
index 0000000..38f1418
--- /dev/null
+++ b/server/dashboard/src/modules/projects/components/ReindexProjectButton.tsx
@@ -0,0 +1,34 @@
+import { Loader2, RefreshCw } from 'lucide-react';
+import { toast } from 'sonner';
+import { ApiError } from '@/api/client';
+import { Button } from '@/ui/button';
+import { useReindexProject } from '../hooks';
+
+export function ReindexProjectButton({ hash, hostPath }: { hash: string; hostPath: string }) {
+  const reindex = useReindexProject();
+
+  async function onClick() {
+    try {
+      const res = await reindex.mutateAsync(hash);
+      if (res.status === 'already_running') {
+        toast.info('Reindex already running', { description: hostPath });
+      } else {
+        toast.success('Reindex enqueued', { description: hostPath });
+      }
+    } catch (err) {
+      const detail = err instanceof ApiError ? err.detail : String(err);
+      toast.error('Failed to enqueue reindex', { description: detail });
+    }
+  }
+
+  return (
+    <Button variant="outline" size="sm" onClick={onClick} disabled={reindex.isPending}>
+      {reindex.isPending ? (
+        <Loader2 className="mr-1 h-4 w-4 animate-spin" />
+      ) : (
+        <RefreshCw className="mr-1 h-4 w-4" />
+      )}
+      Reindex
+    </Button>
+  );
+}
diff --git a/server/dashboard/src/modules/projects/hooks.ts b/server/dashboard/src/modules/projects/hooks.ts
index 38d19be..73b85a4 100644
--- a/server/dashboard/src/modules/projects/hooks.ts
+++ b/server/dashboard/src/modules/projects/hooks.ts
@@ -14,16 +14,17 @@ export const projectKeys = {
 };
 
 // ProjectWorkspaceEntry mirrors the Go response shape from
-// /api/v1/projects/{hash}/workspaces — one row per workspace_repo
-// pointing at this project. Defined locally so the hook doesn't
-// depend on a regen of generated.ts every time the page renders.
+// /api/v1/projects/{hash}/workspaces — one row per workspace_projects
+// membership pointing at this project. The server returns just three
+// fields: the workspace it's linked into and the timestamp it was
+// added. Branch / status / owner-vs-linked concepts no longer exist
+// on this endpoint — projects are uniformly first-class members.
+// Defined locally so the hook doesn't depend on a regen of
+// generated.ts every time the page renders.
 export type ProjectWorkspaceEntry = {
   workspace_id: string;
   workspace_name: string;
-  repo_id: string;
-  branch: string;
-  status: 'pending' | 'cloning' | 'indexing' | 'indexed' | 'failed';
-  is_linked: boolean;
+  added_at: string;
 };
 
 export type ProjectWorkspaceList = {
@@ -42,6 +43,9 @@ export function useProject(hash: string | undefined) {
     queryKey: hash ? projectKeys.detail(hash) : ['projects', 'unknown'],
     queryFn: ({ signal }) => api.get<Project>(`/projects/${hash}`, { signal }),
     enabled: Boolean(hash),
+    // Poll while the project is mid-index so the page reflects completion
+    // without a manual refresh. Stops as soon as status flips to indexed/error.
+    refetchInterval: (q) => (q.state.data?.status === 'indexing' ? 3000 : false),
   });
 }
 
@@ -74,8 +78,17 @@ export function useDeleteProject() {
   });
 }
 
-// NOTE: a "Reindex" button is intentionally absent. The server's three-phase
-// indexing protocol (begin → files → finish) requires a producer with filesystem
-// access to upload file contents. That is the CLI's job (`cix reindex` /
-// `cix watch`). The browser cannot drive this — it has no local filesystem.
-// The detail page surfaces this expectation in copy.
+// Reindex is only meaningful for GitHub-cloned projects — the server enqueues a
+// clone_repo job that chains into index_repo. Local projects must reindex via
+// the CLI (`cix reindex` / `cix watch`); the endpoint returns 422 for those.
+export function useReindexProject() {
+  const qc = useQueryClient();
+  return useMutation({
+    mutationFn: (hash: string) =>
+      api.post<{ status: 'enqueued' | 'already_running' }>(`/projects/${hash}/reindex`, undefined),
+    onSuccess: (_data, hash) => {
+      qc.invalidateQueries({ queryKey: projectKeys.detail(hash) });
+      qc.invalidateQueries({ queryKey: projectKeys.all });
+    },
+  });
+}
diff --git a/server/dashboard/src/modules/workspaces/WorkspaceDetailPage.tsx b/server/dashboard/src/modules/workspaces/WorkspaceDetailPage.tsx
index 0efd737..99c3bf4 100644
--- a/server/dashboard/src/modules/workspaces/WorkspaceDetailPage.tsx
+++ b/server/dashboard/src/modules/workspaces/WorkspaceDetailPage.tsx
@@ -7,47 +7,38 @@ import { Button } from '@/ui/button';
 import { Skeleton } from '@/ui/skeleton';
 import { AddExistingProjectDialog } from './components/AddExistingProjectDialog';
 import { AddRepoDialog } from './components/AddRepoDialog';
-import { RepoCard } from './components/RepoCard';
+import { WorkspaceProjectRow } from './components/WorkspaceProjectRow';
 import { WorkspaceSearchDialog } from './components/WorkspaceSearchDialog';
 import { isInFlight } from './types';
 import type {
   Workspace,
-  WorkspaceRepo,
-  WorkspaceRepoListResponse,
+  WorkspaceProject,
+  WorkspaceProjectListResponse,
 } from './types';
 
-// Auto-dismiss the "indexing finished" toast after this many ms. Long
-// enough to read, short enough not to linger past when the user has
-// likely moved on.
 const INDEX_DONE_TOAST_MS = 5000;
-
-// Background polling cadence. Three seconds is short enough that the
-// "indexing" → "indexed" transition is visible while you watch the
-// dashboard, long enough that the cost of polling for a workspace
-// with many repos stays modest. Only runs while at least one repo is
-// in flight.
 const POLL_MS = 3000;
 
 export function WorkspaceDetailPage() {
   const { id = '' } = useParams<{ id: string }>();
   const navigate = useNavigate();
   const [workspace, setWorkspace] = useState<Workspace | null>(null);
-  const [repos, setRepos] = useState<WorkspaceRepo[] | null>(null);
+  const [projects, setProjects] = useState<WorkspaceProject[] | null>(null);
   const [error, setError] = useState<string | null>(null);
   const [notFound, setNotFound] = useState(false);
   const [indexDoneMsg, setIndexDoneMsg] = useState<string | null>(null);
 
-  const loadRepos = useCallback(async () => {
+  const loadProjects = useCallback(async () => {
     try {
-      const r = await api.get<WorkspaceRepoListResponse>(`/workspaces/${id}/repos`);
-      setRepos(r.repos);
+      const r = await api.get<WorkspaceProjectListResponse>(
+        `/workspaces/${id}/projects`,
+      );
+      setProjects(r.projects);
     } catch (e) {
-      const msg = e instanceof Error ? e.message : String(e);
-      setError(msg);
+      setError(e instanceof Error ? e.message : String(e));
     }
   }, [id]);
 
-  // Initial workspace + repo fetch.
   useEffect(() => {
     let cancelled = false;
     api
@@ -63,37 +54,27 @@ export function WorkspaceDetailPage() {
         }
         setError(e instanceof Error ? e.message : String(e));
       });
-    void loadRepos();
+    void loadProjects();
     return () => {
       cancelled = true;
     };
-  }, [id, loadRepos]);
+  }, [id, loadProjects]);
 
-  // Live progress polling. Active only while at least one repo is
-  // in pending/cloning/indexing — terminal states stop the tick so we
-  // don't burn CPU on an idle workspace.
+  // Poll while any project is still being cloned/indexed.
   useEffect(() => {
-    if (!repos || repos.length === 0) return;
-    const anyBusy = repos.some((r) => isInFlight(r.status));
+    if (!projects || projects.length === 0) return;
+    const anyBusy = projects.some((p) => isInFlight(p.project.status));
     if (!anyBusy) return;
     const handle = setInterval(() => {
-      void loadRepos();
+      void loadProjects();
     }, POLL_MS);
     return () => clearInterval(handle);
-  }, [repos, loadRepos]);
+  }, [projects, loadProjects]);
 
-  // Detect the "last in-flight repo just finished" transition. Workspace
-  // search is live (no centroid rebuild step) so we just confirm to
-  // the user that the new repo is now searchable.
-  //
-  // wasInflightRef is the gate: we only fire the toast on a
-  // true → false transition, not on the initial page load where
-  // everything was already indexed. Reset back to false after firing
-  // so a second indexing wave (add another repo later) re-arms it.
   const wasInflightRef = useRef(false);
   useEffect(() => {
-    if (!repos) return;
-    const anyBusy = repos.some((r) => isInFlight(r.status));
+    if (!projects) return;
+    const anyBusy = projects.some((p) => isInFlight(p.project.status));
     if (anyBusy) {
       wasInflightRef.current = true;
       return;
@@ -102,9 +83,8 @@ export function WorkspaceDetailPage() {
       wasInflightRef.current = false;
       setIndexDoneMsg('Indexing finished — workspace search is ready.');
     }
-  }, [repos]);
+  }, [projects]);
 
-  // Auto-dismiss the toast so it doesn't linger after the user moves on.
   useEffect(() => {
     if (!indexDoneMsg) return;
     const handle = setTimeout(() => setIndexDoneMsg(null), INDEX_DONE_TOAST_MS);
@@ -115,7 +95,7 @@ export function WorkspaceDetailPage() {
     if (!workspace) return;
     if (
       !confirm(
-        `Delete workspace "${workspace.name}"?\n\nThis removes all attached repos and the indexed projects.`,
+        `Delete workspace "${workspace.name}"?\n\nThe projects themselves stay — only this workspace is removed.`,
       )
     ) {
       return;
@@ -168,11 +148,15 @@ export function WorkspaceDetailPage() {
         </div>
         <div className="flex flex-wrap gap-2">
           <WorkspaceSearchDialog workspace={workspace} />
-          <AddRepoDialog workspaceID={workspace.id} onAdded={loadRepos} />
+          {/* Add repo here clones + indexes a new external project AND
+              links it into this workspace in one step. The dialog
+              accepts an optional workspaceID — when supplied, it
+              chains POST /git-repos with POST /workspaces/{id}/projects. */}
+          <AddRepoDialog workspaceID={workspace.id} onAdded={loadProjects} />
           <AddExistingProjectDialog
             workspaceID={workspace.id}
-            existingProjectPaths={(repos ?? []).map((r) => r.project_path)}
-            onAdded={loadRepos}
+            existingProjectPaths={(projects ?? []).map((p) => p.project.host_path)}
+            onAdded={loadProjects}
           />
           <Button variant="outline" onClick={handleDeleteWorkspace}>
             <Trash2 className="mr-1 size-4" /> Delete
@@ -190,40 +174,40 @@ export function WorkspaceDetailPage() {
       {error && (
         <Alert variant="destructive">
           <AlertCircle className="size-4" />
-          <AlertTitle>Could not load repositories</AlertTitle>
+          <AlertTitle>Could not load projects</AlertTitle>
           <AlertDescription>{error}</AlertDescription>
         </Alert>
       )}
 
       <section className="space-y-3">
         <div className="flex items-baseline justify-between">
-          <h2 className="text-base font-medium">Repositories</h2>
-          {repos && (
+          <h2 className="text-base font-medium">Projects</h2>
+          {projects && (
             <span className="text-xs text-muted-foreground">
-              {repos.length === 0
+              {projects.length === 0
                 ? 'none'
-                : `${repos.filter((r) => r.status === 'indexed').length} of ${
-                    repos.length
+                : `${projects.filter((p) => p.project.status === 'indexed').length} of ${
+                    projects.length
                   } indexed`}
             </span>
           )}
         </div>
 
-        {repos === null ? (
+        {projects === null ? (
           <div className="space-y-2">
             <Skeleton className="h-24 w-full" />
             <Skeleton className="h-24 w-full" />
           </div>
-        ) : repos.length === 0 ? (
-          <ReposEmptyState />
+        ) : projects.length === 0 ? (
+          <ProjectsEmptyState />
         ) : (
           <div className="grid gap-3">
-            {repos.map((repo) => (
-              <RepoCard
-                key={repo.id}
-                repo={repo}
-                onDeleted={loadRepos}
-                onReindexed={loadRepos}
+            {projects.map((p) => (
+              <WorkspaceProjectRow
+                key={p.project.host_path}
+                workspaceID={workspace.id}
+                wp={p}
+                onUnlinked={loadProjects}
               />
             ))}
           </div>
@@ -244,12 +228,14 @@ function BackLink() {
   );
 }
 
-function ReposEmptyState() {
+function ProjectsEmptyState() {
   return (
     <div className="rounded-md border border-dashed bg-muted/20 p-8 text-center">
-      <p className="text-sm font-medium">No repositories yet</p>
+      <p className="text-sm font-medium">No projects in this workspace</p>
       <p className="mt-1 text-xs text-muted-foreground">
-        Click <strong>Add repo</strong> above to attach the first one.
+        Use <strong>Add repo</strong> to clone + index a new GitHub project, or{' '}
+        <strong>Add Existing Project</strong> to link a project that already
+        lives in <code>/projects</code>.
       </p>
     </div>
   );
diff --git a/server/dashboard/src/modules/workspaces/components/AddExistingProjectDialog.tsx b/server/dashboard/src/modules/workspaces/components/AddExistingProjectDialog.tsx
index 9f8eddd..8ffaf66 100644
--- a/server/dashboard/src/modules/workspaces/components/AddExistingProjectDialog.tsx
+++ b/server/dashboard/src/modules/workspaces/components/AddExistingProjectDialog.tsx
@@ -16,18 +16,14 @@ import {
 import { Input } from '@/ui/input';
 import { Label } from '@/ui/label';
 import type { Project, ProjectListResponse } from '@/api/types';
-import type { WorkspaceRepo, WorkspaceRepoCreated } from '../types';
 
-// Per-row disabled reason. null means the row is selectable.
-// "already-in-workspace" is NOT included here — those projects are
-// filtered out of the list entirely rather than rendered as disabled,
-// per the operator's request: a workspace's own projects shouldn't be
-// noise in the "add more" picker.
-type LinkDisabledReason = 'not-indexed' | 'not-github';
+// Per-row disabled reason. null means the row is selectable. Local
+// projects are now first-class linkable rows — only "not yet indexed"
+// disables them.
+type LinkDisabledReason = 'not-indexed';
 
 function disabledReasonFor(p: Project): LinkDisabledReason | null {
   if (p.status !== 'indexed') return 'not-indexed';
-  if (!p.host_path.startsWith('github.com/') || !p.host_path.includes('@')) return 'not-github';
   return null;
 }
 
@@ -35,8 +31,6 @@ function disabledLabel(r: LinkDisabledReason): string {
   switch (r) {
     case 'not-indexed':
       return 'not indexed yet';
-    case 'not-github':
-      return 'local path (cannot link)';
   }
 }
 
@@ -46,7 +40,7 @@ function disabledLabel(r: LinkDisabledReason): string {
 // rows are rendered as disabled with a short reason so the operator
 // understands why they can't be picked.
 //
-// Submit fans out N POSTs to /workspaces/{id}/repos/link sequentially.
+// Submit fans out N POSTs to /workspaces/{id}/projects sequentially.
 // We chose sequential over parallel because: (a) it makes per-project
 // error reporting trivial, (b) the per-call cost is tiny (no clone, no
 // index), (c) a backend hiccup mid-batch leaves the workspace in a
@@ -147,8 +141,8 @@ export function AddExistingProjectDialog({
     const toLink = projects.filter((p) => selected.has(p.path_hash));
     for (const p of toLink) {
       try {
-        await api.post<WorkspaceRepoCreated>(
-          `/workspaces/${workspaceID}/repos/link`,
+        await api.post(
+          `/workspaces/${workspaceID}/projects`,
           { project_hash: p.path_hash },
         );
         succeeded.add(p.path_hash);
@@ -216,7 +210,7 @@ export function AddExistingProjectDialog({
             <Label htmlFor="proj-filter">Filter</Label>
             <Input
               id="proj-filter"
-              placeholder="github.com/owner/repo"
+              placeholder="github.com/owner/repo or /local/path"
               value={query}
               onChange={(e) => setQuery(e.target.value)}
               disabled={projects === null}
@@ -332,5 +326,3 @@ export function AddExistingProjectDialog({
   );
 }
 
-// Re-export the row shape so consumers don't need to dig into types.ts.
-export type { WorkspaceRepo };
diff --git a/server/dashboard/src/modules/workspaces/components/AddRepoDialog.tsx b/server/dashboard/src/modules/workspaces/components/AddRepoDialog.tsx
index 88a3ce1..c53d971 100644
--- a/server/dashboard/src/modules/workspaces/components/AddRepoDialog.tsx
+++ b/server/dashboard/src/modules/workspaces/components/AddRepoDialog.tsx
@@ -29,8 +29,8 @@ import type {
   GithubRepoListResponse,
   GithubToken,
   GithubTokenListResponse,
+  GitRepoCreated,
   WebhookMode,
-  WorkspaceRepoCreated,
 } from '../types';
 
 // Sentinel value for the "(public repo, no token)" Select option. Radix
@@ -41,12 +41,22 @@ const NO_TOKEN = '__none__';
 // AddRepoDialog is a staged form: each step gates the next so the user
 // can't pick a repository before choosing a token, and can't submit
 // before pinning down a branch + webhook mode. The shape mirrors how
-// people actually fill it in: PAT → repo → branch → webhook policy.
+// people actually fill it in: PAT → account → repo → branch → webhook.
+//
+// Scope:
+//   - workspaceID provided  → after POST /git-repos, additionally
+//     POST /workspaces/{id}/projects so the new project is linked
+//     into that workspace. Note: the link call only succeeds once
+//     the project finishes indexing; we kick off the link request
+//     fire-and-forget here, the dashboard's polling will surface
+//     the membership once indexing completes.
+//   - workspaceID omitted  → just POST /git-repos. The new project
+//     lives standalone in /projects and can be linked later.
 export function AddRepoDialog({
   workspaceID,
   onAdded,
 }: {
-  workspaceID: string;
+  workspaceID?: string;
   onAdded: () => void;
 }) {
   const [open, setOpen] = useState(false);
@@ -78,7 +88,7 @@ export function AddRepoDialog({
 
   const [submitting, setSubmitting] = useState(false);
   const [submitErr, setSubmitErr] = useState<string | null>(null);
-  const [created, setCreated] = useState<WorkspaceRepoCreated | null>(null);
+  const [created, setCreated] = useState<GitRepoCreated | null>(null);
 
   // Load tokens when the dialog opens — keep the request out of the
   // page mount path so users who never open the dialog don't pay for
@@ -193,11 +203,25 @@ export function AddRepoDialog({
       if (tokenID && tokenID !== NO_TOKEN) {
         payload.token_id = tokenID;
       }
-      const resp = await api.post<WorkspaceRepoCreated>(
-        `/workspaces/${workspaceID}/repos`,
-        payload,
-      );
+      const resp = await api.post<GitRepoCreated>(`/git-repos`, payload);
       setCreated(resp);
+      // If we're in workspace context, link the freshly-created
+      // project. The link call may 422 if indexing isn't done yet —
+      // that's fine for the dashboard UX. We fire it off and rely on
+      // polling in the parent page to pick up the membership once
+      // indexing finishes. A more robust approach (retry-on-422) lives
+      // in a follow-up if users complain.
+      if (workspaceID) {
+        try {
+          await api.post(`/workspaces/${workspaceID}/projects`, {
+            project_hash: resp.git_repo.path_hash,
+          });
+        } catch {
+          // Swallow — workspace polling will pick up the project once
+          // indexing completes and operators can manually link via
+          // "Add Existing Project" if anything goes wrong.
+        }
+      }
       onAdded();
     } catch (e) {
       const msg =
@@ -580,14 +604,14 @@ function CreatedResult({
   created,
   mode,
 }: {
-  created: WorkspaceRepoCreated;
+  created: GitRepoCreated;
   mode: WebhookMode;
 }) {
   return (
     <div className="space-y-3 text-sm">
       <div>
         <span className="text-muted-foreground">Project:</span>{' '}
-        <span className="font-mono">{created.repo.project_path}</span>
+        <span className="font-mono">{created.git_repo.project_path}</span>
       </div>
 
       {mode === 'auto' && (
diff --git a/server/dashboard/src/modules/workspaces/components/RepoCard.tsx b/server/dashboard/src/modules/workspaces/components/RepoCard.tsx
deleted file mode 100644
index 990d493..0000000
--- a/server/dashboard/src/modules/workspaces/components/RepoCard.tsx
+++ /dev/null
@@ -1,221 +0,0 @@
-import { useEffect, useState } from 'react';
-import {
-  AlertTriangle,
-  CheckCircle2,
-  Link2,
-  Loader2,
-  RefreshCw,
-  Trash2,
-  Webhook,
-  WebhookOff,
-} from 'lucide-react';
-import { api } from '@/api/client';
-import { Badge } from '@/ui/badge';
-import { Button } from '@/ui/button';
-import { Card, CardContent } from '@/ui/card';
-import { formatRelative } from '@/lib/formatDate';
-import type { WorkspaceRepo } from '../types';
-import { isInFlight } from '../types';
-
-// RepoCard renders one workspace_repo as a self-contained card. Status
-// drives the visual treatment — a spinner with an elapsed-time counter
-// is shown while clone/index is in flight so the operator gets feedback
-// without staring at a stale page.
-export function RepoCard({
-  repo,
-  onDeleted,
-  onReindexed,
-}: {
-  repo: WorkspaceRepo;
-  onDeleted: () => void;
-  onReindexed: () => void;
-}) {
-  const [busy, setBusy] = useState<'delete' | 'reindex' | null>(null);
-  const inFlight = isInFlight(repo.status);
-
-  async function handleDelete() {
-    const detachMsg = repo.is_linked
-      ? `Detach the linked project "${repo.github_url}@${repo.branch}" from this workspace?\n\nThe project itself stays — only this workspace's link to it is removed.`
-      : `Detach "${repo.github_url}@${repo.branch}" from this workspace?\n\nThe indexed project will also be removed.`;
-    if (!confirm(detachMsg)) {
-      return;
-    }
-    setBusy('delete');
-    try {
-      await api.delete<void>(`/workspaces/${repo.workspace_id}/repos/${repo.id}`);
-      onDeleted();
-    } catch (e) {
-      alert(e instanceof Error ? e.message : String(e));
-    } finally {
-      setBusy(null);
-    }
-  }
-
-  async function handleReindex() {
-    setBusy('reindex');
-    try {
-      await api.post(
-        `/workspaces/${repo.workspace_id}/repos/${repo.id}/reindex`,
-        {},
-      );
-      onReindexed();
-    } catch (e) {
-      alert(e instanceof Error ? e.message : String(e));
-    } finally {
-      setBusy(null);
-    }
-  }
-
-  return (
-    <Card
-      className={
-        repo.status === 'failed'
-          ? 'border-destructive/60'
-          : inFlight
-          ? 'border-amber-500/40'
-          : ''
-      }
-    >
-      <CardContent className="space-y-3 p-4">
-        <div className="flex items-start justify-between gap-2">
-          <div className="min-w-0 flex-1">
-            <div className="truncate font-medium">
-              {repo.github_url}
-              <span className="text-muted-foreground"> @ {repo.branch}</span>
-            </div>
-            <div
-              className="mt-0.5 truncate text-xs text-muted-foreground"
-              title={repo.project_path}
-            >
-              {repo.project_path}
-            </div>
-          </div>
-          <div className="flex shrink-0 items-center gap-1">
-            {/* Reindex is a no-op for linked rows — they don't own the
-                clone, so the canonical workspace must trigger it. Hide
-                the button to make that contract obvious. */}
-            {!repo.is_linked && (
-              <Button
-                variant="ghost"
-                size="sm"
-                disabled={busy !== null || inFlight}
-                title="Reindex"
-                onClick={handleReindex}
-              >
-                <RefreshCw className={`size-4 ${busy === 'reindex' ? 'animate-spin' : ''}`} />
-              </Button>
-            )}
-            <Button
-              variant="ghost"
-              size="sm"
-              disabled={busy !== null}
-              title={repo.is_linked ? 'Detach linked project' : 'Detach repo'}
-              onClick={handleDelete}
-            >
-              <Trash2 className="size-4" />
-            </Button>
-          </div>
-        </div>
-
-        <div className="flex flex-wrap items-center gap-1.5 text-xs">
-          <StatusBadge repo={repo} />
-          {repo.is_linked ? (
-            <Badge variant="outline" className="gap-1 font-normal">
-              <Link2 className="size-3" /> linked
-            </Badge>
-          ) : (
-            <WebhookBadge repo={repo} />
-          )}
-          {repo.last_indexed_at && (
-            <span className="text-muted-foreground">
-              · indexed {formatRelative(repo.last_indexed_at)}
-            </span>
-          )}
-        </div>
-
-        {repo.last_error && (
-          <div className="rounded bg-destructive/10 px-2 py-1 text-xs text-destructive">
-            {repo.last_error}
-          </div>
-        )}
-      </CardContent>
-    </Card>
-  );
-}
-
-// StatusBadge renders the colour-coded status + an elapsed-time read
-// while a clone/index job is running. The elapsed counter ticks once a
-// second so the user can tell the job hasn't silently stalled.
-function StatusBadge({ repo }: { repo: WorkspaceRepo }) {
-  const inFlight = isInFlight(repo.status);
-  const elapsed = useElapsedSince(inFlight ? repo.updated_at : null);
-
-  if (repo.status === 'indexed') {
-    return (
-      <Badge className="gap-1">
-        <CheckCircle2 className="size-3" /> indexed
-      </Badge>
-    );
-  }
-  if (repo.status === 'failed') {
-    return (
-      <Badge variant="destructive" className="gap-1">
-        <AlertTriangle className="size-3" /> failed
-      </Badge>
-    );
-  }
-  return (
-    <Badge variant="secondary" className="gap-1">
-      <Loader2 className="size-3 animate-spin" />
-      {repo.status}
-      {elapsed !== null && (
-        <span className="font-mono text-muted-foreground">· {formatDuration(elapsed)}</span>
-      )}
-    </Badge>
-  );
-}
-
-function WebhookBadge({ repo }: { repo: WorkspaceRepo }) {
-  switch (repo.webhook_mode) {
-    case 'auto':
-      return (
-        <Badge variant="outline" className="gap-1 font-normal">
-          <Webhook className="size-3" /> auto
-        </Badge>
-      );
-    case 'manual':
-      return (
-        <Badge variant="outline" className="gap-1 font-normal">
-          <Webhook className="size-3" /> manual
-        </Badge>
-      );
-    case 'disabled':
-      return (
-        <Badge variant="outline" className="gap-1 font-normal text-muted-foreground">
-          <WebhookOff className="size-3" /> disabled
-        </Badge>
-      );
-  }
-}
-
-// useElapsedSince ticks once a second so the in-flight badge shows
-// elapsed time without re-fetching from the server.
-function useElapsedSince(iso: string | null): number | null {
-  const [now, setNow] = useState(() => Date.now());
-  useEffect(() => {
-    if (iso === null) return;
-    const t = setInterval(() => setNow(Date.now()), 1000);
-    return () => clearInterval(t);
-  }, [iso]);
-  if (iso === null) return null;
-  const ts = Date.parse(iso);
-  if (Number.isNaN(ts)) return null;
-  return Math.max(0, Math.floor((now - ts) / 1000));
-}
-
-function formatDuration(seconds: number): string {
-  if (seconds < 60) return `${seconds}s`;
-  const m = Math.floor(seconds / 60);
-  const s = seconds % 60;
-  return `${m}m ${s}s`;
-}
diff --git a/server/dashboard/src/modules/workspaces/components/WorkspaceCard.tsx b/server/dashboard/src/modules/workspaces/components/WorkspaceCard.tsx
index 6400b32..7427224 100644
--- a/server/dashboard/src/modules/workspaces/components/WorkspaceCard.tsx
+++ b/server/dashboard/src/modules/workspaces/components/WorkspaceCard.tsx
@@ -4,33 +4,35 @@ import { Boxes, ChevronRight, Loader2 } from 'lucide-react';
 import { api } from '@/api/client';
 import { Badge } from '@/ui/badge';
 import { Card, CardContent } from '@/ui/card';
-import type { Workspace, WorkspaceRepo, WorkspaceRepoListResponse } from '../types';
+import type {
+  Workspace,
+  WorkspaceProject,
+  WorkspaceProjectListResponse,
+} from '../types';
 import { isInFlight } from '../types';
 import { formatRelative } from '@/lib/formatDate';
 
 // WorkspaceCard mirrors the projects ProjectCard so the dashboard reads
-// with one visual language: counts at-a-glance, status badge, "click
-// anywhere" surface. Repos are loaded lazily so the list page renders
-// instantly and each card fills in as soon as its summary arrives.
+// with one visual language. Project memberships load lazily.
 export function WorkspaceCard({ workspace }: { workspace: Workspace }) {
-  const [repos, setRepos] = useState<WorkspaceRepo[] | null>(null);
+  const [projects, setProjects] = useState<WorkspaceProject[] | null>(null);
 
   useEffect(() => {
     let cancelled = false;
     api
-      .get<WorkspaceRepoListResponse>(`/workspaces/${workspace.id}/repos`)
+      .get<WorkspaceProjectListResponse>(`/workspaces/${workspace.id}/projects`)
       .then((r) => {
-        if (!cancelled) setRepos(r.repos);
+        if (!cancelled) setProjects(r.projects);
       })
       .catch(() => {
-        if (!cancelled) setRepos([]);
+        if (!cancelled) setProjects([]);
       });
     return () => {
       cancelled = true;
     };
   }, [workspace.id]);
 
-  const summary = computeSummary(repos);
+  const summary = computeSummary(projects);
 
   return (
     <Link to={`/workspaces/${workspace.id}`} className="group">
@@ -60,30 +62,30 @@ export function WorkspaceCard({ workspace }: { workspace: Workspace }) {
                 <Loader2 className="size-3 animate-spin" />
                 {summary.busy === 1 ? '1 in progress' : `${summary.busy} in progress`}
               </Badge>
-            ) : repos === null ? (
+            ) : projects === null ? (
               <Badge variant="outline" className="font-normal">
                 Loading…
               </Badge>
-            ) : repos.length === 0 ? (
+            ) : projects.length === 0 ? (
               <Badge variant="outline" className="font-normal">
-                No repos yet
+                No projects yet
               </Badge>
             ) : summary.failed > 0 ? (
               <Badge variant="destructive">{summary.failed} failed</Badge>
             ) : (
               <Badge>Ready</Badge>
             )}
-            {repos !== null && repos.length > 0 && (
+            {projects !== null && projects.length > 0 && (
               <Badge variant="outline" className="font-normal text-xs">
-                {summary.indexed}/{repos.length} indexed
+                {summary.indexed}/{projects.length} indexed
               </Badge>
             )}
           </div>
 
           <div className="flex items-center gap-4 text-xs text-muted-foreground">
             <span className="ml-auto">
-              {repos !== null && repos.length > 0
-                ? `Updated ${formatRelative(latestUpdate(repos))}`
+              {projects !== null && projects.length > 0
+                ? `Updated ${formatRelative(latestUpdate(projects))}`
                 : `Created ${formatRelative(workspace.created_at)}`}
             </span>
           </div>
@@ -93,33 +95,28 @@ export function WorkspaceCard({ workspace }: { workspace: Workspace }) {
   );
 }
 
-// computeSummary turns the repo list into the three numbers the card
-// surface needs. Lives in this file because no other view computes the
-// same shape.
-function computeSummary(repos: WorkspaceRepo[] | null): {
+function computeSummary(projects: WorkspaceProject[] | null): {
   indexed: number;
   busy: number;
   failed: number;
 } {
-  if (!repos) return { indexed: 0, busy: 0, failed: 0 };
+  if (!projects) return { indexed: 0, busy: 0, failed: 0 };
   let indexed = 0;
   let busy = 0;
   let failed = 0;
-  for (const r of repos) {
-    if (r.status === 'indexed') indexed++;
-    else if (r.status === 'failed') failed++;
-    else if (isInFlight(r.status)) busy++;
+  for (const p of projects) {
+    const s = p.project.status;
+    if (s === 'indexed') indexed++;
+    else if (s === 'failed' || s === 'error') failed++;
+    else if (isInFlight(s)) busy++;
   }
   return { indexed, busy, failed };
 }
 
-// latestUpdate returns the most recent updated_at across a repo list.
-// Used so the card's "Updated …" footer tracks the freshest signal
-// rather than the workspace row's stale updated_at.
-function latestUpdate(repos: WorkspaceRepo[]): string {
-  let best = repos[0]?.updated_at ?? '';
-  for (const r of repos) {
-    if (r.updated_at > best) best = r.updated_at;
+function latestUpdate(projects: WorkspaceProject[]): string {
+  let best = projects[0]?.added_at ?? '';
+  for (const p of projects) {
+    if (p.added_at > best) best = p.added_at;
   }
   return best;
 }
diff --git a/server/dashboard/src/modules/workspaces/components/WorkspaceProjectRow.tsx b/server/dashboard/src/modules/workspaces/components/WorkspaceProjectRow.tsx
new file mode 100644
index 0000000..834002d
--- /dev/null
+++ b/server/dashboard/src/modules/workspaces/components/WorkspaceProjectRow.tsx
@@ -0,0 +1,138 @@
+import { useState } from 'react';
+import { Link as RouterLink } from 'react-router-dom';
+import {
+  AlertTriangle,
+  CheckCircle2,
+  Folder,
+  Github,
+  Loader2,
+  Trash2,
+} from 'lucide-react';
+import { api } from '@/api/client';
+import { Badge } from '@/ui/badge';
+import { Button } from '@/ui/button';
+import { Card, CardContent } from '@/ui/card';
+import { formatRelative } from '@/lib/formatDate';
+import type { ProjectStatus, WorkspaceProject } from '../types';
+import { isInFlight } from '../types';
+
+// WorkspaceProjectRow renders one project as it appears inside a
+// workspace. Unlink is the only action — the project itself is
+// managed on its own detail page (reindex, webhook config, delete
+// all live there). Click anywhere on the row to navigate to that
+// page; the Unlink button stops propagation so it doesn't trigger
+// the link.
+export function WorkspaceProjectRow({
+  workspaceID,
+  wp,
+  onUnlinked,
+}: {
+  workspaceID: string;
+  wp: WorkspaceProject;
+  onUnlinked: () => void;
+}) {
+  const [busy, setBusy] = useState(false);
+  const inFlight = isInFlight(wp.project.status);
+  const isExternal = wp.project.host_path.startsWith('github.com/');
+  const hash = wp.project.path_hash ?? '';
+
+  async function handleUnlink(e: React.MouseEvent) {
+    e.preventDefault();
+    e.stopPropagation();
+    if (
+      !confirm(
+        `Remove "${wp.project.host_path}" from this workspace?\n\nThe project itself stays — only this workspace's link is removed.`,
+      )
+    ) {
+      return;
+    }
+    setBusy(true);
+    try {
+      await api.delete<void>(`/workspaces/${workspaceID}/projects/${hash}`);
+      onUnlinked();
+    } catch (err) {
+      alert(err instanceof Error ? err.message : String(err));
+    } finally {
+      setBusy(false);
+    }
+  }
+
+  return (
+    <Card
+      className={
+        wp.project.status === 'failed' || wp.project.status === 'error'
+          ? 'border-destructive/60'
+          : inFlight
+          ? 'border-amber-500/40'
+          : ''
+      }
+    >
+      <CardContent className="space-y-3 p-4">
+        <div className="flex items-start justify-between gap-2">
+          <RouterLink
+            to={`/projects/${hash}`}
+            className="min-w-0 flex-1 hover:underline"
+          >
+            <div className="flex items-center gap-2 truncate font-medium">
+              {isExternal ? (
+                <Github className="size-4 shrink-0 text-muted-foreground" />
+              ) : (
+                <Folder className="size-4 shrink-0 text-muted-foreground" />
+              )}
+              {wp.project.host_path}
+            </div>
+            <div className="mt-0.5 text-xs text-muted-foreground">
+              linked {formatRelative(wp.added_at)}
+            </div>
+          </RouterLink>
+          <Button
+            variant="ghost"
+            size="sm"
+            disabled={busy}
+            title="Remove from workspace (project itself stays)"
+            onClick={handleUnlink}
+          >
+            <Trash2 className="size-4" />
+          </Button>
+        </div>
+
+        <div className="flex flex-wrap items-center gap-1.5 text-xs">
+          <StatusBadge status={wp.project.status} />
+          {wp.project.last_indexed_at && (
+            <span className="text-muted-foreground">
+              · indexed {formatRelative(wp.project.last_indexed_at)}
+            </span>
+          )}
+          {wp.project.languages.slice(0, 4).map((l) => (
+            <span key={l} className="text-muted-foreground">
+              {l}
+            </span>
+          ))}
+        </div>
+      </CardContent>
+    </Card>
+  );
+}
+
+function StatusBadge({ status }: { status: ProjectStatus }) {
+  if (status === 'indexed') {
+    return (
+      <Badge className="gap-1">
+        <CheckCircle2 className="size-3" /> indexed
+      </Badge>
+    );
+  }
+  if (status === 'error' || status === 'failed') {
+    return (
+      <Badge variant="destructive" className="gap-1">
+        <AlertTriangle className="size-3" /> {status}
+      </Badge>
+    );
+  }
+  return (
+    <Badge variant="secondary" className="gap-1">
+      <Loader2 className="size-3 animate-spin" />
+      {status}
+    </Badge>
+  );
+}
diff --git a/server/dashboard/src/modules/workspaces/types.ts b/server/dashboard/src/modules/workspaces/types.ts
index 6000cb8..7b72222 100644
--- a/server/dashboard/src/modules/workspaces/types.ts
+++ b/server/dashboard/src/modules/workspaces/types.ts
@@ -18,33 +18,53 @@ export type WorkspaceListResponse = {
 
 export type WebhookMode = 'manual' | 'auto' | 'disabled';
 
-export type RepoStatus =
+// Project lifecycle status — single source of truth lives on the
+// projects row. Surfaces directly on Project (from the projects module)
+// and on the WorkspaceProject decorator below.
+export type ProjectStatus =
+  | 'created'
   | 'pending'
   | 'cloning'
   | 'indexing'
   | 'indexed'
+  | 'error'
   | 'failed';
 
-export type WorkspaceRepo = {
-  id: string;
-  workspace_id: string;
+// GitRepo carries the clone + webhook metadata for an external project.
+// Local projects have no GitRepo row at all — that's how the dashboard
+// tells them apart from cloneable repos.
+export type GitRepo = {
+  project_path: string;
+  path_hash: string;
   github_url: string;
   branch: string;
-  project_path: string;
   token_id: string | null;
   auto_webhook: boolean;
   webhook_mode: WebhookMode;
-  status: RepoStatus;
   last_sha: string | null;
   last_error: string | null;
-  last_indexed_at: string | null;
-  is_linked: boolean;
   created_at: string;
   updated_at: string;
 };
 
-export type WorkspaceRepoListResponse = {
-  repos: WorkspaceRepo[];
+// WorkspaceProject is what /workspaces/{id}/projects returns: the
+// embedded Project plus the membership timestamp.
+export type WorkspaceProject = {
+  project: {
+    host_path: string;
+    container_path: string;
+    languages: string[];
+    status: ProjectStatus;
+    path_hash?: string;
+    last_indexed_at?: string | null;
+    created_at?: string;
+    updated_at?: string;
+  };
+  added_at: string;
+};
+
+export type WorkspaceProjectListResponse = {
+  projects: WorkspaceProject[];
   total: number;
 };
 
@@ -87,16 +107,23 @@ export type GithubAccountListResponse = {
   total: number;
 };
 
-export type WorkspaceRepoCreated = {
-  repo: WorkspaceRepo;
+// GitRepoCreated is the POST /git-repos response shape.
+export type GitRepoCreated = {
+  project: WorkspaceProject['project'];
+  git_repo: GitRepo;
   webhook_url: string;
   webhook_secret: string;
   auto_registered?: boolean;
   auto_register_note?: string;
 };
 
-// Whether the repo's status counts as "still doing something". Polling
-// stops as soon as every repo in the workspace is in a terminal state.
-export function isInFlight(status: RepoStatus): boolean {
-  return status === 'pending' || status === 'cloning' || status === 'indexing';
+// Whether a project's status counts as "still doing something". The
+// workspace detail page polls until every linked project is in a
+// terminal state.
+export function isInFlight(status: ProjectStatus): boolean {
+  return (
+    status === 'pending' ||
+    status === 'cloning' ||
+    status === 'indexing'
+  );
 }
diff --git a/server/dashboard/tsconfig.tsbuildinfo b/server/dashboard/tsconfig.tsbuildinfo
deleted file mode 100644
index 9a79695..0000000
--- a/server/dashboard/tsconfig.tsbuildinfo
+++ /dev/null
@@ -1 +0,0 @@
-{"root":["./src/main.tsx","./src/vite-env.d.ts","./src/api/client.ts","./src/api/generated.ts","./src/api/types.ts","./src/app/app.tsx","./src/app/footer.tsx","./src/app/shell.tsx","./src/app/sidebar.tsx","./src/app/themeprovider.tsx","./src/app/updatebanner.tsx","./src/app/providers.tsx","./src/auth/authprovider.tsx","./src/auth/bootstrapneededpage.tsx","./src/auth/changepasswordpage.tsx","./src/auth/loginpage.tsx","./src/auth/useauth.ts","./src/lib/cn.ts","./src/lib/editorpreference.ts","./src/lib/formatdate.ts","./src/lib/theme.ts","./src/lib/useserverstatus.ts","./src/modules/registry.ts","./src/modules/types.ts","./src/modules/api-keys/apikeyspage.tsx","./src/modules/api-keys/hooks.ts","./src/modules/api-keys/index.ts","./src/modules/api-keys/components/apikeytable.tsx","./src/modules/api-keys/components/createapikeydialog.tsx","./src/modules/api-keys/components/revokeapikeydialog.tsx","./src/modules/github-tokens/githubtokenspage.tsx","./src/modules/github-tokens/index.ts","./src/modules/home/homepage.tsx","./src/modules/home/index.ts","./src/modules/projects/projectdetailpage.tsx","./src/modules/projects/projectslistpage.tsx","./src/modules/projects/projectspage.tsx","./src/modules/projects/hooks.ts","./src/modules/projects/index.ts","./src/modules/projects/components/deleteprojectdialog.tsx","./src/modules/projects/components/projectcard.tsx","./src/modules/projects/components/projectinfocard.tsx","./src/modules/search/searchpage.tsx","./src/modules/search/hooks.ts","./src/modules/search/index.ts","./src/modules/search/components/filters.tsx","./src/modules/search/components/resultfilecard.tsx","./src/modules/search/components/resultsnippet.tsx","./src/modules/search/components/searchinput.tsx","./src/modules/server/serverpage.tsx","./src/modules/server/hooks.ts","./src/modules/server/index.ts","./src/modules/server/components/saveandrestartdialog.tsx","./src/modules/server/components/sidecarstatebadge.tsx","./src/modules/server/components/sourcepill.tsx","./src/modules/server/sections/advancedsection.tsx","./src/modules/server/sections/embeddingmodelsection.tsx","./src/modules/server/sections/runtimeparamssection.tsx","./src/modules/server/sections/sidecarsection.tsx","./src/modules/settings/settingspage.tsx","./src/modules/settings/hooks.ts","./src/modules/settings/index.ts","./src/modules/settings/components/changepasswordform.tsx","./src/modules/settings/components/sessionrow.tsx","./src/modules/settings/sections/editorsection.tsx","./src/modules/settings/sections/profilesection.tsx","./src/modules/settings/sections/sessionssection.tsx","./src/modules/settings/sections/themesection.tsx","./src/modules/users/userspage.tsx","./src/modules/users/hooks.ts","./src/modules/users/index.ts","./src/modules/users/components/deleteuserdialog.tsx","./src/modules/users/components/disableuserbutton.tsx","./src/modules/users/components/inviteuserdialog.tsx","./src/modules/users/components/userroleselect.tsx","./src/modules/users/components/userstable.tsx","./src/modules/workspaces/workspacedetailpage.tsx","./src/modules/workspaces/workspaceslistpage.tsx","./src/modules/workspaces/workspacespage.tsx","./src/modules/workspaces/index.ts","./src/modules/workspaces/types.ts","./src/modules/workspaces/components/addexistingprojectdialog.tsx","./src/modules/workspaces/components/addrepodialog.tsx","./src/modules/workspaces/components/createworkspacedialog.tsx","./src/modules/workspaces/components/repocard.tsx","./src/modules/workspaces/components/workspacecard.tsx","./src/modules/workspaces/components/workspacesearchdialog.tsx","./src/ui/alert.tsx","./src/ui/badge.tsx","./src/ui/button.tsx","./src/ui/card.tsx","./src/ui/dialog.tsx","./src/ui/input.tsx","./src/ui/label.tsx","./src/ui/radio-group.tsx","./src/ui/scroll-area.tsx","./src/ui/select.tsx","./src/ui/skeleton.tsx","./src/ui/slider.tsx","./src/ui/sonner.tsx","./src/ui/switch.tsx","./src/ui/table.tsx","./src/ui/tabs.tsx","./src/ui/tooltip.tsx"],"version":"5.9.3"}
\ No newline at end of file
diff --git a/server/internal/callgraph/callgraph.go b/server/internal/callgraph/callgraph.go
index 75a9a9d..fd0da66 100644
--- a/server/internal/callgraph/callgraph.go
+++ b/server/internal/callgraph/callgraph.go
@@ -305,7 +305,7 @@ func loadCallees(ctx context.Context, db *sql.DB, projectPath string) (map[strin
 }
 
 // CountEdges returns the number of rows in call_edges for a project.
-// Used by /api/v1/workspaces/{id}/repos to surface graph completion
+// Used by /api/v1/workspaces/{id}/projects to surface graph completion
 // state in the dashboard ("graph: 1234 edges").
 func CountEdges(ctx context.Context, db *sql.DB, projectPath string) (int, error) {
 	var n int
diff --git a/server/internal/config/config.go b/server/internal/config/config.go
index b2e1bb9..a900204 100644
--- a/server/internal/config/config.go
+++ b/server/internal/config/config.go
@@ -122,7 +122,8 @@ type Config struct {
 	SecretsDataDir string
 
 	// WorkspacesDataDir is the parent directory the worker pool clones
-	// GitHub repositories under (workspace_repos.{id}/). Defaults to
+	// GitHub repositories under (each clone lives at
+	// <WorkspacesDataDir>/<path_hash>/). Defaults to
 	// <SQLite parent>/repos. Source: CIX_WORKSPACES_DATA_DIR.
 	WorkspacesDataDir string
 
diff --git a/server/internal/db/db.go b/server/internal/db/db.go
index c696718..473f46c 100644
--- a/server/internal/db/db.go
+++ b/server/internal/db/db.go
@@ -12,17 +12,80 @@ import (
 	"os"
 	"path/filepath"
 	"strings"
+	"time"
 
 	_ "modernc.org/sqlite"
 )
 
+// migrationFn applies a single schema migration. The opts parameter carries
+// OpenOptions through to migrations that touch on-disk artefacts (the split
+// migration renames clone dirs under opts.DataDir); migrations that only
+// touch SQL ignore it.
+type migrationFn func(*sql.DB, OpenOptions) error
+
+// migration is one row in the registeredMigrations slice. version is the
+// permanent identifier recorded in schema_migrations; name is a human-readable
+// label surfaced in error messages and ops logs.
+type migration struct {
+	version int
+	name    string
+	fn      migrationFn
+}
+
+// registeredMigrations is the canonical migration ledger, in apply order.
+// schema_migrations records (version, name) after each successful run; on
+// subsequent boots applyMigrations skips every entry whose version is
+// <= MAX(schema_migrations.version), so each migration runs at most once
+// per database.
+//
+// Rules for editing this list:
+//
+//  1. Append new migrations with the next sequential version number. Never
+//     renumber, never remove — production schema_migrations rows reference
+//     these version/name tuples and a collision would silently skip work
+//     that was supposed to run.
+//  2. Keep each migration idempotent. Bootstrap (DB exists but
+//     schema_migrations is empty) runs all of them from scratch, so each
+//     must detect already-applied state via PRAGMA / sqlite_master /
+//     IF NOT EXISTS and short-circuit.
+//  3. Migrations run outside any wrapping transaction; some take their own
+//     internal tx (the split migration does). If a migration fails part-way,
+//     its schema_migrations row is NOT inserted, so the next boot retries
+//     end-to-end — which is why idempotency is non-negotiable.
+var registeredMigrations = []migration{
+	{1, "path_hash", func(db *sql.DB, _ OpenOptions) error { return migratePathHash(db) }},
+	{2, "indexed_with_model", func(db *sql.DB, _ OpenOptions) error { return migrateIndexedWithModel(db) }},
+	{3, "webhook_mode", func(db *sql.DB, _ OpenOptions) error { return migrateWebhookMode(db) }},
+	{4, "workspace_repos_linked", func(db *sql.DB, _ OpenOptions) error { return migrateWorkspaceReposLinked(db) }},
+	{5, "split_workspace_repos", func(db *sql.DB, opts OpenOptions) error { return migrateSplitWorkspaceRepos(db, opts.DataDir) }},
+	{6, "drop_communities", func(db *sql.DB, _ OpenOptions) error { return migrateDropCommunities(db) }},
+}
+
 // DriverName is the registered database/sql driver name for modernc.org/sqlite.
 const DriverName = "sqlite"
 
-// Open opens (and creates if necessary) the SQLite database at path, sets the
-// required PRAGMAs via the DSN, and runs the schema migration. Pass ":memory:"
-// for an in-memory DB (used by tests).
+// OpenOptions configures Open. DataDir is only consulted by migrations
+// that need to rename on-disk artefacts (e.g. the split of workspace_repos
+// into git_repos renamed clone directories from {workspace_repos.id} to
+// {path_hash}). Empty DataDir means "skip filesystem-touching migrations
+// in this call" — tests use this.
+type OpenOptions struct {
+	Path    string
+	DataDir string
+}
+
+// Open is the conventional entry point used everywhere except main.go.
+// It defers to OpenWith with an empty DataDir, so any migration that
+// wants to rename on-disk files becomes a no-op for tests + in-memory DBs.
 func Open(path string) (*sql.DB, error) {
+	return OpenWith(OpenOptions{Path: path})
+}
+
+// OpenWith opens (and creates if necessary) the SQLite database at
+// opts.Path, sets the required PRAGMAs via the DSN, and runs the
+// schema migrations.
+func OpenWith(opts OpenOptions) (*sql.DB, error) {
+	path := opts.Path
 	dsn, err := buildDSN(path)
 	if err != nil {
 		return nil, err
@@ -62,50 +125,63 @@ func Open(path string) (*sql.DB, error) {
 		return nil, fmt.Errorf("apply schema: %w", err)
 	}
 
-	// m7 — migrate existing databases that pre-date the path_hash column.
-	// We add the column + index if absent, then backfill in a single pass.
-	if err := migratePathHash(db); err != nil {
+	if err := applyMigrations(db, opts); err != nil {
 		_ = db.Close()
-		return nil, fmt.Errorf("migrate path_hash: %w", err)
+		return nil, err
 	}
 
-	// PR-E — add indexed_with_model to projects on pre-PR-E databases. Same
-	// PRAGMA-table_info pattern as migratePathHash; no backfill (NULL means
-	// "indexed before drift tracking landed" — UI renders this as Unknown,
-	// not as a stale-model warning).
-	if err := migrateIndexedWithModel(db); err != nil {
-		_ = db.Close()
-		return nil, fmt.Errorf("migrate indexed_with_model: %w", err)
-	}
+	return db, nil
+}
 
-	// PR10 — extend workspace_repos with webhook_mode so the dashboard
-	// can distinguish manual/auto/disabled intents. Older databases get
-	// the column with a sensible default; rows where auto_webhook=1 are
-	// retro-fitted to 'auto' so they keep the same effective behaviour.
-	if err := migrateWebhookMode(db); err != nil {
-		_ = db.Close()
-		return nil, fmt.Errorf("migrate webhook_mode: %w", err)
+// applyMigrations runs every entry in registeredMigrations whose version is
+// greater than the current high-water mark in schema_migrations. Each
+// successful migration records a (version, name, applied_at) row so the
+// same migration never runs twice on the same database.
+//
+// Bootstrap behaviour: when schema_migrations is empty (fresh DB or any
+// production DB that pre-dates this ledger), MAX(version) reads as 0 and
+// every registered migration runs. The migrations are individually
+// idempotent — they short-circuit on already-current state — so this
+// is the same cost as the pre-ledger code path. The benefit kicks in
+// from the SECOND boot onwards: applyMigrations sees MAX = N and skips
+// every entry <= N, turning warm boots into a single SELECT.
+//
+// schema_migrations itself is created here, not in Schema, so the bootstrap
+// path on a legacy DB (which never ran Schema with the row) still gets a
+// ledger. Schema.Exec runs first in OpenWith and uses IF NOT EXISTS, so the
+// table is harmlessly recreated by this function on the same boot.
+func applyMigrations(db *sql.DB, opts OpenOptions) error {
+	if _, err := db.Exec(`CREATE TABLE IF NOT EXISTS schema_migrations (
+        version    INTEGER PRIMARY KEY,
+        name       TEXT    NOT NULL,
+        applied_at TEXT    NOT NULL
+    )`); err != nil {
+		return fmt.Errorf("create schema_migrations: %w", err)
 	}
 
-	// PR13 — workspace_repos.is_linked + drop the legacy global UNIQUE
-	// on project_path. The rebuild path is taken only when the old
-	// constraint is still present; freshly-created DBs hit the new
-	// CREATE TABLE shape via Schema and the rebuild becomes a no-op.
-	if err := migrateWorkspaceReposLinked(db); err != nil {
-		_ = db.Close()
-		return nil, fmt.Errorf("migrate workspace_repos is_linked: %w", err)
+	var currentMax sql.NullInt64
+	if err := db.QueryRow(
+		`SELECT MAX(version) FROM schema_migrations`,
+	).Scan(&currentMax); err != nil {
+		return fmt.Errorf("read schema_migrations max version: %w", err)
 	}
+	threshold := currentMax.Int64
 
-	// PR14 — workspace search switched from the Louvain-centroid two-
-	// stage pipeline to a weighted fan-out. The communities +
-	// community_members tables stop being written; drop them on
-	// upgrade so the schema reflects what's actually used.
-	if err := migrateDropCommunities(db); err != nil {
-		_ = db.Close()
-		return nil, fmt.Errorf("migrate drop communities: %w", err)
+	for _, m := range registeredMigrations {
+		if int64(m.version) <= threshold {
+			continue
+		}
+		if err := m.fn(db, opts); err != nil {
+			return fmt.Errorf("migration %d (%s): %w", m.version, m.name, err)
+		}
+		if _, err := db.Exec(
+			`INSERT INTO schema_migrations (version, name, applied_at) VALUES (?, ?, ?)`,
+			m.version, m.name, time.Now().UTC().Format(time.RFC3339Nano),
+		); err != nil {
+			return fmt.Errorf("record migration %d (%s): %w", m.version, m.name, err)
+		}
 	}
-
-	return db, nil
+	return nil
 }
 
 // migrateDropCommunities removes the PR5–PR12 communities +
@@ -436,6 +512,265 @@ func migrateWebhookMode(db *sql.DB) error {
 	return nil
 }
 
+// migrateSplitWorkspaceRepos converts a legacy workspace_repos table
+// into two new tables: git_repos (clone + webhook metadata, 1:1 with
+// projects for external repos) and workspace_projects (workspace ↔
+// project junction). After the table is consumed it is dropped, so
+// re-running the migration on already-migrated DBs is a fast no-op.
+//
+// dataDir, when non-empty, points at the on-disk workspace data root.
+// External (owned, non-linked) workspace_repos rows used to keep their
+// clone in {dataDir}/repos/{workspace_repos.id}; we rename those dirs
+// to {dataDir}/repos/{path_hash} so the new gitrepos service finds
+// them.
+//
+// Crash-safety contract — FS renames run BEFORE the DB transaction:
+// a kill -9 between commit and rename used to leave the DB split but
+// the clone dirs stranded under their old UUID names (causing silent
+// re-clones on next start). By running renames first and refusing to
+// drop workspace_repos when any rename hard-fails, a retry on next
+// start is fully idempotent (INSERT OR IGNORE on workspace_projects /
+// git_repos, skip-target-exists on the rename loop). Missing source
+// dirs (legacy clone job died before mkdir) and pre-existing targets
+// (partial rename from a previous run) are non-fatal skips.
+//
+// Pre-conditions on the legacy table: the earlier migrateWebhookMode +
+// migrateWorkspaceReposLinked passes brought it up to the richest
+// shape (webhook_mode + is_linked columns present, no global UNIQUE
+// on project_path).
+func migrateSplitWorkspaceRepos(db *sql.DB, dataDir string) error {
+	exists, err := tableExists(db, "workspace_repos")
+	if err != nil {
+		return err
+	}
+	if !exists {
+		return nil
+	}
+
+	type rowSnapshot struct {
+		id            string
+		workspaceID   string
+		githubURL     string
+		branch        string
+		projectPath   string
+		tokenID       sql.NullString
+		webhookSecret string
+		webhookID     sql.NullInt64
+		autoWebhook   int
+		webhookMode   string
+		lastSHA       sql.NullString
+		lastError     sql.NullString
+		isLinked      int
+		createdAt     string
+		updatedAt     string
+	}
+
+	rows, err := db.Query(`
+		SELECT id, workspace_id, github_url, branch, project_path,
+		       token_id, webhook_secret, webhook_id, auto_webhook,
+		       webhook_mode, last_sha, last_error, is_linked,
+		       created_at, updated_at
+		  FROM workspace_repos`)
+	if err != nil {
+		return fmt.Errorf("select workspace_repos: %w", err)
+	}
+	var legacy []rowSnapshot
+	for rows.Next() {
+		var s rowSnapshot
+		if err := rows.Scan(
+			&s.id, &s.workspaceID, &s.githubURL, &s.branch, &s.projectPath,
+			&s.tokenID, &s.webhookSecret, &s.webhookID, &s.autoWebhook,
+			&s.webhookMode, &s.lastSHA, &s.lastError, &s.isLinked,
+			&s.createdAt, &s.updatedAt,
+		); err != nil {
+			rows.Close()
+			return fmt.Errorf("scan workspace_repos row: %w", err)
+		}
+		legacy = append(legacy, s)
+	}
+	rows.Close()
+	if err := rows.Err(); err != nil {
+		return fmt.Errorf("iterate workspace_repos: %w", err)
+	}
+
+	// Build the rename plan from the legacy snapshot. Only owned
+	// external rows (not linked, project_path is github.com/owner/repo@branch)
+	// have a clone directory on disk; linked rows reuse the owner's
+	// clone, and local projects have no on-disk artifact at all.
+	type renamePair struct{ oldID, newHash string }
+	var renames []renamePair
+	for _, s := range legacy {
+		if s.isLinked != 0 || !looksLikeGitHubProjectPath(s.projectPath) {
+			continue
+		}
+		renames = append(renames, renamePair{
+			oldID:   s.id,
+			newHash: HashHostPath(s.projectPath),
+		})
+	}
+
+	// Filesystem renames run BEFORE the SQL transaction. If a hard
+	// failure happens (permissions, EROFS, …) we return an error and
+	// leave workspace_repos intact, so the next process start retries
+	// the migration end-to-end. The DB-side inserts are idempotent
+	// via INSERT OR IGNORE, and the rename loop's skip-target-exists
+	// branch keeps the FS retry idempotent too.
+	if dataDir != "" && len(renames) > 0 {
+		base := filepath.Join(dataDir, "repos")
+		var renamed, skippedMissing, skippedExisting, failed int
+		for _, rp := range renames {
+			oldPath := filepath.Join(base, rp.oldID)
+			newPath := filepath.Join(base, rp.newHash)
+			if _, statErr := os.Stat(oldPath); statErr != nil {
+				// Source missing — legacy clone job died before mkdir,
+				// or a prior run already renamed away. Either way no
+				// FS work needed and the next clone job will recreate.
+				skippedMissing++
+				continue
+			}
+			if _, statErr := os.Stat(newPath); statErr == nil {
+				// Target already there — prior partial run completed
+				// this rename. Safe to skip.
+				skippedExisting++
+				continue
+			}
+			if err := os.Rename(oldPath, newPath); err != nil {
+				failed++
+				fmt.Fprintf(os.Stderr,
+					"db: migrateSplitWorkspaceRepos: rename %s → %s failed: %v\n",
+					oldPath, newPath, err)
+				continue
+			}
+			renamed++
+		}
+		fmt.Fprintf(os.Stderr,
+			"db: migrateSplitWorkspaceRepos: clone-dir renames "+
+				"renamed=%d skipped_missing_source=%d skipped_target_exists=%d failed=%d\n",
+			renamed, skippedMissing, skippedExisting, failed)
+		if failed > 0 {
+			return fmt.Errorf(
+				"migrateSplitWorkspaceRepos: %d clone-dir rename(s) failed; "+
+					"refusing to drop workspace_repos so migration retries on next start",
+				failed,
+			)
+		}
+	}
+
+	tx, err := db.Begin()
+	if err != nil {
+		return fmt.Errorf("begin split tx: %w", err)
+	}
+	defer func() { _ = tx.Rollback() }()
+
+	// Pre-seed projects rows for any project_path that's referenced by
+	// the legacy workspace_repos but doesn't yet exist in projects
+	// (typical state for rows still in clone/index lifecycle when the
+	// upgrade boots). Both workspace_projects and git_repos FK to
+	// projects(host_path), so the membership + clone-metadata inserts
+	// below would fail without this.
+	for _, s := range legacy {
+		if _, err := tx.Exec(`
+			INSERT OR IGNORE INTO projects (
+				host_path, container_path, languages, settings, stats,
+				status, created_at, updated_at, path_hash
+			) VALUES (?, ?, '[]', '{}', '{}', 'pending', ?, ?, ?)`,
+			s.projectPath, s.projectPath,
+			s.createdAt, s.updatedAt, HashHostPath(s.projectPath),
+		); err != nil {
+			return fmt.Errorf("pre-seed projects row for %s: %w", s.projectPath, err)
+		}
+	}
+
+	for _, s := range legacy {
+		// Every legacy row becomes a workspace_projects membership.
+		if _, err := tx.Exec(`
+			INSERT OR IGNORE INTO workspace_projects
+				(workspace_id, project_path, added_at)
+			VALUES (?, ?, ?)`,
+			s.workspaceID, s.projectPath, s.createdAt,
+		); err != nil {
+			return fmt.Errorf("insert workspace_projects: %w", err)
+		}
+
+		// Owned + external rows additionally seed a git_repos row.
+		// Linked rows reuse the canonical owner's git_repos row, so we
+		// skip them here. Local rows (project_path doesn't look like
+		// github.com/owner/repo@branch) have no git_repos representation.
+		if s.isLinked != 0 || !looksLikeGitHubProjectPath(s.projectPath) {
+			continue
+		}
+		webhookMode := s.webhookMode
+		if webhookMode == "" {
+			webhookMode = "manual"
+		}
+		if _, err := tx.Exec(`
+			INSERT OR IGNORE INTO git_repos (
+				project_path, github_url, branch,
+				token_id, webhook_secret, webhook_id,
+				webhook_mode, auto_webhook,
+				last_sha, last_error,
+				created_at, updated_at
+			) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)`,
+			s.projectPath, s.githubURL, s.branch,
+			nullableSQL(s.tokenID), s.webhookSecret, nullableSQLInt(s.webhookID),
+			webhookMode, s.autoWebhook,
+			nullableSQL(s.lastSHA), nullableSQL(s.lastError),
+			s.createdAt, s.updatedAt,
+		); err != nil {
+			return fmt.Errorf("insert git_repos for %s: %w", s.projectPath, err)
+		}
+	}
+
+	if _, err := tx.Exec(`DROP TABLE workspace_repos`); err != nil {
+		return fmt.Errorf("drop workspace_repos: %w", err)
+	}
+	if err := tx.Commit(); err != nil {
+		return fmt.Errorf("commit split tx: %w", err)
+	}
+	return nil
+}
+
+// looksLikeGitHubProjectPath decides whether a workspace_repos.project_path
+// follows the canonical "github.com/owner/repo@branch" shape used for
+// external repos. Local-path projects (absolute filesystem paths) fail this
+// check and are handled as workspace-only memberships during the split.
+func looksLikeGitHubProjectPath(projectPath string) bool {
+	s := strings.TrimSpace(projectPath)
+	if !strings.HasPrefix(s, "github.com/") {
+		return false
+	}
+	return strings.LastIndex(s, "@") > 0
+}
+
+// tableExists returns whether a table with the given name is registered in
+// sqlite_master. Used by migrations to short-circuit on already-migrated DBs.
+func tableExists(db *sql.DB, name string) (bool, error) {
+	row := db.QueryRow(
+		`SELECT 1 FROM sqlite_master WHERE type = 'table' AND name = ?`, name)
+	var dummy int
+	if err := row.Scan(&dummy); err != nil {
+		if errors.Is(err, sql.ErrNoRows) {
+			return false, nil
+		}
+		return false, fmt.Errorf("sqlite_master lookup for %q: %w", name, err)
+	}
+	return true, nil
+}
+
+func nullableSQL(s sql.NullString) any {
+	if !s.Valid {
+		return nil
+	}
+	return s.String
+}
+
+func nullableSQLInt(n sql.NullInt64) any {
+	if !n.Valid {
+		return nil
+	}
+	return n.Int64
+}
+
 // HashHostPath returns the 16-char SHA1 prefix used as the URL segment for
 // projects. Exported so projects.Create and the migration share one
 // implementation (keep it byte-identical to projects.HashPath).
diff --git a/server/internal/db/db_test.go b/server/internal/db/db_test.go
index f0cfba9..d690d38 100644
--- a/server/internal/db/db_test.go
+++ b/server/internal/db/db_test.go
@@ -4,7 +4,9 @@ import (
 	"database/sql"
 	"os"
 	"path/filepath"
+	"runtime"
 	"sort"
+	"strings"
 	"testing"
 
 	_ "modernc.org/sqlite"
@@ -227,30 +229,180 @@ func TestSymbolsIndexExists(t *testing.T) {
 	}
 }
 
-// TestMigrate_DropsGlobalUniqueOnProjectPath verifies that opening a
-// pre-PR13 database (workspace_repos with `project_path TEXT NOT NULL UNIQUE`)
-// migrates it to the current shape, dropping the global UNIQUE so the
-// same indexed project can live in multiple workspaces.
+// TestMigrate_SplitWorkspaceRepos verifies the conversion from the
+// legacy workspace_repos table into the new git_repos + workspace_projects
+// shape. Three legacy rows are seeded covering all three flavours that
+// existed before the split: an owned external repo, a linked external
+// repo (is_linked=1), and a local-path repo (host_path doesn't match
+// github.com/owner/repo@branch). After Open():
 //
-// Strategy: create a fresh file-backed DB, manually lay down the
-// legacy table shape + seed one row, close, reopen via Open() so the
-// migration runs, then try inserting a second row with the same
-// project_path in a different workspace_id — pre-migration this would
-// fail with UNIQUE constraint failed; post-migration it must succeed.
-func TestMigrate_DropsGlobalUniqueOnProjectPath(t *testing.T) {
+//   - workspace_repos is gone.
+//   - git_repos has exactly one row — for the owned external; linked +
+//     local rows must not seed git_repos.
+//   - workspace_projects has three rows — every legacy membership is
+//     preserved, regardless of flavour.
+//   - The on-disk clone directory for the owned row is renamed from
+//     {workspace_repos.id} to {path_hash}; the linked + local IDs have
+//     no on-disk artifacts to begin with so the migration leaves the
+//     filesystem alone for them.
+func TestMigrate_SplitWorkspaceRepos(t *testing.T) {
 	dir := t.TempDir()
-	path := filepath.Join(dir, "test.db")
+	dbPath := filepath.Join(dir, "test.db")
+	dataDir := filepath.Join(dir, "data")
+	if err := os.MkdirAll(filepath.Join(dataDir, "repos", "owned-id"), 0o755); err != nil {
+		t.Fatalf("mkdir owned clone: %v", err)
+	}
 
-	// Open with the regular driver (bypass Schema by hand-rolling DDL).
-	raw, err := sql.Open(DriverName, "file:"+path+"?_pragma=foreign_keys(ON)")
+	raw, err := sql.Open(DriverName, "file:"+dbPath+"?_pragma=foreign_keys(ON)")
 	if err != nil {
 		t.Fatalf("raw open: %v", err)
 	}
 
-	// Lay down only the minimum tables the legacy workspace_repos needs:
-	// workspaces (FK target) + the OLD workspace_repos shape with the
-	// inline UNIQUE on project_path. github_tokens is FK-referenced but
-	// nullable, so we can skip it for this test.
+	// Lay down the post-PR13 / pre-split shape (matches what an upgraded
+	// prod DB looks like just before this migration ran for the first time).
+	legacy := `
+		CREATE TABLE workspaces (
+			id TEXT PRIMARY KEY,
+			name TEXT NOT NULL UNIQUE,
+			description TEXT NOT NULL DEFAULT '',
+			created_at TEXT NOT NULL,
+			updated_at TEXT NOT NULL
+		);
+		CREATE TABLE workspace_repos (
+			id              TEXT PRIMARY KEY,
+			workspace_id    TEXT NOT NULL,
+			github_url      TEXT NOT NULL,
+			branch          TEXT NOT NULL,
+			project_path    TEXT NOT NULL,
+			token_id        TEXT,
+			webhook_secret  TEXT NOT NULL,
+			webhook_id      INTEGER,
+			auto_webhook    INTEGER NOT NULL DEFAULT 0,
+			webhook_mode    TEXT NOT NULL DEFAULT 'manual',
+			status          TEXT NOT NULL DEFAULT 'pending',
+			last_sha        TEXT,
+			last_error      TEXT,
+			last_indexed_at TEXT,
+			is_linked       INTEGER NOT NULL DEFAULT 0,
+			created_at      TEXT NOT NULL,
+			updated_at      TEXT NOT NULL,
+			UNIQUE(workspace_id, github_url, branch),
+			FOREIGN KEY (workspace_id) REFERENCES workspaces(id) ON DELETE CASCADE
+		);
+		INSERT INTO workspaces (id, name, created_at, updated_at) VALUES
+			('ws-a', 'alpha', '2026-05-14T00:00:00Z', '2026-05-14T00:00:00Z'),
+			('ws-b', 'beta',  '2026-05-14T00:00:00Z', '2026-05-14T00:00:00Z');
+		INSERT INTO workspace_repos
+			(id, workspace_id, github_url, branch, project_path,
+			 webhook_secret, status, is_linked, webhook_mode,
+			 created_at, updated_at)
+		VALUES
+			('owned-id', 'ws-a', 'https://github.com/x/y', 'main',
+				'github.com/x/y@main', 's-owned', 'indexed', 0, 'manual',
+				'2026-05-14T00:00:00Z', '2026-05-14T00:00:00Z'),
+			('linked-id', 'ws-b', 'https://github.com/x/y', 'main',
+				'github.com/x/y@main', 's-linked', 'indexed', 1, 'disabled',
+				'2026-05-14T00:00:00Z', '2026-05-14T00:00:00Z'),
+			('local-id', 'ws-a', '/Users/x/local-proj', '',
+				'/Users/x/local-proj', 's-local', 'indexed', 1, 'disabled',
+				'2026-05-14T00:00:00Z', '2026-05-14T00:00:00Z');
+	`
+	if _, err := raw.Exec(legacy); err != nil {
+		_ = raw.Close()
+		t.Fatalf("seed legacy: %v", err)
+	}
+	_ = raw.Close()
+
+	migrated, err := OpenWith(OpenOptions{Path: dbPath, DataDir: dataDir})
+	if err != nil {
+		t.Fatalf("OpenWith: %v", err)
+	}
+	defer migrated.Close()
+
+	// workspace_repos is gone.
+	var n int
+	if err := migrated.QueryRow(
+		`SELECT COUNT(*) FROM sqlite_master WHERE type='table' AND name='workspace_repos'`,
+	).Scan(&n); err != nil {
+		t.Fatalf("count workspace_repos: %v", err)
+	}
+	if n != 0 {
+		t.Fatalf("workspace_repos should be dropped after migration, count=%d", n)
+	}
+
+	// git_repos has exactly the one owned-external row.
+	if err := migrated.QueryRow(`SELECT COUNT(*) FROM git_repos`).Scan(&n); err != nil {
+		t.Fatalf("count git_repos: %v", err)
+	}
+	if n != 1 {
+		t.Fatalf("expected 1 git_repos row, got %d", n)
+	}
+	var gh, branch, secret string
+	if err := migrated.QueryRow(
+		`SELECT github_url, branch, webhook_secret FROM git_repos WHERE project_path = ?`,
+		"github.com/x/y@main",
+	).Scan(&gh, &branch, &secret); err != nil {
+		t.Fatalf("read git_repos: %v", err)
+	}
+	if gh != "https://github.com/x/y" || branch != "main" || secret != "s-owned" {
+		t.Fatalf("git_repos row mismatch: gh=%q branch=%q secret=%q", gh, branch, secret)
+	}
+
+	// workspace_projects holds three rows — one per legacy workspace_repos.
+	if err := migrated.QueryRow(`SELECT COUNT(*) FROM workspace_projects`).Scan(&n); err != nil {
+		t.Fatalf("count workspace_projects: %v", err)
+	}
+	if n != 3 {
+		t.Fatalf("expected 3 workspace_projects rows, got %d", n)
+	}
+
+	// On-disk clone for the owned row was renamed from {old id} → {path_hash}.
+	expectedPath := filepath.Join(dataDir, "repos", HashHostPath("github.com/x/y@main"))
+	if _, err := os.Stat(expectedPath); err != nil {
+		t.Fatalf("clone dir was not renamed to %s: %v", expectedPath, err)
+	}
+	if _, err := os.Stat(filepath.Join(dataDir, "repos", "owned-id")); err == nil {
+		t.Fatalf("legacy clone dir still exists after rename")
+	}
+
+	// Re-running Open() must be a no-op — workspace_repos is already
+	// gone so the migration short-circuits at tableExists().
+	migrated.Close()
+	again, err := OpenWith(OpenOptions{Path: dbPath, DataDir: dataDir})
+	if err != nil {
+		t.Fatalf("second OpenWith: %v", err)
+	}
+	defer again.Close()
+}
+
+// TestMigrate_SplitWorkspaceRepos_PartialRename covers Fix #3 of the
+// branch review: when a clone-dir rename hard-fails (permissions, EROFS,
+// …) the migration must NOT drop workspace_repos. The old code dropped
+// the table first and then attempted renames; a kill -9 in the gap
+// stranded clone dirs and silently re-cloned on next start. The new
+// code does renames before the SQL transaction and returns an error
+// on any real failure, so the next process start retries end-to-end.
+//
+// On Unix we drop write on the repos parent dir to force EACCES from
+// rename(2). Skipped on Windows where the permission model differs and
+// we can't reliably trigger the same failure mode portably.
+func TestMigrate_SplitWorkspaceRepos_PartialRename(t *testing.T) {
+	if runtime.GOOS == "windows" {
+		t.Skip("permission-based rename failure not portable to Windows")
+	}
+
+	dir := t.TempDir()
+	dbPath := filepath.Join(dir, "test.db")
+	dataDir := filepath.Join(dir, "data")
+	reposDir := filepath.Join(dataDir, "repos")
+	if err := os.MkdirAll(filepath.Join(reposDir, "owned-id"), 0o755); err != nil {
+		t.Fatalf("mkdir owned clone: %v", err)
+	}
+
+	raw, err := sql.Open(DriverName, "file:"+dbPath+"?_pragma=foreign_keys(ON)")
+	if err != nil {
+		t.Fatalf("raw open: %v", err)
+	}
 	legacy := `
 		CREATE TABLE workspaces (
 			id TEXT PRIMARY KEY,
@@ -264,7 +416,7 @@ func TestMigrate_DropsGlobalUniqueOnProjectPath(t *testing.T) {
 			workspace_id    TEXT NOT NULL,
 			github_url      TEXT NOT NULL,
 			branch          TEXT NOT NULL,
-			project_path    TEXT NOT NULL UNIQUE,
+			project_path    TEXT NOT NULL,
 			token_id        TEXT,
 			webhook_secret  TEXT NOT NULL,
 			webhook_id      INTEGER,
@@ -274,73 +426,577 @@ func TestMigrate_DropsGlobalUniqueOnProjectPath(t *testing.T) {
 			last_sha        TEXT,
 			last_error      TEXT,
 			last_indexed_at TEXT,
+			is_linked       INTEGER NOT NULL DEFAULT 0,
 			created_at      TEXT NOT NULL,
 			updated_at      TEXT NOT NULL,
 			UNIQUE(workspace_id, github_url, branch),
 			FOREIGN KEY (workspace_id) REFERENCES workspaces(id) ON DELETE CASCADE
 		);
-		INSERT INTO workspaces (id, name, created_at, updated_at)
-			VALUES ('ws-a', 'alpha', '2026-05-11T00:00:00Z', '2026-05-11T00:00:00Z');
-		INSERT INTO workspaces (id, name, created_at, updated_at)
-			VALUES ('ws-b', 'beta',  '2026-05-11T00:00:00Z', '2026-05-11T00:00:00Z');
-		INSERT INTO workspace_repos (id, workspace_id, github_url, branch, project_path,
-			webhook_secret, created_at, updated_at)
-			VALUES ('repo-1', 'ws-a', 'https://github.com/x/y', 'main',
-			        'github.com/x/y@main', 's', '2026-05-11T00:00:00Z', '2026-05-11T00:00:00Z');
+		INSERT INTO workspaces (id, name, created_at, updated_at) VALUES
+			('ws-a', 'alpha', '2026-05-14T00:00:00Z', '2026-05-14T00:00:00Z');
+		INSERT INTO workspace_repos
+			(id, workspace_id, github_url, branch, project_path,
+			 webhook_secret, status, is_linked, webhook_mode,
+			 created_at, updated_at)
+		VALUES
+			('owned-id', 'ws-a', 'https://github.com/x/y', 'main',
+				'github.com/x/y@main', 's-owned', 'indexed', 0, 'manual',
+				'2026-05-14T00:00:00Z', '2026-05-14T00:00:00Z');
 	`
 	if _, err := raw.Exec(legacy); err != nil {
+		_ = raw.Close()
 		t.Fatalf("seed legacy: %v", err)
 	}
+	_ = raw.Close()
+
+	// Drop write on the parent of source+target. rename(2) needs write
+	// on both parents (which here are the same dir) so the syscall
+	// will return EACCES. Restore in cleanup so t.TempDir can run.
+	if err := os.Chmod(reposDir, 0o500); err != nil {
+		t.Fatalf("chmod %s to read-only: %v", reposDir, err)
+	}
+	t.Cleanup(func() {
+		_ = os.Chmod(reposDir, 0o755)
+	})
 
-	// Confirm pre-migration: the second insert with same project_path
-	// would fail. We catch the error so the test is honest about the
-	// invariant we're removing.
-	_, err = raw.Exec(`INSERT INTO workspace_repos (id, workspace_id, github_url, branch, project_path,
-		webhook_secret, created_at, updated_at) VALUES ('repo-bad', 'ws-b', 'https://github.com/x/y', 'main',
-		'github.com/x/y@main', 's', '2026-05-11T00:00:00Z', '2026-05-11T00:00:00Z')`)
+	// OpenWith must surface the rename failure and refuse to drop
+	// workspace_repos.
+	_, err = OpenWith(OpenOptions{Path: dbPath, DataDir: dataDir})
 	if err == nil {
+		t.Fatalf("expected OpenWith to fail when rename is denied, got nil")
+	}
+	if !strings.Contains(err.Error(), "rename") {
+		t.Fatalf("expected error to mention rename, got: %v", err)
+	}
+
+	// Restore perms so we can inspect the DB and run the retry.
+	if err := os.Chmod(reposDir, 0o755); err != nil {
+		t.Fatalf("chmod %s restore: %v", reposDir, err)
+	}
+
+	raw2, err := sql.Open(DriverName, "file:"+dbPath+"?_pragma=foreign_keys(ON)")
+	if err != nil {
+		t.Fatalf("raw open #2: %v", err)
+	}
+	var n int
+	if err := raw2.QueryRow(
+		`SELECT COUNT(*) FROM sqlite_master WHERE type='table' AND name='workspace_repos'`,
+	).Scan(&n); err != nil {
+		_ = raw2.Close()
+		t.Fatalf("count workspace_repos: %v", err)
+	}
+	_ = raw2.Close()
+	if n != 1 {
+		t.Fatalf("workspace_repos should still exist (migration must be retry-safe), got count=%d", n)
+	}
+
+	// Source dir untouched (still under old id, no target created).
+	if _, err := os.Stat(filepath.Join(reposDir, "owned-id")); err != nil {
+		t.Fatalf("source clone dir should still exist: %v", err)
+	}
+	if _, err := os.Stat(filepath.Join(reposDir, HashHostPath("github.com/x/y@main"))); err == nil {
+		t.Fatalf("target clone dir should not have been created on failure")
+	}
+
+	// Retry — with perms restored, OpenWith finishes the migration
+	// end-to-end. INSERT OR IGNORE on workspace_projects / git_repos
+	// and skip-target-exists on rename keep it idempotent.
+	db, err := OpenWith(OpenOptions{Path: dbPath, DataDir: dataDir})
+	if err != nil {
+		t.Fatalf("OpenWith retry: %v", err)
+	}
+	defer db.Close()
+
+	if err := db.QueryRow(
+		`SELECT COUNT(*) FROM sqlite_master WHERE type='table' AND name='workspace_repos'`,
+	).Scan(&n); err != nil {
+		t.Fatalf("count workspace_repos post-retry: %v", err)
+	}
+	if n != 0 {
+		t.Fatalf("workspace_repos should be dropped after successful retry, got count=%d", n)
+	}
+	expected := filepath.Join(reposDir, HashHostPath("github.com/x/y@main"))
+	if _, err := os.Stat(expected); err != nil {
+		t.Fatalf("clone dir was not renamed on retry: %v", err)
+	}
+	if _, err := os.Stat(filepath.Join(reposDir, "owned-id")); err == nil {
+		t.Fatalf("legacy clone dir still exists after retry")
+	}
+}
+
+// TestMigrate_SplitWorkspaceRepos_EdgeCases — Fix #14 coverage. Each
+// subtest exercises one corner of the migration's rename loop or DB-side
+// insert pass:
+//
+//   - PreExistingTarget_Skipped: target dir already exists under the new
+//     path_hash (prior partial-run did this rename). The migration must
+//     skip the rename — neither overwriting the existing target nor
+//     erroring — and the DB split must proceed.
+//   - MissingSourceDir_Skipped: DB row references a clone that never
+//     materialised on disk (legacy clone job died before mkdir). The
+//     migration must treat the missing source as a no-op rename and
+//     still complete the DB split.
+//   - DuplicatePathInLegacy: two legacy rows in the same workspace map
+//     to the same (workspace_id, project_path) tuple. INSERT OR IGNORE
+//     into workspace_projects must collapse them to a single membership
+//     row without erroring on the PK collision.
+//
+// PartialRename_ReturnsError (the fifth review-doc case) is already
+// covered by TestMigrate_SplitWorkspaceRepos_PartialRename above; not
+// duplicated here.
+//
+// TokenDeletedConcurrently (review-doc case 5) is intentionally NOT
+// implemented — simulating a token row vanishing mid-migration requires
+// either a mock of the github_tokens FK or a goroutine deleting from a
+// parallel connection, both of which are out of scope for a DB-only
+// migration test. Tracked as a TODO; reintroduce when there's a
+// workspacejobs integration suite that can drive token lifecycle
+// alongside the migration.
+func TestMigrate_SplitWorkspaceRepos_EdgeCases(t *testing.T) {
+	t.Run("PreExistingTarget_Skipped", func(t *testing.T) {
+		dir := t.TempDir()
+		dbPath := filepath.Join(dir, "test.db")
+		dataDir := filepath.Join(dir, "data")
+		reposDir := filepath.Join(dataDir, "repos")
+
+		projectPath := "github.com/x/y@main"
+		targetHash := HashHostPath(projectPath)
+
+		// Legacy source dir with a sentinel so we can tell whether it
+		// survived (skip path) or got renamed away (would be a regression).
+		if err := os.MkdirAll(filepath.Join(reposDir, "owned-id"), 0o755); err != nil {
+			t.Fatalf("mkdir source: %v", err)
+		}
+		if err := os.WriteFile(
+			filepath.Join(reposDir, "owned-id", "src.sentinel"), []byte("src"), 0o644,
+		); err != nil {
+			t.Fatalf("write source sentinel: %v", err)
+		}
+
+		// Pre-existing TARGET dir under the new path_hash with its own
+		// sentinel — simulates a partial-run that already finished this
+		// rename. The migration must preserve this content untouched.
+		if err := os.MkdirAll(filepath.Join(reposDir, targetHash), 0o755); err != nil {
+			t.Fatalf("mkdir pre-existing target: %v", err)
+		}
+		if err := os.WriteFile(
+			filepath.Join(reposDir, targetHash, "target.sentinel"), []byte("preserved"), 0o644,
+		); err != nil {
+			t.Fatalf("write target sentinel: %v", err)
+		}
+
+		seedSplitLegacyDB(t, dbPath, false, []legacyRow{{
+			id: "owned-id", workspaceID: "ws-a",
+			githubURL: "https://github.com/x/y", branch: "main",
+			projectPath: projectPath,
+			isLinked:    0,
+		}})
+
+		d, err := OpenWith(OpenOptions{Path: dbPath, DataDir: dataDir})
+		if err != nil {
+			t.Fatalf("OpenWith: %v", err)
+		}
+		defer d.Close()
+
+		// Target survived with its original content (rename skipped).
+		got, err := os.ReadFile(filepath.Join(reposDir, targetHash, "target.sentinel"))
+		if err != nil {
+			t.Errorf("target dir / sentinel missing after migration: %v", err)
+		} else if string(got) != "preserved" {
+			t.Errorf("target sentinel overwritten: got %q, want %q", got, "preserved")
+		}
+		// Source dir still there (the rename was a no-op, didn't move it).
+		if _, err := os.Stat(filepath.Join(reposDir, "owned-id")); err != nil {
+			t.Errorf("source dir was unexpectedly removed: %v", err)
+		}
+		// DB split happened — workspace_repos dropped, git_repos populated.
+		assertWorkspaceReposDropped(t, d)
+		assertGitReposCount(t, d, 1)
+		assertWorkspaceProjectsCount(t, d, 1)
+	})
+
+	t.Run("MissingSourceDir_Skipped", func(t *testing.T) {
+		dir := t.TempDir()
+		dbPath := filepath.Join(dir, "test.db")
+		dataDir := filepath.Join(dir, "data")
+		reposDir := filepath.Join(dataDir, "repos")
+		// reposDir exists but no per-id subdir — simulates a legacy clone
+		// job that died before mkdir, leaving an orphan workspace_repos
+		// row pointing at a directory that never materialised.
+		if err := os.MkdirAll(reposDir, 0o755); err != nil {
+			t.Fatalf("mkdir reposDir: %v", err)
+		}
+
+		projectPath := "github.com/x/y@main"
+		seedSplitLegacyDB(t, dbPath, false, []legacyRow{{
+			id: "ghost-id", workspaceID: "ws-a",
+			githubURL: "https://github.com/x/y", branch: "main",
+			projectPath: projectPath,
+			isLinked:    0,
+		}})
+
+		d, err := OpenWith(OpenOptions{Path: dbPath, DataDir: dataDir})
+		if err != nil {
+			t.Fatalf("OpenWith: %v", err)
+		}
+		defer d.Close()
+
+		// No target dir got created — the rename was skipped because
+		// there was no source. A future clone_repo job will mkdir the
+		// target when it runs against the new path_hash.
+		targetHash := HashHostPath(projectPath)
+		if _, err := os.Stat(filepath.Join(reposDir, targetHash)); err == nil {
+			t.Errorf("target dir created from nothing: %s", filepath.Join(reposDir, targetHash))
+		}
+		// DB split still happened — the absent on-disk clone doesn't
+		// block the SQL inserts.
+		assertWorkspaceReposDropped(t, d)
+		assertGitReposCount(t, d, 1)
+		assertWorkspaceProjectsCount(t, d, 1)
+	})
+
+	t.Run("DuplicatePathInLegacy", func(t *testing.T) {
+		dir := t.TempDir()
+		dbPath := filepath.Join(dir, "test.db")
+		dataDir := filepath.Join(dir, "data")
+
+		// Two legacy rows in ws-a that map to the same project_path —
+		// possible on a pre-PR12/13 schema (no UNIQUE on workspace_id +
+		// github_url + branch) or on a hand-edited DB. The owned row
+		// uses the bare URL, the linked row uses the ".git" suffix
+		// variant; both deterministically produce the same project_path
+		// `github.com/x/y@main` and so collide on the workspace_projects
+		// PK (workspace_id, project_path).
+		seedSplitLegacyDB(t, dbPath, true /* skipUnique */, []legacyRow{
+			{
+				id: "row-owned", workspaceID: "ws-a",
+				githubURL: "https://github.com/x/y", branch: "main",
+				projectPath: "github.com/x/y@main",
+				isLinked:    0,
+			},
+			{
+				id: "row-linked", workspaceID: "ws-a",
+				githubURL: "https://github.com/x/y.git", branch: "main",
+				projectPath: "github.com/x/y@main",
+				isLinked:    1,
+			},
+		})
+
+		d, err := OpenWith(OpenOptions{Path: dbPath, DataDir: dataDir})
+		if err != nil {
+			t.Fatalf("OpenWith: %v", err)
+		}
+		defer d.Close()
+
+		// Exactly one workspace_projects row survived the INSERT OR
+		// IGNORE pass; the second legacy row was suppressed by the
+		// (workspace_id, project_path) PK collision.
+		var n int
+		if err := d.QueryRow(
+			`SELECT COUNT(*) FROM workspace_projects WHERE workspace_id = ? AND project_path = ?`,
+			"ws-a", "github.com/x/y@main",
+		).Scan(&n); err != nil {
+			t.Fatalf("count membership: %v", err)
+		}
+		if n != 1 {
+			t.Errorf("workspace_projects membership count for duplicate path: got %d, want 1", n)
+		}
+		// git_repos also collapses — only the owned row contributes (linked
+		// rows skip the git_repos insert), and the project_path PK guards
+		// against double-insert anyway.
+		assertGitReposCount(t, d, 1)
+		assertWorkspaceReposDropped(t, d)
+	})
+}
+
+// legacyRow models the minimal subset of pre-split workspace_repos fields
+// the migration cares about. Defaults that don't matter to the migration
+// (webhook_mode, status, timestamps) are filled in by seedSplitLegacyDB.
+type legacyRow struct {
+	id          string
+	workspaceID string
+	githubURL   string
+	branch      string
+	projectPath string
+	isLinked    int
+}
+
+// seedSplitLegacyDB lays down the pre-split schema (workspaces +
+// workspace_repos in the post-PR13 shape) and inserts the given rows.
+// When skipUnique is true the composite UNIQUE on (workspace_id,
+// github_url, branch) is omitted so duplicate-path scenarios can be
+// constructed; otherwise the schema mirrors what
+// migrateWorkspaceReposLinked leaves behind.
+func seedSplitLegacyDB(t *testing.T, dbPath string, skipUnique bool, rows []legacyRow) {
+	t.Helper()
+	raw, err := sql.Open(DriverName, "file:"+dbPath+"?_pragma=foreign_keys(ON)")
+	if err != nil {
+		t.Fatalf("raw open: %v", err)
+	}
+	defer raw.Close()
+
+	uniqueClause := "UNIQUE(workspace_id, github_url, branch),"
+	if skipUnique {
+		uniqueClause = ""
+	}
+	schema := `
+		CREATE TABLE workspaces (
+			id TEXT PRIMARY KEY,
+			name TEXT NOT NULL UNIQUE,
+			description TEXT NOT NULL DEFAULT '',
+			created_at TEXT NOT NULL,
+			updated_at TEXT NOT NULL
+		);
+		CREATE TABLE workspace_repos (
+			id              TEXT PRIMARY KEY,
+			workspace_id    TEXT NOT NULL,
+			github_url      TEXT NOT NULL,
+			branch          TEXT NOT NULL,
+			project_path    TEXT NOT NULL,
+			token_id        TEXT,
+			webhook_secret  TEXT NOT NULL,
+			webhook_id      INTEGER,
+			auto_webhook    INTEGER NOT NULL DEFAULT 0,
+			webhook_mode    TEXT NOT NULL DEFAULT 'manual',
+			status          TEXT NOT NULL DEFAULT 'pending',
+			last_sha        TEXT,
+			last_error      TEXT,
+			last_indexed_at TEXT,
+			is_linked       INTEGER NOT NULL DEFAULT 0,
+			created_at      TEXT NOT NULL,
+			updated_at      TEXT NOT NULL,
+			` + uniqueClause + `
+			FOREIGN KEY (workspace_id) REFERENCES workspaces(id) ON DELETE CASCADE
+		);
+		INSERT INTO workspaces (id, name, created_at, updated_at) VALUES
+			('ws-a', 'alpha', '2026-05-14T00:00:00Z', '2026-05-14T00:00:00Z');
+	`
+	if _, err := raw.Exec(schema); err != nil {
+		t.Fatalf("seed schema: %v", err)
+	}
+	for _, r := range rows {
+		if _, err := raw.Exec(`
+			INSERT INTO workspace_repos (id, workspace_id, github_url, branch, project_path,
+				webhook_secret, status, is_linked, webhook_mode, created_at, updated_at)
+			VALUES (?, ?, ?, ?, ?, ?, 'indexed', ?, 'manual',
+				'2026-05-14T00:00:00Z', '2026-05-14T00:00:00Z')`,
+			r.id, r.workspaceID, r.githubURL, r.branch, r.projectPath,
+			"secret-"+r.id, r.isLinked,
+		); err != nil {
+			t.Fatalf("seed legacy row %s: %v", r.id, err)
+		}
+	}
+}
+
+func assertWorkspaceReposDropped(t *testing.T, d *sql.DB) {
+	t.Helper()
+	var n int
+	if err := d.QueryRow(
+		`SELECT COUNT(*) FROM sqlite_master WHERE type='table' AND name='workspace_repos'`,
+	).Scan(&n); err != nil {
+		t.Fatalf("check workspace_repos drop: %v", err)
+	}
+	if n != 0 {
+		t.Errorf("workspace_repos should be dropped, count=%d", n)
+	}
+}
+
+func assertGitReposCount(t *testing.T, d *sql.DB, want int) {
+	t.Helper()
+	var n int
+	if err := d.QueryRow(`SELECT COUNT(*) FROM git_repos`).Scan(&n); err != nil {
+		t.Fatalf("count git_repos: %v", err)
+	}
+	if n != want {
+		t.Errorf("git_repos count: got %d, want %d", n, want)
+	}
+}
+
+func assertWorkspaceProjectsCount(t *testing.T, d *sql.DB, want int) {
+	t.Helper()
+	var n int
+	if err := d.QueryRow(`SELECT COUNT(*) FROM workspace_projects`).Scan(&n); err != nil {
+		t.Fatalf("count workspace_projects: %v", err)
+	}
+	if n != want {
+		t.Errorf("workspace_projects count: got %d, want %d", n, want)
+	}
+}
+
+// TestApplyMigrations_FreshDBRecordsAll — fresh Open() must record every
+// registered migration in schema_migrations. The acceptance criterion for
+// Fix #7: `SELECT version FROM schema_migrations` returns the full ledger
+// in order. Pins both the count (regression guard against silent skipping)
+// and the name sequence (regression guard against accidental renumber).
+func TestApplyMigrations_FreshDBRecordsAll(t *testing.T) {
+	d, err := Open(":memory:")
+	if err != nil {
+		t.Fatalf("Open: %v", err)
+	}
+	defer d.Close()
+
+	rows, err := d.Query(
+		`SELECT version, name FROM schema_migrations ORDER BY version`)
+	if err != nil {
+		t.Fatalf("query schema_migrations: %v", err)
+	}
+	defer rows.Close()
+
+	type entry struct {
+		version int
+		name    string
+	}
+	var got []entry
+	for rows.Next() {
+		var e entry
+		if err := rows.Scan(&e.version, &e.name); err != nil {
+			t.Fatalf("scan: %v", err)
+		}
+		got = append(got, e)
+	}
+	if err := rows.Err(); err != nil {
+		t.Fatalf("rows.Err: %v", err)
+	}
+
+	if len(got) != len(registeredMigrations) {
+		t.Fatalf("schema_migrations row count = %d, want %d (got=%+v)",
+			len(got), len(registeredMigrations), got)
+	}
+	for i, m := range registeredMigrations {
+		if got[i].version != m.version || got[i].name != m.name {
+			t.Errorf("row %d = {%d, %q}, want {%d, %q}",
+				i, got[i].version, got[i].name, m.version, m.name)
+		}
+	}
+}
+
+// TestApplyMigrations_ReopenIsNoOp — opening the same file-backed DB twice
+// must leave schema_migrations untouched: same row count, same applied_at
+// strings. If a migration accidentally re-ran on warm boot, applied_at
+// would be re-stamped to the second open's time. The acceptance criterion
+// from Fix #7: "повторний запуск — no-op".
+func TestApplyMigrations_ReopenIsNoOp(t *testing.T) {
+	dbPath := filepath.Join(t.TempDir(), "reopen.db")
+
+	d, err := Open(dbPath)
+	if err != nil {
+		t.Fatalf("first Open: %v", err)
+	}
+	first := readMigrationLedger(t, d)
+	if err := d.Close(); err != nil {
+		t.Fatalf("close: %v", err)
+	}
+
+	again, err := Open(dbPath)
+	if err != nil {
+		t.Fatalf("second Open: %v", err)
+	}
+	defer again.Close()
+	second := readMigrationLedger(t, again)
+
+	if len(first) != len(second) {
+		t.Fatalf("ledger row count changed: first=%d second=%d", len(first), len(second))
+	}
+	for i := range first {
+		if first[i] != second[i] {
+			t.Errorf("ledger row %d changed: first=%+v second=%+v",
+				i, first[i], second[i])
+		}
+	}
+}
+
+// TestApplyMigrations_BootstrapFromLegacyDB — production DBs created before
+// the schema_migrations ledger landed start out with no rows in
+// schema_migrations even though their tables are already at the modern
+// shape. applyMigrations must bootstrap them by running every registered
+// migration (each idempotent, so the SQL is mostly a no-op on already-current
+// state) and recording all version rows. Without this, every boot would
+// re-run every migration forever.
+//
+// We simulate the pre-ledger state by opening the DB via Schema.Exec alone
+// (skipping applyMigrations), then re-opening via the normal path.
+func TestApplyMigrations_BootstrapFromLegacyDB(t *testing.T) {
+	dbPath := filepath.Join(t.TempDir(), "legacy.db")
+
+	// Seed: schema applied, but schema_migrations not populated (mimicking
+	// any prod DB that booted before this ledger existed).
+	raw, err := sql.Open(DriverName, "file:"+dbPath+"?_pragma=foreign_keys(ON)")
+	if err != nil {
+		t.Fatalf("raw open: %v", err)
+	}
+	if _, err := raw.Exec(Schema); err != nil {
 		_ = raw.Close()
-		t.Fatalf("pre-migration insert should fail UNIQUE — test setup is wrong")
+		t.Fatalf("exec Schema: %v", err)
+	}
+	if _, err := raw.Exec(`DROP TABLE IF EXISTS schema_migrations`); err != nil {
+		_ = raw.Close()
+		t.Fatalf("drop schema_migrations: %v", err)
 	}
 	_ = raw.Close()
 
-	// Now reopen via the real Open() so the migration runs.
-	migrated, err := Open(path)
+	// Confirm the seeded DB really has no ledger before we bootstrap.
+	seedDB, err := sql.Open(DriverName, "file:"+dbPath)
+	if err != nil {
+		t.Fatalf("verify seed open: %v", err)
+	}
+	var seedHasLedger int
+	if err := seedDB.QueryRow(
+		`SELECT COUNT(*) FROM sqlite_master WHERE type='table' AND name='schema_migrations'`,
+	).Scan(&seedHasLedger); err != nil {
+		_ = seedDB.Close()
+		t.Fatalf("verify seed: %v", err)
+	}
+	_ = seedDB.Close()
+	if seedHasLedger != 0 {
+		t.Fatalf("seed precondition: schema_migrations should be absent, found %d", seedHasLedger)
+	}
+
+	// Now boot through the normal path — applyMigrations should bootstrap.
+	d, err := Open(dbPath)
 	if err != nil {
 		t.Fatalf("Open: %v", err)
 	}
-	defer migrated.Close()
+	defer d.Close()
 
-	// is_linked column should be present and default to 0 on the
-	// migrated row.
-	var isLinked int
-	if err := migrated.QueryRow(
-		`SELECT is_linked FROM workspace_repos WHERE id = 'repo-1'`,
-	).Scan(&isLinked); err != nil {
-		t.Fatalf("read is_linked: %v", err)
-	}
-	if isLinked != 0 {
-		t.Fatalf("pre-existing rows must keep is_linked=0, got %d", isLinked)
-	}
-
-	// And the post-migration invariant we care about: same project_path
-	// in a different workspace now succeeds.
-	if _, err := migrated.Exec(`INSERT INTO workspace_repos (id, workspace_id, github_url, branch, project_path,
-		webhook_secret, status, is_linked, created_at, updated_at)
-		VALUES ('repo-2', 'ws-b', 'https://github.com/x/y', 'main',
-		'github.com/x/y@main', 's', 'indexed', 1,
-		'2026-05-11T00:00:00Z', '2026-05-11T00:00:00Z')`); err != nil {
-		t.Fatalf("post-migration cross-workspace insert should succeed: %v", err)
-	}
-
-	// Per-workspace UNIQUE must still bite — adding the same repo+branch
-	// to ws-b a second time should fail.
-	_, err = migrated.Exec(`INSERT INTO workspace_repos (id, workspace_id, github_url, branch, project_path,
-		webhook_secret, status, is_linked, created_at, updated_at)
-		VALUES ('repo-3', 'ws-b', 'https://github.com/x/y', 'main',
-		'github.com/x/y@main', 's', 'indexed', 1,
-		'2026-05-11T00:00:00Z', '2026-05-11T00:00:00Z')`)
-	if err == nil {
-		t.Fatalf("per-workspace UNIQUE should still reject duplicate (workspace_id, github_url, branch)")
+	ledger := readMigrationLedger(t, d)
+	if len(ledger) != len(registeredMigrations) {
+		t.Fatalf("post-bootstrap ledger has %d rows, want %d",
+			len(ledger), len(registeredMigrations))
+	}
+	for i, m := range registeredMigrations {
+		if ledger[i].version != m.version || ledger[i].name != m.name {
+			t.Errorf("ledger row %d = {%d, %q}, want {%d, %q}",
+				i, ledger[i].version, ledger[i].name, m.version, m.name)
+		}
+	}
+}
+
+// migrationLedgerRow mirrors a schema_migrations row for test assertions.
+type migrationLedgerRow struct {
+	version   int
+	name      string
+	appliedAt string
+}
+
+// readMigrationLedger snapshots the schema_migrations table in version order.
+func readMigrationLedger(t *testing.T, d *sql.DB) []migrationLedgerRow {
+	t.Helper()
+	rows, err := d.Query(
+		`SELECT version, name, applied_at FROM schema_migrations ORDER BY version`)
+	if err != nil {
+		t.Fatalf("query schema_migrations: %v", err)
+	}
+	defer rows.Close()
+	var out []migrationLedgerRow
+	for rows.Next() {
+		var r migrationLedgerRow
+		if err := rows.Scan(&r.version, &r.name, &r.appliedAt); err != nil {
+			t.Fatalf("scan ledger row: %v", err)
+		}
+		out = append(out, r)
+	}
+	if err := rows.Err(); err != nil {
+		t.Fatalf("ledger rows.Err: %v", err)
 	}
+	return out
 }
diff --git a/server/internal/db/schema.go b/server/internal/db/schema.go
index d55f788..abe2ecc 100644
--- a/server/internal/db/schema.go
+++ b/server/internal/db/schema.go
@@ -150,11 +150,11 @@ CREATE TABLE IF NOT EXISTS runtime_settings (
     updated_by TEXT
 );
 
--- Workspaces feature (PR1 — skeleton). Workspaces group GitHub repositories
--- for cross-project semantic search. Server-wide shared: every authenticated
+-- Workspaces group indexed projects (rows in the projects table,
+-- optionally with their git_repos peer) for cross-project semantic
+-- search. Membership lives in workspace_projects; clone + webhook
+-- metadata lives in git_repos. Server-wide shared: every authenticated
 -- user can see and modify any workspace (per the chosen visibility model).
--- The richer workspace_repos / call_edges / communities tables land in
--- subsequent PRs of the workspaces feature branch.
 CREATE TABLE IF NOT EXISTS workspaces (
     id          TEXT PRIMARY KEY,
     name        TEXT NOT NULL UNIQUE,
@@ -177,51 +177,52 @@ CREATE TABLE IF NOT EXISTS github_tokens (
     last_used_at TEXT
 );
 
--- Workspaces feature PR2 — workspace_repos + jobs.
+-- git_repos holds clone + webhook metadata for projects that come from a
+-- git remote (currently GitHub-only). Exactly 1:1 with the corresponding
+-- projects row — keyed by project_path = projects.host_path. Local
+-- projects (indexed via the CLI) have no git_repos row at all, which
+-- is how the server tells them apart from cloneable repos.
 --
--- One workspace_repos row per (repo, branch). project_path is the canonical
--- "github.com/owner/repo@branch" string used as host_path in projects, so
--- existing per-project SQL stays uniform across local + remote sources.
--- webhook_secret is generated server-side at create time and shown exactly
--- once to the operator (or used by the auto-register flow added in PR3).
--- token_id stays nullable so public repos can be added without storing a PAT.
--- last_sha / last_indexed_at survive across reindexes so an incremental
--- fetch_repo job can short-circuit when HEAD hasn't moved.
--- is_linked discriminates owned rows (the canonical Add Repo flow that
--- clones + indexes + owns a webhook) from linked rows (a lightweight
--- membership pointer to an already-indexed project — no clone, no
--- webhook). Uniqueness is per-workspace; the same project_path may live
--- in many workspaces as long as it appears at most once in each.
-CREATE TABLE IF NOT EXISTS workspace_repos (
-    id              TEXT PRIMARY KEY,
-    workspace_id    TEXT NOT NULL,
+-- webhook_secret is generated server-side at create time and shown
+-- exactly once to the operator (or consumed by the auto-register flow).
+-- token_id stays nullable so public repos can be cloned without a PAT.
+-- last_sha lets an incremental fetch short-circuit when HEAD hasn't
+-- moved; status lives on the projects row (single source of truth).
+CREATE TABLE IF NOT EXISTS git_repos (
+    project_path    TEXT PRIMARY KEY,
     github_url      TEXT NOT NULL,
     branch          TEXT NOT NULL,
-    project_path    TEXT NOT NULL,
     token_id        TEXT,
     webhook_secret  TEXT NOT NULL,
     webhook_id      INTEGER,
-    auto_webhook    INTEGER NOT NULL DEFAULT 0,
-    -- webhook_mode is the operator's stated intent for how this repo gets
-    -- kept fresh: 'auto' (server calls GitHub to register the hook),
-    -- 'manual' (operator pastes the URL+secret into GitHub themselves),
-    -- 'disabled' (no auto-sync, reindex via the dashboard button only).
-    -- Stored separately from auto_webhook so the dashboard can distinguish
-    -- "manual, still pending operator action" from "deliberately disabled".
+    -- webhook_mode = 'auto' | 'manual' | 'disabled'. See workspaces docs.
     webhook_mode    TEXT NOT NULL DEFAULT 'manual',
-    status          TEXT NOT NULL DEFAULT 'pending',
+    auto_webhook    INTEGER NOT NULL DEFAULT 0,
     last_sha        TEXT,
     last_error      TEXT,
-    last_indexed_at TEXT,
-    is_linked       INTEGER NOT NULL DEFAULT 0,
     created_at      TEXT NOT NULL,
     updated_at      TEXT NOT NULL,
-    UNIQUE(workspace_id, github_url, branch),
-    FOREIGN KEY (workspace_id) REFERENCES workspaces(id) ON DELETE CASCADE,
+    UNIQUE (github_url, branch),
+    FOREIGN KEY (project_path) REFERENCES projects(host_path) ON DELETE CASCADE,
     FOREIGN KEY (token_id) REFERENCES github_tokens(id) ON DELETE SET NULL
 );
-CREATE INDEX IF NOT EXISTS idx_workspace_repos_workspace ON workspace_repos(workspace_id);
-CREATE INDEX IF NOT EXISTS idx_workspace_repos_project ON workspace_repos(project_path);
+
+-- workspace_projects is the many-to-many junction between workspaces
+-- and projects. A workspace is just a labelled collection — adding a
+-- project = INSERT here, removing = DELETE here. The project itself
+-- is untouched. The same project can live in any number of workspaces.
+-- ON DELETE CASCADE on both FKs keeps memberships consistent: deleting
+-- a workspace or a project automatically clears the rows that name it.
+CREATE TABLE IF NOT EXISTS workspace_projects (
+    workspace_id  TEXT NOT NULL,
+    project_path  TEXT NOT NULL,
+    added_at      TEXT NOT NULL,
+    PRIMARY KEY (workspace_id, project_path),
+    FOREIGN KEY (workspace_id) REFERENCES workspaces(id) ON DELETE CASCADE,
+    FOREIGN KEY (project_path) REFERENCES projects(host_path) ON DELETE CASCADE
+);
+CREATE INDEX IF NOT EXISTS idx_workspace_projects_project
+    ON workspace_projects(project_path);
 
 -- jobs is the persistent worker queue. Survives process restarts; one
 -- worker pool drains it. dedupe_key is the partial-unique mechanism that
@@ -341,9 +342,11 @@ var ExpectedTables = []string{
 	"runtime_settings",
 	"workspaces",
 	"github_tokens",
-	"workspace_repos",
+	"git_repos",
+	"workspace_projects",
 	"jobs",
 	"call_edges",
 	"chunks_meta",
 	"chunks_fts",
+	"schema_migrations",
 }
diff --git a/server/internal/githubapi/githubapi.go b/server/internal/githubapi/githubapi.go
index f30ee4c..b577f5a 100644
--- a/server/internal/githubapi/githubapi.go
+++ b/server/internal/githubapi/githubapi.go
@@ -554,7 +554,7 @@ func githubMessage(body []byte) string {
 }
 
 // ParseOwnerRepo extracts {owner, repo} from an https://github.com/owner/repo URL.
-// Mirrors the same logic as workspacerepos.parseGitHubURL but kept private
+// Mirrors the same logic as gitrepos.parseGitHubURL but kept private
 // to that package — we re-implement here to avoid an import cycle.
 func ParseOwnerRepo(githubURL string) (owner, repo string, err error) {
 	u, perr := url.Parse(strings.TrimSpace(githubURL))
diff --git a/server/internal/gitrepos/gitrepos.go b/server/internal/gitrepos/gitrepos.go
new file mode 100644
index 0000000..4b91d79
--- /dev/null
+++ b/server/internal/gitrepos/gitrepos.go
@@ -0,0 +1,362 @@
+// Package gitrepos is the service layer for the git_repos table —
+// clone + webhook metadata for projects that come from a git remote
+// (currently GitHub-only). A row exists exactly 1:1 with the projects
+// row whose host_path matches project_path; local projects (CLI-indexed
+// filesystem paths) have no git_repos row, which is how the rest of the
+// system tells them apart from cloneable repos.
+//
+// Workspace membership lives in a separate junction table —
+// workspace_projects — owned by the workspaceprojects package. This
+// package knows nothing about workspaces.
+package gitrepos
+
+import (
+	"context"
+	"crypto/rand"
+	"database/sql"
+	"encoding/base64"
+	"errors"
+	"fmt"
+	"net/url"
+	"strings"
+	"time"
+
+	"github.com/dvcdsys/code-index/server/internal/db"
+)
+
+// Webhook modes. Stored verbatim in the webhook_mode column so the
+// dashboard renders the operator's stated intent.
+const (
+	WebhookModeManual   = "manual"
+	WebhookModeAuto     = "auto"
+	WebhookModeDisabled = "disabled"
+)
+
+// Errors.
+var (
+	ErrNotFound           = errors.New("git repo not found")
+	ErrDuplicate          = errors.New("a git repo with this (github_url, branch) already exists")
+	ErrInvalidURL         = errors.New("github_url must be an https://github.com/owner/repo URL")
+	ErrBranchEmpty        = errors.New("branch is required")
+	ErrInvalidWebhookMode = errors.New("webhook_mode must be one of manual, auto, disabled")
+)
+
+// GitRepo is the wire view. The webhook_secret is in the response of
+// Create only — subsequent reads must call WebhookInfo to fetch it
+// (kept out of bulk lists so secrets don't fan out unnecessarily).
+type GitRepo struct {
+	ProjectPath   string
+	PathHash      string
+	GitHubURL     string
+	Branch        string
+	TokenID       string
+	WebhookSecret string
+	WebhookID     *int64
+	WebhookMode   string
+	AutoWebhook   bool
+	LastSHA       string
+	LastError     string
+	CreatedAt     time.Time
+	UpdatedAt     time.Time
+}
+
+// Service wraps the git_repos table.
+type Service struct {
+	DB *sql.DB
+}
+
+func New(db *sql.DB) *Service { return &Service{DB: db} }
+
+// CreateRequest is what handlers pass in. ProjectPath is computed from
+// GitHubURL + Branch; callers don't supply it directly.
+type CreateRequest struct {
+	GitHubURL   string
+	Branch      string
+	TokenID     string // optional
+	WebhookMode string // empty → manual
+}
+
+// Create inserts a git_repos row. The caller is responsible for
+// ensuring the matching projects row exists (FK target). The resulting
+// ProjectPath is "github.com/owner/repo@branch".
+func (s *Service) Create(ctx context.Context, req CreateRequest) (GitRepo, error) {
+	owner, repo, err := parseGitHubURL(req.GitHubURL)
+	if err != nil {
+		return GitRepo{}, err
+	}
+	if strings.TrimSpace(req.Branch) == "" {
+		return GitRepo{}, ErrBranchEmpty
+	}
+	mode, merr := NormaliseWebhookMode(req.WebhookMode)
+	if merr != nil {
+		return GitRepo{}, merr
+	}
+
+	projectPath := fmt.Sprintf("github.com/%s/%s@%s", owner, repo, req.Branch)
+	githubURL := canonicaliseURL(req.GitHubURL)
+	secret, err := generateWebhookSecret()
+	if err != nil {
+		return GitRepo{}, fmt.Errorf("generate webhook secret: %w", err)
+	}
+	auto := 0
+	if mode == WebhookModeAuto {
+		auto = 1
+	}
+	tokenID := nullableString(req.TokenID)
+	now := time.Now().UTC().Format(time.RFC3339Nano)
+
+	if _, err := s.DB.ExecContext(ctx, `
+		INSERT INTO git_repos (
+			project_path, github_url, branch,
+			token_id, webhook_secret,
+			webhook_mode, auto_webhook,
+			created_at, updated_at
+		) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)`,
+		projectPath, githubURL, req.Branch,
+		tokenID, secret, mode, auto,
+		now, now,
+	); err != nil {
+		if isUniqueConstraintViolation(err) {
+			return GitRepo{}, ErrDuplicate
+		}
+		return GitRepo{}, fmt.Errorf("insert git_repo: %w", err)
+	}
+	return s.GetByPath(ctx, projectPath)
+}
+
+// GetByPath returns the git_repos row for the given project_path
+// (= projects.host_path).
+func (s *Service) GetByPath(ctx context.Context, projectPath string) (GitRepo, error) {
+	row := s.DB.QueryRowContext(ctx, selectColumns+` WHERE project_path = ?`, projectPath)
+	return scanRow(row)
+}
+
+// GetByHash resolves a git_repos row by the 16-char SHA1 prefix of
+// project_path (= projects.path_hash). The webhook endpoint uses this
+// — it's stable across the system and doubles as the on-disk clone dir
+// identifier.
+func (s *Service) GetByHash(ctx context.Context, pathHash string) (GitRepo, error) {
+	var path string
+	if err := s.DB.QueryRowContext(ctx,
+		`SELECT host_path FROM projects WHERE path_hash = ?`, pathHash,
+	).Scan(&path); err != nil {
+		if errors.Is(err, sql.ErrNoRows) {
+			return GitRepo{}, ErrNotFound
+		}
+		return GitRepo{}, fmt.Errorf("lookup by path_hash: %w", err)
+	}
+	return s.GetByPath(ctx, path)
+}
+
+// ListAll returns every git_repos row, newest first. Local projects do
+// not appear here — they have no git_repos representation.
+func (s *Service) ListAll(ctx context.Context) ([]GitRepo, error) {
+	rows, err := s.DB.QueryContext(ctx, selectColumns+` ORDER BY created_at DESC`)
+	if err != nil {
+		return nil, fmt.Errorf("list git_repos: %w", err)
+	}
+	defer rows.Close()
+	return scanRows(rows)
+}
+
+// SetWebhookID persists the GitHub-side hook id after the auto-register
+// flow registers the webhook. ErrNotFound when the row is gone.
+func (s *Service) SetWebhookID(ctx context.Context, projectPath string, hookID int64) error {
+	res, err := s.DB.ExecContext(ctx, `
+		UPDATE git_repos SET webhook_id = ?, updated_at = ?
+		WHERE project_path = ?`,
+		hookID, time.Now().UTC().Format(time.RFC3339Nano), projectPath)
+	if err != nil {
+		return fmt.Errorf("set webhook_id: %w", err)
+	}
+	n, _ := res.RowsAffected()
+	if n == 0 {
+		return ErrNotFound
+	}
+	return nil
+}
+
+// SetClone updates last_sha / last_error after a clone job completes.
+// Pass empty strings to leave the corresponding field unchanged (NULL
+// to clear last_error explicitly is not supported — callers should
+// pass "" for "no error" which CASE-clears it).
+func (s *Service) SetClone(ctx context.Context, projectPath, lastSHA, lastError string) error {
+	now := time.Now().UTC().Format(time.RFC3339Nano)
+	res, err := s.DB.ExecContext(ctx, `
+		UPDATE git_repos
+		   SET last_sha   = COALESCE(NULLIF(?, ''), last_sha),
+		       last_error = CASE WHEN ? = '' THEN NULL ELSE ? END,
+		       updated_at = ?
+		 WHERE project_path = ?`,
+		lastSHA, lastError, lastError, now, projectPath)
+	if err != nil {
+		return fmt.Errorf("set clone: %w", err)
+	}
+	n, _ := res.RowsAffected()
+	if n == 0 {
+		return ErrNotFound
+	}
+	return nil
+}
+
+// Delete removes a git_repos row. Idempotent — re-deleting returns
+// ErrNotFound. The matching projects row + on-disk clone are NOT
+// cleaned up here; that's the project-delete handler's job.
+func (s *Service) Delete(ctx context.Context, projectPath string) error {
+	res, err := s.DB.ExecContext(ctx, `DELETE FROM git_repos WHERE project_path = ?`, projectPath)
+	if err != nil {
+		return fmt.Errorf("delete git_repo: %w", err)
+	}
+	n, _ := res.RowsAffected()
+	if n == 0 {
+		return ErrNotFound
+	}
+	return nil
+}
+
+// --- helpers ---
+
+const selectColumns = `
+	SELECT project_path, github_url, branch,
+	       token_id, webhook_secret, webhook_id,
+	       webhook_mode, auto_webhook,
+	       last_sha, last_error,
+	       created_at, updated_at
+	  FROM git_repos`
+
+func scanRow(r interface{ Scan(dest ...any) error }) (GitRepo, error) {
+	var (
+		g           GitRepo
+		tokenID     sql.NullString
+		webhookID   sql.NullInt64
+		webhookMode string
+		autoWebhook int
+		lastSHA     sql.NullString
+		lastError   sql.NullString
+		createdAt   string
+		updatedAt   string
+	)
+	err := r.Scan(&g.ProjectPath, &g.GitHubURL, &g.Branch,
+		&tokenID, &g.WebhookSecret, &webhookID,
+		&webhookMode, &autoWebhook,
+		&lastSHA, &lastError,
+		&createdAt, &updatedAt)
+	if err != nil {
+		if errors.Is(err, sql.ErrNoRows) {
+			return GitRepo{}, ErrNotFound
+		}
+		return GitRepo{}, fmt.Errorf("scan git_repo: %w", err)
+	}
+	g.PathHash = HashHostPath(g.ProjectPath)
+	g.TokenID = tokenID.String
+	if webhookID.Valid {
+		v := webhookID.Int64
+		g.WebhookID = &v
+	}
+	g.WebhookMode = webhookMode
+	if g.WebhookMode == "" {
+		g.WebhookMode = WebhookModeManual
+	}
+	g.AutoWebhook = autoWebhook == 1
+	g.LastSHA = lastSHA.String
+	g.LastError = lastError.String
+	g.CreatedAt, _ = time.Parse(time.RFC3339Nano, createdAt)
+	g.UpdatedAt, _ = time.Parse(time.RFC3339Nano, updatedAt)
+	return g, nil
+}
+
+func scanRows(rows *sql.Rows) ([]GitRepo, error) {
+	out := []GitRepo{}
+	for rows.Next() {
+		g, err := scanRow(rows)
+		if err != nil {
+			return nil, err
+		}
+		out = append(out, g)
+	}
+	return out, rows.Err()
+}
+
+// NormaliseWebhookMode rejects unknown values up front so the DB only
+// ever stores one of the three documented states. Empty input maps to
+// the default 'manual'.
+func NormaliseWebhookMode(s string) (string, error) {
+	switch strings.ToLower(strings.TrimSpace(s)) {
+	case "":
+		return WebhookModeManual, nil
+	case WebhookModeManual:
+		return WebhookModeManual, nil
+	case WebhookModeAuto:
+		return WebhookModeAuto, nil
+	case WebhookModeDisabled:
+		return WebhookModeDisabled, nil
+	default:
+		return "", ErrInvalidWebhookMode
+	}
+}
+
+// ParseGitHubURL extracts owner + repo from an HTTPS GitHub URL.
+// Accepts trailing slash and ".git" suffix; rejects anything not on
+// github.com. Exported so the HTTP handler can resolve the canonical
+// project_path before staging the projects row.
+func ParseGitHubURL(s string) (owner, repo string, err error) {
+	return parseGitHubURL(s)
+}
+
+// parseGitHubURL extracts owner + repo from an HTTPS GitHub URL. Accepts
+// trailing slash and ".git" suffix. Rejects anything not on github.com.
+func parseGitHubURL(s string) (owner, repo string, err error) {
+	s = strings.TrimSpace(s)
+	if s == "" {
+		return "", "", ErrInvalidURL
+	}
+	u, perr := url.Parse(s)
+	if perr != nil {
+		return "", "", ErrInvalidURL
+	}
+	if !strings.EqualFold(u.Host, "github.com") {
+		return "", "", ErrInvalidURL
+	}
+	p := strings.Trim(u.Path, "/")
+	p = strings.TrimSuffix(p, ".git")
+	parts := strings.Split(p, "/")
+	if len(parts) != 2 || parts[0] == "" || parts[1] == "" {
+		return "", "", ErrInvalidURL
+	}
+	return parts[0], parts[1], nil
+}
+
+func canonicaliseURL(s string) string {
+	s = strings.TrimSpace(s)
+	s = strings.TrimSuffix(s, "/")
+	s = strings.TrimSuffix(s, ".git")
+	return s
+}
+
+func generateWebhookSecret() (string, error) {
+	var buf [32]byte
+	if _, err := rand.Read(buf[:]); err != nil {
+		return "", err
+	}
+	return base64.RawURLEncoding.EncodeToString(buf[:]), nil
+}
+
+func nullableString(s string) any {
+	if s == "" {
+		return nil
+	}
+	return s
+}
+
+func isUniqueConstraintViolation(err error) bool {
+	if err == nil {
+		return false
+	}
+	msg := err.Error()
+	return strings.Contains(msg, "UNIQUE constraint failed") ||
+		strings.Contains(msg, "constraint failed: UNIQUE")
+}
+
+// HashHostPath is a thin re-export of db.HashHostPath so callers within
+// the gitrepos package don't need a separate import.
+func HashHostPath(path string) string { return db.HashHostPath(path) }
diff --git a/server/internal/gitrepos/gitrepos_test.go b/server/internal/gitrepos/gitrepos_test.go
new file mode 100644
index 0000000..8ec5fba
--- /dev/null
+++ b/server/internal/gitrepos/gitrepos_test.go
@@ -0,0 +1,187 @@
+package gitrepos
+
+import (
+	"context"
+	"database/sql"
+	"errors"
+	"testing"
+	"time"
+
+	"github.com/dvcdsys/code-index/server/internal/db"
+)
+
+// seedProject inserts the minimum projects row the git_repos FK requires.
+// We don't go through the projects service to keep the test focused on
+// gitrepos and free of any indirect coupling.
+func seedProject(t *testing.T, d *sql.DB, hostPath string) {
+	t.Helper()
+	now := time.Now().UTC().Format(time.RFC3339Nano)
+	if _, err := d.Exec(`
+		INSERT INTO projects (
+			host_path, container_path, languages, settings, stats,
+			status, created_at, updated_at, path_hash
+		) VALUES (?, ?, '[]', '{}', '{}', 'pending', ?, ?, ?)`,
+		hostPath, hostPath, now, now, db.HashHostPath(hostPath),
+	); err != nil {
+		t.Fatalf("seed project %s: %v", hostPath, err)
+	}
+}
+
+func mustOpen(t *testing.T) (*sql.DB, *Service) {
+	t.Helper()
+	d, err := db.Open(":memory:")
+	if err != nil {
+		t.Fatalf("open: %v", err)
+	}
+	t.Cleanup(func() { _ = d.Close() })
+	return d, New(d)
+}
+
+func TestCreate_HappyPath(t *testing.T) {
+	d, svc := mustOpen(t)
+	ctx := context.Background()
+	seedProject(t, d, "github.com/spf13/cobra@main")
+
+	g, err := svc.Create(ctx, CreateRequest{
+		GitHubURL: "https://github.com/spf13/cobra",
+		Branch:    "main",
+	})
+	if err != nil {
+		t.Fatalf("Create: %v", err)
+	}
+	if g.ProjectPath != "github.com/spf13/cobra@main" {
+		t.Errorf("ProjectPath = %q", g.ProjectPath)
+	}
+	if g.GitHubURL != "https://github.com/spf13/cobra" {
+		t.Errorf("GitHubURL = %q", g.GitHubURL)
+	}
+	if g.WebhookMode != WebhookModeManual {
+		t.Errorf("default WebhookMode = %q, want manual", g.WebhookMode)
+	}
+	if g.WebhookSecret == "" {
+		t.Error("WebhookSecret was not generated")
+	}
+	if g.PathHash != db.HashHostPath(g.ProjectPath) {
+		t.Errorf("PathHash mismatch: %q", g.PathHash)
+	}
+}
+
+func TestCreate_RejectsBadURL(t *testing.T) {
+	_, svc := mustOpen(t)
+	cases := []struct {
+		name string
+		body CreateRequest
+		want error
+	}{
+		{"empty url", CreateRequest{GitHubURL: "", Branch: "main"}, ErrInvalidURL},
+		{"non-github host", CreateRequest{GitHubURL: "https://gitlab.com/x/y", Branch: "main"}, ErrInvalidURL},
+		{"missing branch", CreateRequest{GitHubURL: "https://github.com/x/y", Branch: ""}, ErrBranchEmpty},
+		{"missing repo", CreateRequest{GitHubURL: "https://github.com/x", Branch: "main"}, ErrInvalidURL},
+	}
+	for _, tc := range cases {
+		t.Run(tc.name, func(t *testing.T) {
+			if _, err := svc.Create(context.Background(), tc.body); !errors.Is(err, tc.want) {
+				t.Fatalf("got %v, want %v", err, tc.want)
+			}
+		})
+	}
+}
+
+// TestCreate_Duplicate guards the UNIQUE(github_url, branch) constraint
+// — two git_repos rows for the same upstream + branch must not coexist
+// even if the operator typed slightly different casings.
+func TestCreate_Duplicate(t *testing.T) {
+	d, svc := mustOpen(t)
+	ctx := context.Background()
+	seedProject(t, d, "github.com/foo/bar@main")
+
+	if _, err := svc.Create(ctx, CreateRequest{
+		GitHubURL: "https://github.com/foo/bar",
+		Branch:    "main",
+	}); err != nil {
+		t.Fatalf("first create: %v", err)
+	}
+	if _, err := svc.Create(ctx, CreateRequest{
+		GitHubURL: "https://github.com/foo/bar",
+		Branch:    "main",
+	}); !errors.Is(err, ErrDuplicate) {
+		t.Fatalf("second create: got %v, want ErrDuplicate", err)
+	}
+}
+
+func TestGetByHash(t *testing.T) {
+	d, svc := mustOpen(t)
+	ctx := context.Background()
+	seedProject(t, d, "github.com/x/y@main")
+	if _, err := svc.Create(ctx, CreateRequest{
+		GitHubURL: "https://github.com/x/y",
+		Branch:    "main",
+	}); err != nil {
+		t.Fatalf("Create: %v", err)
+	}
+
+	hash := db.HashHostPath("github.com/x/y@main")
+	g, err := svc.GetByHash(ctx, hash)
+	if err != nil {
+		t.Fatalf("GetByHash: %v", err)
+	}
+	if g.ProjectPath != "github.com/x/y@main" {
+		t.Errorf("ProjectPath via hash mismatch: %q", g.ProjectPath)
+	}
+	if _, err := svc.GetByHash(ctx, "0000000000000000"); !errors.Is(err, ErrNotFound) {
+		t.Errorf("unknown hash: got %v, want ErrNotFound", err)
+	}
+}
+
+func TestSetClone_UpdatesLastSHA(t *testing.T) {
+	d, svc := mustOpen(t)
+	ctx := context.Background()
+	seedProject(t, d, "github.com/x/y@main")
+	if _, err := svc.Create(ctx, CreateRequest{GitHubURL: "https://github.com/x/y", Branch: "main"}); err != nil {
+		t.Fatalf("Create: %v", err)
+	}
+	if err := svc.SetClone(ctx, "github.com/x/y@main", "deadbeef", ""); err != nil {
+		t.Fatalf("SetClone: %v", err)
+	}
+	g, err := svc.GetByPath(ctx, "github.com/x/y@main")
+	if err != nil {
+		t.Fatalf("GetByPath: %v", err)
+	}
+	if g.LastSHA != "deadbeef" {
+		t.Errorf("LastSHA = %q, want deadbeef", g.LastSHA)
+	}
+}
+
+func TestDelete_Idempotent(t *testing.T) {
+	d, svc := mustOpen(t)
+	ctx := context.Background()
+	seedProject(t, d, "github.com/x/y@main")
+	if _, err := svc.Create(ctx, CreateRequest{GitHubURL: "https://github.com/x/y", Branch: "main"}); err != nil {
+		t.Fatalf("Create: %v", err)
+	}
+	if err := svc.Delete(ctx, "github.com/x/y@main"); err != nil {
+		t.Fatalf("Delete: %v", err)
+	}
+	if err := svc.Delete(ctx, "github.com/x/y@main"); !errors.Is(err, ErrNotFound) {
+		t.Errorf("second Delete: got %v, want ErrNotFound", err)
+	}
+}
+
+// TestDeletingProject_CascadesToGitRepo guards the schema FK behaviour:
+// removing a row from projects must drop the matching git_repos row via
+// ON DELETE CASCADE so the project-level delete handler can stay simple.
+func TestDeletingProject_CascadesToGitRepo(t *testing.T) {
+	d, svc := mustOpen(t)
+	ctx := context.Background()
+	seedProject(t, d, "github.com/x/y@main")
+	if _, err := svc.Create(ctx, CreateRequest{GitHubURL: "https://github.com/x/y", Branch: "main"}); err != nil {
+		t.Fatalf("Create: %v", err)
+	}
+
+	if _, err := d.ExecContext(ctx, `DELETE FROM projects WHERE host_path = ?`, "github.com/x/y@main"); err != nil {
+		t.Fatalf("delete project: %v", err)
+	}
+	if _, err := svc.GetByPath(ctx, "github.com/x/y@main"); !errors.Is(err, ErrNotFound) {
+		t.Fatalf("git_repos row should have cascade-deleted, got %v", err)
+	}
+}
diff --git a/server/internal/httpapi/gitrepos.go b/server/internal/httpapi/gitrepos.go
new file mode 100644
index 0000000..fdb3154
--- /dev/null
+++ b/server/internal/httpapi/gitrepos.go
@@ -0,0 +1,332 @@
+package httpapi
+
+import (
+	"context"
+	"encoding/json"
+	"errors"
+	"net/http"
+	"strings"
+
+	"github.com/dvcdsys/code-index/server/internal/githubapi"
+	"github.com/dvcdsys/code-index/server/internal/githubtokens"
+	"github.com/dvcdsys/code-index/server/internal/gitrepos"
+	"github.com/dvcdsys/code-index/server/internal/httpapi/openapi"
+	"github.com/dvcdsys/code-index/server/internal/jobs"
+	"github.com/dvcdsys/code-index/server/internal/projects"
+	"github.com/dvcdsys/code-index/server/internal/workspacejobs"
+)
+
+// gitReposUnavailable returns 503 when the workspaces feature flag is
+// off OR any required service is nil. Single source for the message so
+// the dashboard's "feature off" UI key is stable.
+func (s *Server) gitReposUnavailable(w http.ResponseWriter) bool {
+	if !s.Deps.WorkspacesEnabled || s.Deps.GitRepos == nil || s.Deps.Jobs == nil {
+		writeError(w, http.StatusServiceUnavailable, "workspaces feature is disabled (set CIX_WORKSPACES_ENABLED=true and restart)")
+		return true
+	}
+	return false
+}
+
+// gitRepoPayload mirrors the OpenAPI GitRepo schema.
+type gitRepoPayload struct {
+	ProjectPath string  `json:"project_path"`
+	PathHash    string  `json:"path_hash"`
+	GitHubURL   string  `json:"github_url"`
+	Branch      string  `json:"branch"`
+	TokenID     *string `json:"token_id"`
+	AutoWebhook bool    `json:"auto_webhook"`
+	WebhookMode string  `json:"webhook_mode"`
+	LastSHA     *string `json:"last_sha"`
+	LastError   *string `json:"last_error"`
+	CreatedAt   string  `json:"created_at"`
+	UpdatedAt   string  `json:"updated_at"`
+}
+
+func gitRepoToPayload(g gitrepos.GitRepo) gitRepoPayload {
+	var tokenID *string
+	if g.TokenID != "" {
+		v := g.TokenID
+		tokenID = &v
+	}
+	var lastSHA *string
+	if g.LastSHA != "" {
+		v := g.LastSHA
+		lastSHA = &v
+	}
+	var lastErr *string
+	if g.LastError != "" {
+		v := g.LastError
+		lastErr = &v
+	}
+	return gitRepoPayload{
+		ProjectPath: g.ProjectPath,
+		PathHash:    g.PathHash,
+		GitHubURL:   g.GitHubURL,
+		Branch:      g.Branch,
+		TokenID:     tokenID,
+		AutoWebhook: g.AutoWebhook,
+		WebhookMode: g.WebhookMode,
+		LastSHA:     lastSHA,
+		LastError:   lastErr,
+		CreatedAt:   g.CreatedAt.UTC().Format("2006-01-02T15:04:05.999999999Z07:00"),
+		UpdatedAt:   g.UpdatedAt.UTC().Format("2006-01-02T15:04:05.999999999Z07:00"),
+	}
+}
+
+// AddGitRepo — POST /api/v1/git-repos.
+//
+// Creates a projects row (status='pending'), the matching git_repos row,
+// and enqueues a clone_repo job. The resulting project belongs to no
+// workspace — the caller can attach it via POST /workspaces/{id}/projects.
+func (s *Server) AddGitRepo(w http.ResponseWriter, r *http.Request) {
+	if s.gitReposUnavailable(w) {
+		return
+	}
+	var body openapi.AddGitRepoRequest
+	if err := json.NewDecoder(r.Body).Decode(&body); err != nil {
+		writeError(w, http.StatusUnprocessableEntity, "invalid JSON body")
+		return
+	}
+
+	mode := ""
+	if body.WebhookMode != nil {
+		mode = string(*body.WebhookMode)
+	}
+	tokenID := ""
+	if body.TokenId != nil {
+		tokenID = *body.TokenId
+	}
+
+	// Parse the URL up front so we know the canonical project_path and
+	// can stage the projects row before gitrepos.Create runs (the FK
+	// from git_repos.project_path → projects.host_path needs it).
+	owner, repo, perr := gitrepos.ParseGitHubURL(body.GithubUrl)
+	if perr != nil {
+		writeError(w, http.StatusUnprocessableEntity, "github_url must be an https://github.com/owner/repo URL")
+		return
+	}
+	branch := strings.TrimSpace(body.Branch)
+	if branch == "" {
+		writeError(w, http.StatusUnprocessableEntity, "branch is required")
+		return
+	}
+	projectPath := "github.com/" + owner + "/" + repo + "@" + branch
+
+	// Pre-stage the projects row so the git_repos FK can attach.
+	// ErrConflict on a re-add is fine — somebody else (or a previous
+	// half-failed attempt) already wrote it; the gitrepos.Create
+	// below will surface the real duplicate via UNIQUE on (github_url,
+	// branch). ErrOverlap is a hard reject.
+	//
+	// Fix #5: track whether THIS request created the projects row so
+	// we can compensate-delete it on gitrepos.Create failure. Without
+	// the rollback a failed request leaves an operator-visible
+	// 'pending' orphan with no git_repos and no workspace_projects.
+	_, createErr := projects.Create(r.Context(), s.Deps.DB, projects.CreateRequest{HostPath: projectPath})
+	projectCreatedHere := createErr == nil
+	if createErr != nil && !errors.Is(createErr, projects.ErrConflict) {
+		writeError(w, http.StatusUnprocessableEntity, createErr.Error())
+		return
+	}
+
+	g, err := s.Deps.GitRepos.Create(r.Context(), gitrepos.CreateRequest{
+		GitHubURL:   body.GithubUrl,
+		Branch:      body.Branch,
+		TokenID:     tokenID,
+		WebhookMode: mode,
+	})
+	if err != nil {
+		// Compensating delete (Fix #5): drop the project we staged so
+		// the failed flow doesn't leave a 'pending' orphan visible in
+		// /projects. Guarded by two checks:
+		//   (a) projectCreatedHere — never touch a project that
+		//       pre-existed; somebody else owns it.
+		//   (b) no git_repos row currently FK-references this project
+		//       — a concurrent winner may have inserted between our
+		//       projects.Create and our gitrepos.Create. Deleting then
+		//       would cascade away the winner's git_repo row.
+		if projectCreatedHere {
+			if _, gerr := s.Deps.GitRepos.GetByPath(r.Context(), projectPath); errors.Is(gerr, gitrepos.ErrNotFound) {
+				if derr := projects.Delete(r.Context(), s.Deps.DB, projectPath); derr != nil && s.Deps.Logger != nil {
+					s.Deps.Logger.Warn(
+						"AddGitRepo: compensating projects.Delete after gitrepos.Create failure failed; an orphan 'pending' project may need manual cleanup",
+						"project_path", projectPath,
+						"original_err", err,
+						"delete_err", derr,
+					)
+				}
+			}
+		}
+		switch {
+		case errors.Is(err, gitrepos.ErrInvalidURL):
+			writeError(w, http.StatusUnprocessableEntity, "github_url must be an https://github.com/owner/repo URL")
+		case errors.Is(err, gitrepos.ErrBranchEmpty):
+			writeError(w, http.StatusUnprocessableEntity, "branch is required")
+		case errors.Is(err, gitrepos.ErrInvalidWebhookMode):
+			writeError(w, http.StatusUnprocessableEntity, "webhook_mode must be one of manual, auto, disabled")
+		case errors.Is(err, gitrepos.ErrDuplicate):
+			writeError(w, http.StatusConflict, "a project for this github_url + branch already exists")
+		default:
+			writeError(w, http.StatusInternalServerError, "could not register git repo: "+err.Error())
+		}
+		return
+	}
+
+	if err := workspacejobs.EnqueueClone(r.Context(), s.Deps.Jobs, g.ProjectPath); err != nil {
+		writeError(w, http.StatusInternalServerError, "git repo registered but clone could not be enqueued: "+err.Error())
+		return
+	}
+
+	webhookURL := s.buildWebhookURL(g.PathHash)
+	autoRegistered := false
+	autoNote := ""
+	if g.WebhookMode == gitrepos.WebhookModeAuto {
+		ok, note := s.tryAutoRegisterWebhook(r.Context(), g, webhookURL)
+		autoRegistered = ok
+		autoNote = note
+		if ok {
+			// Reload so the response reflects the persisted webhook_id.
+			if fresh, ferr := s.Deps.GitRepos.GetByPath(r.Context(), g.ProjectPath); ferr == nil {
+				g = fresh
+			}
+		}
+	}
+
+	proj, perr := projects.Get(r.Context(), s.Deps.DB, g.ProjectPath)
+	if perr != nil {
+		writeError(w, http.StatusInternalServerError, "could not reload project: "+perr.Error())
+		return
+	}
+	resp := map[string]any{
+		"project":         projectToOpenAPI(proj),
+		"git_repo":        gitRepoToPayload(g),
+		"webhook_url":     webhookURL,
+		"webhook_secret":  g.WebhookSecret,
+		"auto_registered": autoRegistered,
+	}
+	if autoNote != "" {
+		resp["auto_register_note"] = autoNote
+	}
+	writeJSON(w, http.StatusCreated, resp)
+}
+
+// GetProjectGitRepo — GET /api/v1/projects/{hash}/git-repo.
+func (s *Server) GetProjectGitRepo(w http.ResponseWriter, r *http.Request, hash openapi.ProjectHash) {
+	if s.gitReposUnavailable(w) {
+		return
+	}
+	g, err := s.Deps.GitRepos.GetByHash(r.Context(), string(hash))
+	if err != nil {
+		if errors.Is(err, gitrepos.ErrNotFound) {
+			writeError(w, http.StatusNotFound, "no git_repos row for this project (likely a local project)")
+			return
+		}
+		writeError(w, http.StatusInternalServerError, "could not load git_repo: "+err.Error())
+		return
+	}
+	writeJSON(w, http.StatusOK, gitRepoToPayload(g))
+}
+
+// ReindexProject — POST /api/v1/projects/{hash}/reindex.
+//
+// Looks up the matching git_repos row and enqueues a clone_repo job
+// (which chains into index_repo on success). 422 for local projects
+// — they have no clone pipeline and must be reindexed via the CLI.
+func (s *Server) ReindexProject(w http.ResponseWriter, r *http.Request, hash openapi.ProjectHash) {
+	if s.gitReposUnavailable(w) {
+		return
+	}
+	g, err := s.Deps.GitRepos.GetByHash(r.Context(), string(hash))
+	if err != nil {
+		if errors.Is(err, gitrepos.ErrNotFound) {
+			writeError(w, http.StatusUnprocessableEntity, "this project has no git_repos row — reindex via `cix reindex <path>` for local projects")
+			return
+		}
+		writeError(w, http.StatusInternalServerError, "could not load git_repo: "+err.Error())
+		return
+	}
+
+	enqueued := true
+	if _, eerr := s.Deps.Jobs.Enqueue(r.Context(), jobs.EnqueueRequest{
+		Type:      workspacejobs.TypeCloneRepo,
+		DedupeKey: "clone:" + g.PathHash,
+		Payload:   workspacejobs.ClonePayload{ProjectPath: g.ProjectPath},
+	}); eerr != nil {
+		if errors.Is(eerr, jobs.ErrDuplicate) {
+			enqueued = false
+		} else {
+			writeError(w, http.StatusInternalServerError, "could not enqueue reindex")
+			return
+		}
+	}
+	status := "enqueued"
+	if !enqueued {
+		status = "already_running"
+	}
+	proj, _ := projects.Get(r.Context(), s.Deps.DB, g.ProjectPath)
+	resp := map[string]any{"status": status}
+	if proj != nil {
+		resp["project"] = projectToOpenAPI(proj)
+	}
+	writeJSON(w, http.StatusAccepted, resp)
+}
+
+// tryAutoRegisterWebhook calls the GitHub API to register a push hook
+// for the given git_repo. Best-effort — failure does NOT roll back the
+// git_repos row; the operator can rerun manually via webhook-info.
+func (s *Server) tryAutoRegisterWebhook(ctx context.Context, g gitrepos.GitRepo, deliveryURL string) (bool, string) {
+	logger := s.Deps.Logger
+	if !strings.HasPrefix(deliveryURL, "http") {
+		return false, "CIX_PUBLIC_URL is not set — register the webhook manually"
+	}
+	if g.TokenID == "" {
+		return false, "auto webhook_mode requires a token_id with admin:repo_hook scope"
+	}
+	pat, err := s.Deps.GithubTokens.Reveal(ctx, g.TokenID)
+	if err != nil {
+		if errors.Is(err, githubtokens.ErrNotFound) {
+			return false, "token_id not found"
+		}
+		return false, "could not decrypt the GitHub token"
+	}
+	_ = s.Deps.GithubTokens.Touch(ctx, g.TokenID)
+
+	owner, repo, perr := githubapi.ParseOwnerRepo(g.GitHubURL)
+	if perr != nil {
+		return false, "github_url is not a parseable owner/repo URL"
+	}
+	hr, herr := githubapi.New().CreateWebhook(ctx, githubapi.CreateWebhookOptions{
+		Owner:  owner,
+		Repo:   repo,
+		PAT:    pat,
+		URL:    deliveryURL,
+		Secret: g.WebhookSecret,
+	})
+	if herr != nil {
+		if logger != nil {
+			logger.Warn("workspaces: auto-register webhook failed",
+				"project", g.ProjectPath, "owner", owner, "repo", repo, "err", herr)
+		}
+		if errors.Is(herr, githubapi.ErrUnauthorized) {
+			return false, "GitHub rejected the token — add admin:repo_hook scope or register manually"
+		}
+		return false, "GitHub API rejected the call: " + herr.Error()
+	}
+	if uerr := s.Deps.GitRepos.SetWebhookID(ctx, g.ProjectPath, hr.ID); uerr != nil && logger != nil {
+		logger.Warn("workspaces: could not persist webhook id", "project", g.ProjectPath, "err", uerr)
+	}
+	return true, ""
+}
+
+// buildWebhookURL constructs the publicly-reachable webhook delivery URL
+// for a project's path_hash. When PublicBaseURL is empty, returns the
+// path only so the dashboard can render with a helper note.
+func (s *Server) buildWebhookURL(pathHash string) string {
+	path := "/api/v1/webhooks/github/" + pathHash
+	base := strings.TrimRight(s.Deps.PublicBaseURL, "/")
+	if base == "" {
+		return path
+	}
+	return base + path
+}
+
diff --git a/server/internal/httpapi/gitrepos_test.go b/server/internal/httpapi/gitrepos_test.go
new file mode 100644
index 0000000..c098f36
--- /dev/null
+++ b/server/internal/httpapi/gitrepos_test.go
@@ -0,0 +1,358 @@
+package httpapi
+
+import (
+	"context"
+	"encoding/json"
+	"net/http"
+	"sort"
+	"sync"
+	"testing"
+
+	"github.com/dvcdsys/code-index/server/internal/jobs"
+)
+
+func TestAddGitRepo_Succeeds(t *testing.T) {
+	router, jobsSvc := reposRouter(t)
+
+	rr := doJSON(t, router, http.MethodPost, "/api/v1/git-repos", map[string]any{
+		"github_url": "https://github.com/spf13/cobra",
+		"branch":     "main",
+	})
+	if rr.Code != http.StatusCreated {
+		t.Fatalf("add: %d (%s)", rr.Code, rr.Body.String())
+	}
+
+	var resp struct {
+		Project struct {
+			HostPath string `json:"host_path"`
+			Status   string `json:"status"`
+		} `json:"project"`
+		GitRepo struct {
+			ProjectPath string `json:"project_path"`
+			PathHash    string `json:"path_hash"`
+			GitHubURL   string `json:"github_url"`
+			Branch      string `json:"branch"`
+			WebhookMode string `json:"webhook_mode"`
+		} `json:"git_repo"`
+		WebhookURL    string `json:"webhook_url"`
+		WebhookSecret string `json:"webhook_secret"`
+	}
+	if err := json.Unmarshal(rr.Body.Bytes(), &resp); err != nil {
+		t.Fatalf("decode: %v", err)
+	}
+	want := "github.com/spf13/cobra@main"
+	if resp.GitRepo.ProjectPath != want {
+		t.Fatalf("project_path = %q, want %q", resp.GitRepo.ProjectPath, want)
+	}
+	if resp.Project.HostPath != want {
+		t.Fatalf("project.host_path = %q, want %q", resp.Project.HostPath, want)
+	}
+	// Fresh projects.Create returns status='created'; the clone job
+	// flips through 'cloning' → 'indexing' → 'indexed' from there.
+	if resp.Project.Status != "created" {
+		t.Fatalf("project.status = %q, want created", resp.Project.Status)
+	}
+	if resp.WebhookSecret == "" {
+		t.Errorf("webhook_secret was not populated")
+	}
+	if resp.GitRepo.WebhookMode != "manual" {
+		t.Errorf("default webhook_mode = %q, want manual", resp.GitRepo.WebhookMode)
+	}
+
+	// clone_repo job enqueued.
+	jobList, err := jobsSvc.List(context.Background(), jobs.StatusPending, "clone_repo", 10)
+	if err != nil {
+		t.Fatalf("jobs list: %v", err)
+	}
+	if len(jobList) != 1 {
+		t.Fatalf("expected 1 clone_repo job, got %d", len(jobList))
+	}
+	if jobList[0].DedupeKey != "clone:"+resp.GitRepo.PathHash {
+		t.Errorf("dedupe_key = %q, want clone:%s", jobList[0].DedupeKey, resp.GitRepo.PathHash)
+	}
+}
+
+// TestAddGitRepo_Duplicate confirms the UNIQUE(github_url, branch)
+// constraint on git_repos surfaces as 409 from the HTTP handler. Used
+// to be a workspace-scoped duplicate; with the split the same upstream
+// can only be registered once across the whole server.
+func TestAddGitRepo_Duplicate(t *testing.T) {
+	router, _ := reposRouter(t)
+	body := map[string]any{
+		"github_url": "https://github.com/a/b",
+		"branch":     "main",
+	}
+	if rr := doJSON(t, router, http.MethodPost, "/api/v1/git-repos", body); rr.Code != http.StatusCreated {
+		t.Fatalf("first: %d", rr.Code)
+	}
+	if rr := doJSON(t, router, http.MethodPost, "/api/v1/git-repos", body); rr.Code != http.StatusConflict {
+		t.Fatalf("duplicate should 409, got %d (%s)", rr.Code, rr.Body.String())
+	}
+}
+
+func TestReindexProject_RequiresGitRepo(t *testing.T) {
+	router, _ := reposRouter(t)
+
+	// CLI-indexed local project — has a projects row but no git_repos.
+	rr := doJSON(t, router, http.MethodPost, "/api/v1/projects", map[string]any{
+		"host_path": "/Users/x/local-proj",
+	})
+	if rr.Code != http.StatusCreated {
+		t.Fatalf("seed local project: %d (%s)", rr.Code, rr.Body.String())
+	}
+	var p struct {
+		PathHash string `json:"path_hash"`
+	}
+	_ = json.Unmarshal(rr.Body.Bytes(), &p)
+	if p.PathHash == "" {
+		t.Fatalf("local project missing path_hash")
+	}
+
+	rr = doJSON(t, router, http.MethodPost, "/api/v1/projects/"+p.PathHash+"/reindex", nil)
+	if rr.Code != http.StatusUnprocessableEntity {
+		t.Fatalf("expected 422 for local-project reindex, got %d (%s)", rr.Code, rr.Body.String())
+	}
+}
+
+// TestAddGitRepo_FailedGitRepoCreate_RollsBackProject covers Fix #5 of
+// the branch review: when gitrepos.Create fails AFTER projects.Create
+// succeeded, the handler must compensate-delete the freshly created
+// projects row. Without that rollback the operator sees a 'pending'
+// orphan in /projects that can't be linked to a workspace (status !=
+// 'indexed') and can't be reindexed (no git_repos row).
+//
+// Force the gitrepos.Create failure via an invalid webhook_mode — the
+// service-side validation rejects unknown values, by which point the
+// handler has already staged the projects row. (URL + branch are
+// validated by the handler up front so they don't trigger the same
+// orphan window.)
+func TestAddGitRepo_FailedGitRepoCreate_RollsBackProject(t *testing.T) {
+	router, _, d := reposRouterDB(t)
+
+	rr := doJSON(t, router, http.MethodPost, "/api/v1/git-repos", map[string]any{
+		"github_url":   "https://github.com/x/orphan-test",
+		"branch":       "main",
+		"webhook_mode": "totally-bogus-mode",
+	})
+	if rr.Code != http.StatusUnprocessableEntity {
+		t.Fatalf("expected 422 for invalid webhook_mode, got %d (%s)", rr.Code, rr.Body.String())
+	}
+
+	var n int
+	if err := d.QueryRow(
+		`SELECT COUNT(*) FROM projects WHERE host_path = ?`,
+		"github.com/x/orphan-test@main",
+	).Scan(&n); err != nil {
+		t.Fatalf("count projects: %v", err)
+	}
+	if n != 0 {
+		t.Errorf("expected projects row to be rolled back after gitrepos.Create failure, got count=%d", n)
+	}
+
+	// Sanity: no git_repos row either (Create rejected before INSERT).
+	if err := d.QueryRow(
+		`SELECT COUNT(*) FROM git_repos WHERE project_path = ?`,
+		"github.com/x/orphan-test@main",
+	).Scan(&n); err != nil {
+		t.Fatalf("count git_repos: %v", err)
+	}
+	if n != 0 {
+		t.Errorf("expected no git_repos row after validation failure, got %d", n)
+	}
+}
+
+// TestAddGitRepo_FailedGitRepoCreate_PreservesPreExistingProject is the
+// negative half of Fix #5: when the project pre-existed (created by a
+// different flow earlier), a failing AddGitRepo must NOT delete it.
+// projectCreatedHere=false → no compensation, even though gitrepos.Create
+// failed. This guards the cascade-delete corruption case where rolling
+// back would wipe somebody else's git_repos row via FK CASCADE.
+func TestAddGitRepo_FailedGitRepoCreate_PreservesPreExistingProject(t *testing.T) {
+	router, _, d := reposRouterDB(t)
+
+	// Pre-seed an indexed project for the same path the request would
+	// derive. Simulates: a previous successful flow created this row,
+	// and our concurrent request shouldn't blow it away.
+	hostPath := "github.com/x/keepme@main"
+	if _, err := d.Exec(`
+		INSERT INTO projects (host_path, container_path, languages, settings, stats,
+			status, created_at, updated_at, path_hash)
+		VALUES (?, ?, '[]', '{}', '{}', 'indexed', '2026-01-01T00:00:00Z', '2026-01-01T00:00:00Z', ?)`,
+		hostPath, hostPath, "0123456789abcdef",
+	); err != nil {
+		t.Fatalf("seed pre-existing project: %v", err)
+	}
+
+	rr := doJSON(t, router, http.MethodPost, "/api/v1/git-repos", map[string]any{
+		"github_url":   "https://github.com/x/keepme",
+		"branch":       "main",
+		"webhook_mode": "totally-bogus-mode",
+	})
+	if rr.Code != http.StatusUnprocessableEntity {
+		t.Fatalf("expected 422, got %d (%s)", rr.Code, rr.Body.String())
+	}
+
+	var n int
+	if err := d.QueryRow(
+		`SELECT COUNT(*) FROM projects WHERE host_path = ?`, hostPath,
+	).Scan(&n); err != nil {
+		t.Fatalf("count: %v", err)
+	}
+	if n != 1 {
+		t.Errorf("pre-existing project must be preserved on gitrepos.Create failure, got count=%d", n)
+	}
+}
+
+// TestAddGitRepo_ConcurrentDuplicate_NoOrphan covers the Fix #5
+// acceptance criterion literally: two concurrent POSTs with the same
+// github_url + branch should yield one 201 and one 409, with exactly
+// one projects row and one git_repos row at the end. This also covers
+// Fix #15 (concurrent race test) from the same review.
+//
+// The compensating delete guard `if no git_repos row exists` is what
+// makes this safe — without it, the loser's rollback could cascade
+// away the winner's git_repos row.
+func TestAddGitRepo_ConcurrentDuplicate_NoOrphan(t *testing.T) {
+	router, _, d := reposRouterDB(t)
+	body := map[string]any{
+		"github_url": "https://github.com/x/concurrent",
+		"branch":     "main",
+	}
+
+	var wg sync.WaitGroup
+	codes := make(chan int, 2)
+	for i := 0; i < 2; i++ {
+		wg.Add(1)
+		go func() {
+			defer wg.Done()
+			rr := doJSON(t, router, http.MethodPost, "/api/v1/git-repos", body)
+			codes <- rr.Code
+		}()
+	}
+	wg.Wait()
+	close(codes)
+
+	got := []int{<-codes, <-codes}
+	sort.Ints(got)
+	// Exactly one 201 (winner) and one 409 (duplicate).
+	if got[0] != http.StatusCreated || got[1] != http.StatusConflict {
+		t.Fatalf("expected one 201 + one 409, got %v", got)
+	}
+
+	// Single projects row.
+	var n int
+	if err := d.QueryRow(
+		`SELECT COUNT(*) FROM projects WHERE host_path = ?`,
+		"github.com/x/concurrent@main",
+	).Scan(&n); err != nil {
+		t.Fatalf("count projects: %v", err)
+	}
+	if n != 1 {
+		t.Errorf("expected exactly 1 projects row after concurrent race, got %d", n)
+	}
+
+	// Single git_repos row.
+	if err := d.QueryRow(
+		`SELECT COUNT(*) FROM git_repos WHERE project_path = ?`,
+		"github.com/x/concurrent@main",
+	).Scan(&n); err != nil {
+		t.Fatalf("count git_repos: %v", err)
+	}
+	if n != 1 {
+		t.Errorf("expected exactly 1 git_repos row after concurrent race, got %d", n)
+	}
+}
+
+// TestDeleteProject_CascadesGitRepoAndMembership exercises the chained
+// FK ON DELETE CASCADE: removing the project deletes the git_repos row
+// AND every workspace_projects row referencing it. Used to be a
+// manual cleanup in projects.Delete; now the FKs do the work.
+//
+// Fix #16 acceptance: explicit COUNT(*) assertions on both child tables
+// after the DELETE so anyone who later strips `ON DELETE CASCADE` from
+// either FK gets a clear "git_repos should cascade" / "workspace_projects
+// should cascade" failure instead of a downstream behavioural surprise.
+func TestDeleteProject_CascadesGitRepoAndMembership(t *testing.T) {
+	router, _, d := reposRouterDB(t)
+
+	// Add an external project — kicks off project + git_repos rows.
+	rr := doJSON(t, router, http.MethodPost, "/api/v1/git-repos", map[string]any{
+		"github_url": "https://github.com/a/b",
+		"branch":     "main",
+	})
+	if rr.Code != http.StatusCreated {
+		t.Fatalf("add: %d (%s)", rr.Code, rr.Body.String())
+	}
+	var created struct {
+		GitRepo struct {
+			PathHash string `json:"path_hash"`
+		} `json:"git_repo"`
+	}
+	_ = json.Unmarshal(rr.Body.Bytes(), &created)
+	hash := created.GitRepo.PathHash
+	projPath := "github.com/a/b@main"
+
+	// Force status=indexed so workspaceprojects.Link's precondition passes —
+	// the clone+index job chain isn't wired in the test harness so we
+	// satisfy the invariant by hand.
+	if _, err := d.Exec(`UPDATE projects SET status = 'indexed' WHERE host_path = ?`, projPath); err != nil {
+		t.Fatalf("mark indexed: %v", err)
+	}
+
+	// Create a workspace and link the project so the workspace_projects
+	// cascade has a real row to verify (the prior version of this test
+	// asserted nothing on workspace_projects — the FK trigger was untested).
+	rr = doJSON(t, router, http.MethodPost, "/api/v1/workspaces", map[string]any{
+		"name":        "platform",
+		"description": "cascade test",
+	})
+	if rr.Code != http.StatusCreated {
+		t.Fatalf("create workspace: %d (%s)", rr.Code, rr.Body.String())
+	}
+	var ws struct {
+		ID string `json:"id"`
+	}
+	_ = json.Unmarshal(rr.Body.Bytes(), &ws)
+	rr = doJSON(t, router, http.MethodPost, "/api/v1/workspaces/"+ws.ID+"/projects", map[string]any{
+		"project_hash": hash,
+	})
+	if rr.Code != http.StatusCreated {
+		t.Fatalf("link project: %d (%s)", rr.Code, rr.Body.String())
+	}
+
+	// Sanity-pin the pre-delete state — without this, a "0 rows after
+	// delete" assertion can't distinguish "cascade fired" from "row
+	// never existed in the first place".
+	assertCount := func(t *testing.T, q string, want int) {
+		t.Helper()
+		var n int
+		if err := d.QueryRow(q, projPath).Scan(&n); err != nil {
+			t.Fatalf("count %q: %v", q, err)
+		}
+		if n != want {
+			t.Errorf("count %q: got %d, want %d", q, n, want)
+		}
+	}
+	assertCount(t, `SELECT COUNT(*) FROM git_repos WHERE project_path = ?`, 1)
+	assertCount(t, `SELECT COUNT(*) FROM workspace_projects WHERE project_path = ?`, 1)
+
+	// Delete the project — both child rows must cascade.
+	rr = doJSON(t, router, http.MethodDelete, "/api/v1/projects/"+hash, nil)
+	if rr.Code != http.StatusNoContent {
+		t.Fatalf("delete: %d (%s)", rr.Code, rr.Body.String())
+	}
+	assertCount(t, `SELECT COUNT(*) FROM git_repos WHERE project_path = ?`, 0)
+	assertCount(t, `SELECT COUNT(*) FROM workspace_projects WHERE project_path = ?`, 0)
+
+	// Re-adding the exact same upstream must succeed — end-to-end check
+	// that the git_repos row was actually removed (otherwise
+	// UNIQUE(github_url, branch) would 409 here, which is the bug a
+	// previous patch fixed).
+	rr = doJSON(t, router, http.MethodPost, "/api/v1/git-repos", map[string]any{
+		"github_url": "https://github.com/a/b",
+		"branch":     "main",
+	})
+	if rr.Code != http.StatusCreated {
+		t.Fatalf("re-add after delete: %d (%s)", rr.Code, rr.Body.String())
+	}
+}
diff --git a/server/internal/httpapi/openapi/openapi.gen.go b/server/internal/httpapi/openapi/openapi.gen.go
index 94436b0..595ebd4 100644
--- a/server/internal/httpapi/openapi/openapi.gen.go
+++ b/server/internal/httpapi/openapi/openapi.gen.go
@@ -26,21 +26,21 @@ const (
 	BearerAuthScopes bearerAuthContextKey = "bearerAuth.Scopes"
 )
 
-// Defines values for AddWorkspaceRepoRequestWebhookMode.
+// Defines values for AddGitRepoRequestWebhookMode.
 const (
-	AddWorkspaceRepoRequestWebhookModeAuto     AddWorkspaceRepoRequestWebhookMode = "auto"
-	AddWorkspaceRepoRequestWebhookModeDisabled AddWorkspaceRepoRequestWebhookMode = "disabled"
-	AddWorkspaceRepoRequestWebhookModeManual   AddWorkspaceRepoRequestWebhookMode = "manual"
+	AddGitRepoRequestWebhookModeAuto     AddGitRepoRequestWebhookMode = "auto"
+	AddGitRepoRequestWebhookModeDisabled AddGitRepoRequestWebhookMode = "disabled"
+	AddGitRepoRequestWebhookModeManual   AddGitRepoRequestWebhookMode = "manual"
 )
 
-// Valid indicates whether the value is a known member of the AddWorkspaceRepoRequestWebhookMode enum.
-func (e AddWorkspaceRepoRequestWebhookMode) Valid() bool {
+// Valid indicates whether the value is a known member of the AddGitRepoRequestWebhookMode enum.
+func (e AddGitRepoRequestWebhookMode) Valid() bool {
 	switch e {
-	case AddWorkspaceRepoRequestWebhookModeAuto:
+	case AddGitRepoRequestWebhookModeAuto:
 		return true
-	case AddWorkspaceRepoRequestWebhookModeDisabled:
+	case AddGitRepoRequestWebhookModeDisabled:
 		return true
-	case AddWorkspaceRepoRequestWebhookModeManual:
+	case AddGitRepoRequestWebhookModeManual:
 		return true
 	default:
 		return false
@@ -65,6 +65,27 @@ func (e CreateUserRequestRole) Valid() bool {
 	}
 }
 
+// Defines values for GitRepoWebhookMode.
+const (
+	GitRepoWebhookModeAuto     GitRepoWebhookMode = "auto"
+	GitRepoWebhookModeDisabled GitRepoWebhookMode = "disabled"
+	GitRepoWebhookModeManual   GitRepoWebhookMode = "manual"
+)
+
+// Valid indicates whether the value is a known member of the GitRepoWebhookMode enum.
+func (e GitRepoWebhookMode) Valid() bool {
+	switch e {
+	case GitRepoWebhookModeAuto:
+		return true
+	case GitRepoWebhookModeDisabled:
+		return true
+	case GitRepoWebhookModeManual:
+		return true
+	default:
+		return false
+	}
+}
+
 // Defines values for GithubAccountType.
 const (
 	GithubAccountTypeOrg  GithubAccountType = "org"
@@ -266,33 +287,6 @@ func (e ProjectStatus) Valid() bool {
 	}
 }
 
-// Defines values for ProjectWorkspaceEntryStatus.
-const (
-	ProjectWorkspaceEntryStatusCloning  ProjectWorkspaceEntryStatus = "cloning"
-	ProjectWorkspaceEntryStatusFailed   ProjectWorkspaceEntryStatus = "failed"
-	ProjectWorkspaceEntryStatusIndexed  ProjectWorkspaceEntryStatus = "indexed"
-	ProjectWorkspaceEntryStatusIndexing ProjectWorkspaceEntryStatus = "indexing"
-	ProjectWorkspaceEntryStatusPending  ProjectWorkspaceEntryStatus = "pending"
-)
-
-// Valid indicates whether the value is a known member of the ProjectWorkspaceEntryStatus enum.
-func (e ProjectWorkspaceEntryStatus) Valid() bool {
-	switch e {
-	case ProjectWorkspaceEntryStatusCloning:
-		return true
-	case ProjectWorkspaceEntryStatusFailed:
-		return true
-	case ProjectWorkspaceEntryStatusIndexed:
-		return true
-	case ProjectWorkspaceEntryStatusIndexing:
-		return true
-	case ProjectWorkspaceEntryStatusPending:
-		return true
-	default:
-		return false
-	}
-}
-
 // Defines values for ReferenceItemChunkType.
 const (
 	Reference ReferenceItemChunkType = "reference"
@@ -467,54 +461,6 @@ func (e WebhookAcceptedStatus) Valid() bool {
 	}
 }
 
-// Defines values for WorkspaceRepoStatus.
-const (
-	WorkspaceRepoStatusCloning  WorkspaceRepoStatus = "cloning"
-	WorkspaceRepoStatusFailed   WorkspaceRepoStatus = "failed"
-	WorkspaceRepoStatusIndexed  WorkspaceRepoStatus = "indexed"
-	WorkspaceRepoStatusIndexing WorkspaceRepoStatus = "indexing"
-	WorkspaceRepoStatusPending  WorkspaceRepoStatus = "pending"
-)
-
-// Valid indicates whether the value is a known member of the WorkspaceRepoStatus enum.
-func (e WorkspaceRepoStatus) Valid() bool {
-	switch e {
-	case WorkspaceRepoStatusCloning:
-		return true
-	case WorkspaceRepoStatusFailed:
-		return true
-	case WorkspaceRepoStatusIndexed:
-		return true
-	case WorkspaceRepoStatusIndexing:
-		return true
-	case WorkspaceRepoStatusPending:
-		return true
-	default:
-		return false
-	}
-}
-
-// Defines values for WorkspaceRepoWebhookMode.
-const (
-	Auto     WorkspaceRepoWebhookMode = "auto"
-	Disabled WorkspaceRepoWebhookMode = "disabled"
-	Manual   WorkspaceRepoWebhookMode = "manual"
-)
-
-// Valid indicates whether the value is a known member of the WorkspaceRepoWebhookMode enum.
-func (e WorkspaceRepoWebhookMode) Valid() bool {
-	switch e {
-	case Auto:
-		return true
-	case Disabled:
-		return true
-	case Manual:
-		return true
-	default:
-		return false
-	}
-}
-
 // Defines values for WorkspaceSearchPendingRepoStatus.
 const (
 	WorkspaceSearchPendingRepoStatusCloning  WorkspaceSearchPendingRepoStatus = "cloning"
@@ -595,22 +541,22 @@ func (e ListTokenReposParamsAccountType) Valid() bool {
 
 // Defines values for ListJobsParamsStatus.
 const (
-	ListJobsParamsStatusCompleted ListJobsParamsStatus = "completed"
-	ListJobsParamsStatusFailed    ListJobsParamsStatus = "failed"
-	ListJobsParamsStatusPending   ListJobsParamsStatus = "pending"
-	ListJobsParamsStatusRunning   ListJobsParamsStatus = "running"
+	Completed ListJobsParamsStatus = "completed"
+	Failed    ListJobsParamsStatus = "failed"
+	Pending   ListJobsParamsStatus = "pending"
+	Running   ListJobsParamsStatus = "running"
 )
 
 // Valid indicates whether the value is a known member of the ListJobsParamsStatus enum.
 func (e ListJobsParamsStatus) Valid() bool {
 	switch e {
-	case ListJobsParamsStatusCompleted:
+	case Completed:
 		return true
-	case ListJobsParamsStatusFailed:
+	case Failed:
 		return true
-	case ListJobsParamsStatusPending:
+	case Pending:
 		return true
-	case ListJobsParamsStatusRunning:
+	case Running:
 		return true
 	default:
 		return false
@@ -635,39 +581,20 @@ func (e IndexFilesParamsAccept) Valid() bool {
 	}
 }
 
-// AddWorkspaceRepoRequest defines model for AddWorkspaceRepoRequest.
-type AddWorkspaceRepoRequest struct {
-	// AutoWebhook Legacy field. New clients should send `webhook_mode` instead.
-	// When both are provided, `webhook_mode` wins; when only the
-	// bool is set, `true` is mapped to `webhook_mode = "auto"`.
-	// Deprecated: this property has been marked as deprecated upstream, but no `x-deprecated-reason` was set
-	AutoWebhook *bool  `json:"auto_webhook,omitempty"`
-	Branch      string `json:"branch"`
+// AddGitRepoRequest defines model for AddGitRepoRequest.
+type AddGitRepoRequest struct {
+	Branch string `json:"branch"`
 
 	// GithubUrl https://github.com/owner/repo URL.
 	GithubUrl string `json:"github_url"`
 
-	// TokenId Optional id of a stored GitHub PAT. Required for private repos.
-	TokenId *string `json:"token_id,omitempty"`
-
-	// WebhookMode How the server should keep this repo fresh:
-	// - `auto` — server registers the webhook in GitHub on your
-	//   behalf (requires admin:repo_hook on the PAT).
-	// - `manual` — server stores a webhook_secret and returns it
-	//   once; you paste the URL + secret into GitHub yourself.
-	// - `disabled` — no auto-sync at all; reindex via the
-	//   dashboard button only.
-	WebhookMode *AddWorkspaceRepoRequestWebhookMode `json:"webhook_mode,omitempty"`
+	// TokenId Optional id of a stored GitHub PAT (required for private repos).
+	TokenId     *string                       `json:"token_id,omitempty"`
+	WebhookMode *AddGitRepoRequestWebhookMode `json:"webhook_mode,omitempty"`
 }
 
-// AddWorkspaceRepoRequestWebhookMode How the server should keep this repo fresh:
-//   - `auto` — server registers the webhook in GitHub on your
-//     behalf (requires admin:repo_hook on the PAT).
-//   - `manual` — server stores a webhook_secret and returns it
-//     once; you paste the URL + secret into GitHub yourself.
-//   - `disabled` — no auto-sync at all; reindex via the
-//     dashboard button only.
-type AddWorkspaceRepoRequestWebhookMode string
+// AddGitRepoRequestWebhookMode defines model for AddGitRepoRequest.WebhookMode.
+type AddGitRepoRequestWebhookMode string
 
 // ApiKey defines model for ApiKey.
 type ApiKey struct {
@@ -857,6 +784,56 @@ type FileSearchResponse struct {
 	Total   int              `json:"total"`
 }
 
+// GitRepo Clone + webhook metadata for an external (git-cloned) project.
+// Exactly 1:1 with the matching projects row; local projects have
+// no GitRepo row.
+type GitRepo struct {
+	// AutoWebhook Legacy alias for `webhook_mode == "auto"`.
+	AutoWebhook bool      `json:"auto_webhook"`
+	Branch      string    `json:"branch"`
+	CreatedAt   time.Time `json:"created_at"`
+	GithubUrl   string    `json:"github_url"`
+	LastError   *string   `json:"last_error,omitempty"`
+	LastSha     *string   `json:"last_sha,omitempty"`
+
+	// PathHash 16-hex SHA1 prefix of project_path, used in URLs.
+	PathHash string `json:"path_hash"`
+
+	// ProjectPath Matches projects.host_path — canonical
+	// "github.com/owner/repo@branch" string.
+	ProjectPath string             `json:"project_path"`
+	TokenId     *string            `json:"token_id,omitempty"`
+	UpdatedAt   time.Time          `json:"updated_at"`
+	WebhookMode GitRepoWebhookMode `json:"webhook_mode"`
+}
+
+// GitRepoWebhookMode defines model for GitRepo.WebhookMode.
+type GitRepoWebhookMode string
+
+// GitRepoCreated defines model for GitRepoCreated.
+type GitRepoCreated struct {
+	// AutoRegisterNote Human-readable reason when auto_registered is false.
+	AutoRegisterNote *string `json:"auto_register_note,omitempty"`
+
+	// AutoRegistered True when webhook_mode was 'auto' AND the server
+	// successfully registered the hook with GitHub.
+	AutoRegistered *bool `json:"auto_registered,omitempty"`
+
+	// GitRepo Clone + webhook metadata for an external (git-cloned) project.
+	// Exactly 1:1 with the matching projects row; local projects have
+	// no GitRepo row.
+	GitRepo GitRepo `json:"git_repo"`
+	Project Project `json:"project"`
+
+	// WebhookSecret HMAC secret. **Returned once on create + once via
+	// /projects/{hash}/webhook-info.**
+	WebhookSecret string `json:"webhook_secret"`
+
+	// WebhookUrl Publicly-reachable POST endpoint to register in GitHub when
+	// doing webhook setup manually.
+	WebhookUrl string `json:"webhook_url"`
+}
+
 // GithubAccount A GitHub account the PAT can see. The user owning the PAT is
 // returned first, followed by every org accessible via /user/orgs.
 // The dashboard's add-repo flow shows these in a Select before
@@ -1051,13 +1028,11 @@ type JobListResponse struct {
 	Total int   `json:"total"`
 }
 
-// LinkExistingProjectRequest defines model for LinkExistingProjectRequest.
-type LinkExistingProjectRequest struct {
-	// ProjectHash The 16-hex `path_hash` of an indexed project — the same value
-	// used in /api/v1/projects/{path}. The server resolves it to
-	// the canonical `host_path` and inserts a linked workspace_repo
-	// row. The project must already be in status='indexed' and have
-	// a host_path of the form "github.com/owner/repo@branch".
+// LinkProjectRequest defines model for LinkProjectRequest.
+type LinkProjectRequest struct {
+	// ProjectHash The 16-hex `path_hash` of an indexed project. The server
+	// resolves it to host_path and inserts the (workspace_id,
+	// project_path) row. The project must be in status='indexed'.
 	ProjectHash string `json:"project_hash"`
 }
 
@@ -1182,19 +1157,11 @@ type ProjectSummary struct {
 
 // ProjectWorkspaceEntry defines model for ProjectWorkspaceEntry.
 type ProjectWorkspaceEntry struct {
-	Branch   string `json:"branch"`
-	IsLinked bool   `json:"is_linked"`
-
-	// RepoId workspace_repos.id — same value used in /repos endpoints.
-	RepoId        string                      `json:"repo_id"`
-	Status        ProjectWorkspaceEntryStatus `json:"status"`
-	WorkspaceId   string                      `json:"workspace_id"`
-	WorkspaceName string                      `json:"workspace_name"`
+	AddedAt       time.Time `json:"added_at"`
+	WorkspaceId   string    `json:"workspace_id"`
+	WorkspaceName string    `json:"workspace_name"`
 }
 
-// ProjectWorkspaceEntryStatus defines model for ProjectWorkspaceEntry.Status.
-type ProjectWorkspaceEntryStatus string
-
 // ProjectWorkspaceList defines model for ProjectWorkspaceList.
 type ProjectWorkspaceList struct {
 	Workspaces []ProjectWorkspaceEntry `json:"workspaces"`
@@ -1233,8 +1200,8 @@ type ReferenceResponse struct {
 
 // ReindexEnqueuedResponse defines model for ReindexEnqueuedResponse.
 type ReindexEnqueuedResponse struct {
-	Repo   *WorkspaceRepo                `json:"repo,omitempty"`
-	Status ReindexEnqueuedResponseStatus `json:"status"`
+	Project *Project                      `json:"project,omitempty"`
+	Status  ReindexEnqueuedResponseStatus `json:"status"`
 }
 
 // ReindexEnqueuedResponseStatus defines model for ReindexEnqueuedResponse.Status.
@@ -1308,8 +1275,10 @@ type SemanticSearchRequest struct {
 	// Limit Maximum number of FILE groups (not chunks) to return.
 	Limit *int `json:"limit,omitempty"`
 
-	// MinScore Minimum cosine similarity. Omit for server default (0.4 for
-	// CodeRankEmbed-Q8). Send `0` explicitly to disable the floor.
+	// MinScore Minimum cosine similarity. Omit for server default (0.2 —
+	// light floor that keeps abstract NL queries non-empty). Send
+	// `0` to disable; pass `0.4+` for strict code-symbol searches
+	// calibrated for CodeRankEmbed-Q8.
 	MinScore *float32 `json:"min_score,omitempty"`
 
 	// Paths Whitelist — keep only results whose path matches any prefix or substring.
@@ -1572,81 +1541,26 @@ type WorkspaceListResponse struct {
 	Workspaces []Workspace `json:"workspaces"`
 }
 
-// WorkspaceRepo defines model for WorkspaceRepo.
-type WorkspaceRepo struct {
-	// AutoWebhook Legacy alias for `webhook_mode == "auto"`. Always present so
-	// old clients keep working; new clients should consult
-	// `webhook_mode` instead.
-	AutoWebhook bool      `json:"auto_webhook"`
-	Branch      string    `json:"branch"`
-	CreatedAt   time.Time `json:"created_at"`
-
-	// GithubUrl Canonical https://github.com/owner/repo URL.
-	GithubUrl string `json:"github_url"`
-	Id        string `json:"id"`
-
-	// IsLinked True when this row is a lightweight pointer to a project
-	// already owned by another workspace_repo — added via the
-	// "Add Existing Project" flow. Linked rows have no clone on
-	// disk, no webhook, and no token; reindex is a no-op (must
-	// be triggered from the canonical owning row).
-	IsLinked      bool       `json:"is_linked"`
-	LastError     *string    `json:"last_error,omitempty"`
-	LastIndexedAt *time.Time `json:"last_indexed_at,omitempty"`
-
-	// LastSha HEAD SHA at last successful clone.
-	LastSha *string `json:"last_sha,omitempty"`
-
-	// ProjectPath Indexed project's host_path — "github.com/owner/repo@branch".
-	// Use this with the existing /api/v1/projects/{path}/* endpoints
-	// (path = first 16 hex chars of SHA1).
-	ProjectPath string              `json:"project_path"`
-	Status      WorkspaceRepoStatus `json:"status"`
-
-	// TokenId GitHub token used for clone+webhook calls. Null when the
-	// repo is public.
-	TokenId   *string   `json:"token_id,omitempty"`
-	UpdatedAt time.Time `json:"updated_at"`
-
-	// WebhookMode Operator's intent for how this repo gets kept fresh. `auto`
-	// asks the server to register the GitHub webhook; `manual`
-	// means the operator pastes the URL+secret into GitHub
-	// themselves; `disabled` skips auto-sync entirely — reindex
-	// via the dashboard button only.
-	WebhookMode WorkspaceRepoWebhookMode `json:"webhook_mode"`
-	WorkspaceId string                   `json:"workspace_id"`
+// WorkspaceProject A project listed under a workspace, decorated with the membership
+// timestamp. The embedded Project carries the full project info
+// (status, languages, last_indexed_at) so the dashboard doesn't
+// need a second roundtrip.
+type WorkspaceProject struct {
+	AddedAt time.Time `json:"added_at"`
+	Project Project   `json:"project"`
 }
 
-// WorkspaceRepoStatus defines model for WorkspaceRepo.Status.
-type WorkspaceRepoStatus string
-
-// WorkspaceRepoWebhookMode Operator's intent for how this repo gets kept fresh. `auto`
-// asks the server to register the GitHub webhook; `manual`
-// means the operator pastes the URL+secret into GitHub
-// themselves; `disabled` skips auto-sync entirely — reindex
-// via the dashboard button only.
-type WorkspaceRepoWebhookMode string
-
-// WorkspaceRepoCreated defines model for WorkspaceRepoCreated.
-type WorkspaceRepoCreated struct {
-	Repo WorkspaceRepo `json:"repo"`
-
-	// WebhookSecret HMAC secret. **Returned once on create + once via
-	// webhook-info.** Use as the "Secret" field in GitHub's webhook
-	// UI; deliveries are validated by HMAC-SHA256 over the body.
-	// Empty string for linked rows (no webhook).
-	WebhookSecret string `json:"webhook_secret"`
-
-	// WebhookUrl Publicly-reachable POST endpoint to register in GitHub when
-	// doing the webhook setup manually. Includes the workspace_repo
-	// id segment. Empty string for linked rows (no webhook).
-	WebhookUrl string `json:"webhook_url"`
+// WorkspaceProjectListResponse defines model for WorkspaceProjectListResponse.
+type WorkspaceProjectListResponse struct {
+	Projects []WorkspaceProject `json:"projects"`
+	Total    int                `json:"total"`
 }
 
-// WorkspaceRepoListResponse defines model for WorkspaceRepoListResponse.
-type WorkspaceRepoListResponse struct {
-	Repos []WorkspaceRepo `json:"repos"`
-	Total int             `json:"total"`
+// WorkspaceProjectMembership defines model for WorkspaceProjectMembership.
+type WorkspaceProjectMembership struct {
+	AddedAt     time.Time `json:"added_at"`
+	ProjectPath string    `json:"project_path"`
+	WorkspaceId string    `json:"workspace_id"`
 }
 
 // WorkspaceSearchChunk defines model for WorkspaceSearchChunk.
@@ -1682,15 +1596,13 @@ type WorkspaceSearchFailedRepo struct {
 type WorkspaceSearchPendingRepo struct {
 	ProjectPath string `json:"project_path"`
 
-	// Status Current row state in `workspace_repos.status`. Anything
-	// other than `indexed` means the repo hasn't contributed to
-	// this response.
+	// Status Current per-project status. Anything other than `indexed`
+	// means the project hasn't contributed to this response.
 	Status WorkspaceSearchPendingRepoStatus `json:"status"`
 }
 
-// WorkspaceSearchPendingRepoStatus Current row state in `workspace_repos.status`. Anything
-// other than `indexed` means the repo hasn't contributed to
-// this response.
+// WorkspaceSearchPendingRepoStatus Current per-project status. Anything other than `indexed`
+// means the project hasn't contributed to this response.
 type WorkspaceSearchPendingRepoStatus string
 
 // WorkspaceSearchProject defines model for WorkspaceSearchProject.
@@ -1863,11 +1775,13 @@ type WorkspaceSearchParams struct {
 	TopChunks   *int   `form:"top_chunks,omitempty" json:"top_chunks,omitempty"`
 
 	// MinScore Floor on raw cosine similarity. Chunks below this are
-	// dropped before aggregation. Default 0 — relies on
-	// chromem's natural ordering. Set higher (e.g. 0.3) to cut
-	// noise when querying long natural-language sentences;
-	// keep at 0 for short tokens / acronyms where embedding
-	// magnitudes are inherently smaller.
+	// dropped before aggregation. Default 0.4 — symmetric with
+	// per-project search default so an unfiltered workspace
+	// query doesn't return cross-repo noise that a single-repo
+	// query would have rejected. Pass 0 explicitly for
+	// intentional cross-project sweeps that need long-tail
+	// recall (e.g. "authentication and authorization" across a
+	// mixed-domain workspace).
 	MinScore *float32 `form:"min_score,omitempty" json:"min_score,omitempty"`
 }
 
@@ -1889,6 +1803,9 @@ type ChangePasswordJSONRequestBody = ChangePasswordRequest
 // LoginJSONRequestBody defines body for Login for application/json ContentType.
 type LoginJSONRequestBody = LoginRequest
 
+// AddGitRepoJSONRequestBody defines body for AddGitRepo for application/json ContentType.
+type AddGitRepoJSONRequestBody = AddGitRepoRequest
+
 // CreateGithubTokenJSONRequestBody defines body for CreateGithubToken for application/json ContentType.
 type CreateGithubTokenJSONRequestBody = CreateGithubTokenRequest
 
@@ -1931,11 +1848,8 @@ type CreateWorkspaceJSONRequestBody = CreateWorkspaceRequest
 // UpdateWorkspaceJSONRequestBody defines body for UpdateWorkspace for application/json ContentType.
 type UpdateWorkspaceJSONRequestBody = UpdateWorkspaceRequest
 
-// AddWorkspaceRepoJSONRequestBody defines body for AddWorkspaceRepo for application/json ContentType.
-type AddWorkspaceRepoJSONRequestBody = AddWorkspaceRepoRequest
-
-// LinkExistingProjectJSONRequestBody defines body for LinkExistingProject for application/json ContentType.
-type LinkExistingProjectJSONRequestBody = LinkExistingProjectRequest
+// LinkProjectToWorkspaceJSONRequestBody defines body for LinkProjectToWorkspace for application/json ContentType.
+type LinkProjectToWorkspaceJSONRequestBody = LinkProjectRequest
 
 // ServerInterface represents all server handlers.
 type ServerInterface interface {
@@ -1996,6 +1910,9 @@ type ServerInterface interface {
 	// End one of my sessions (sign out a single device)
 	// (DELETE /api/v1/auth/sessions/{id})
 	DeleteMySession(w http.ResponseWriter, r *http.Request, id string)
+	// Clone + index a GitHub repository as a standalone project
+	// (POST /api/v1/git-repos)
+	AddGitRepo(w http.ResponseWriter, r *http.Request)
 	// List stored GitHub PATs (metadata only)
 	// (GET /api/v1/github-tokens)
 	ListGithubTokens(w http.ResponseWriter, r *http.Request)
@@ -2020,6 +1937,15 @@ type ServerInterface interface {
 	// Register a new project
 	// (POST /api/v1/projects)
 	CreateProject(w http.ResponseWriter, r *http.Request)
+	// Read the git_repos metadata for an external project
+	// (GET /api/v1/projects/{hash}/git-repo)
+	GetProjectGitRepo(w http.ResponseWriter, r *http.Request, hash string)
+	// Manually re-trigger the clone + index pipeline
+	// (POST /api/v1/projects/{hash}/reindex)
+	ReindexProject(w http.ResponseWriter, r *http.Request, hash string)
+	// Webhook URL + secret for manual GitHub setup
+	// (GET /api/v1/projects/{hash}/webhook-info)
+	GetProjectWebhookInfo(w http.ResponseWriter, r *http.Request, hash string)
 	// Delete a project and all its indexed data (admin only)
 	// (DELETE /api/v1/projects/{path})
 	DeleteProject(w http.ResponseWriter, r *http.Request, path ProjectHash)
@@ -2069,8 +1995,8 @@ type ServerInterface interface {
 	// (GET /api/v1/status)
 	GetStatus(w http.ResponseWriter, r *http.Request)
 	// Receive a GitHub webhook delivery (public, HMAC-authenticated)
-	// (POST /api/v1/webhooks/github/{repo_id})
-	ReceiveGithubWebhook(w http.ResponseWriter, r *http.Request, repoId string, params ReceiveGithubWebhookParams)
+	// (POST /api/v1/webhooks/github/{hash})
+	ReceiveGithubWebhook(w http.ResponseWriter, r *http.Request, hash string, params ReceiveGithubWebhookParams)
 	// List all workspaces
 	// (GET /api/v1/workspaces)
 	ListWorkspaces(w http.ResponseWriter, r *http.Request)
@@ -2086,24 +2012,15 @@ type ServerInterface interface {
 	// Update workspace metadata
 	// (PATCH /api/v1/workspaces/{id})
 	UpdateWorkspace(w http.ResponseWriter, r *http.Request, id string)
-	// List repositories attached to a workspace
-	// (GET /api/v1/workspaces/{id}/repos)
-	ListWorkspaceRepos(w http.ResponseWriter, r *http.Request, id string)
-	// Attach a GitHub repository to a workspace
-	// (POST /api/v1/workspaces/{id}/repos)
-	AddWorkspaceRepo(w http.ResponseWriter, r *http.Request, id string)
-	// Attach an already-indexed project to a workspace
-	// (POST /api/v1/workspaces/{id}/repos/link)
-	LinkExistingProject(w http.ResponseWriter, r *http.Request, id string)
-	// Detach a repository from a workspace
-	// (DELETE /api/v1/workspaces/{id}/repos/{repo_id})
-	DeleteWorkspaceRepo(w http.ResponseWriter, r *http.Request, id string, repoId string)
-	// Manually re-trigger the clone + index pipeline
-	// (POST /api/v1/workspaces/{id}/repos/{repo_id}/reindex)
-	ReindexWorkspaceRepo(w http.ResponseWriter, r *http.Request, id string, repoId string)
-	// Get the webhook URL + secret for manual GitHub setup
-	// (GET /api/v1/workspaces/{id}/repos/{repo_id}/webhook-info)
-	GetWorkspaceRepoWebhookInfo(w http.ResponseWriter, r *http.Request, id string, repoId string)
+	// List projects currently linked to a workspace
+	// (GET /api/v1/workspaces/{id}/projects)
+	ListWorkspaceProjects(w http.ResponseWriter, r *http.Request, id string)
+	// Link an existing project into this workspace
+	// (POST /api/v1/workspaces/{id}/projects)
+	LinkProjectToWorkspace(w http.ResponseWriter, r *http.Request, id string)
+	// Remove a project from this workspace (does not delete the project)
+	// (DELETE /api/v1/workspaces/{id}/projects/{hash})
+	UnlinkProjectFromWorkspace(w http.ResponseWriter, r *http.Request, id string, hash string)
 	// Hybrid BM25+dense search across all repos in a workspace
 	// (GET /api/v1/workspaces/{id}/search)
 	WorkspaceSearch(w http.ResponseWriter, r *http.Request, id string, params WorkspaceSearchParams)
@@ -2230,6 +2147,12 @@ func (_ Unimplemented) DeleteMySession(w http.ResponseWriter, r *http.Request, i
 	w.WriteHeader(http.StatusNotImplemented)
 }
 
+// Clone + index a GitHub repository as a standalone project
+// (POST /api/v1/git-repos)
+func (_ Unimplemented) AddGitRepo(w http.ResponseWriter, r *http.Request) {
+	w.WriteHeader(http.StatusNotImplemented)
+}
+
 // List stored GitHub PATs (metadata only)
 // (GET /api/v1/github-tokens)
 func (_ Unimplemented) ListGithubTokens(w http.ResponseWriter, r *http.Request) {
@@ -2278,6 +2201,24 @@ func (_ Unimplemented) CreateProject(w http.ResponseWriter, r *http.Request) {
 	w.WriteHeader(http.StatusNotImplemented)
 }
 
+// Read the git_repos metadata for an external project
+// (GET /api/v1/projects/{hash}/git-repo)
+func (_ Unimplemented) GetProjectGitRepo(w http.ResponseWriter, r *http.Request, hash string) {
+	w.WriteHeader(http.StatusNotImplemented)
+}
+
+// Manually re-trigger the clone + index pipeline
+// (POST /api/v1/projects/{hash}/reindex)
+func (_ Unimplemented) ReindexProject(w http.ResponseWriter, r *http.Request, hash string) {
+	w.WriteHeader(http.StatusNotImplemented)
+}
+
+// Webhook URL + secret for manual GitHub setup
+// (GET /api/v1/projects/{hash}/webhook-info)
+func (_ Unimplemented) GetProjectWebhookInfo(w http.ResponseWriter, r *http.Request, hash string) {
+	w.WriteHeader(http.StatusNotImplemented)
+}
+
 // Delete a project and all its indexed data (admin only)
 // (DELETE /api/v1/projects/{path})
 func (_ Unimplemented) DeleteProject(w http.ResponseWriter, r *http.Request, path ProjectHash) {
@@ -2375,8 +2316,8 @@ func (_ Unimplemented) GetStatus(w http.ResponseWriter, r *http.Request) {
 }
 
 // Receive a GitHub webhook delivery (public, HMAC-authenticated)
-// (POST /api/v1/webhooks/github/{repo_id})
-func (_ Unimplemented) ReceiveGithubWebhook(w http.ResponseWriter, r *http.Request, repoId string, params ReceiveGithubWebhookParams) {
+// (POST /api/v1/webhooks/github/{hash})
+func (_ Unimplemented) ReceiveGithubWebhook(w http.ResponseWriter, r *http.Request, hash string, params ReceiveGithubWebhookParams) {
 	w.WriteHeader(http.StatusNotImplemented)
 }
 
@@ -2410,39 +2351,21 @@ func (_ Unimplemented) UpdateWorkspace(w http.ResponseWriter, r *http.Request, i
 	w.WriteHeader(http.StatusNotImplemented)
 }
 
-// List repositories attached to a workspace
-// (GET /api/v1/workspaces/{id}/repos)
-func (_ Unimplemented) ListWorkspaceRepos(w http.ResponseWriter, r *http.Request, id string) {
-	w.WriteHeader(http.StatusNotImplemented)
-}
-
-// Attach a GitHub repository to a workspace
-// (POST /api/v1/workspaces/{id}/repos)
-func (_ Unimplemented) AddWorkspaceRepo(w http.ResponseWriter, r *http.Request, id string) {
+// List projects currently linked to a workspace
+// (GET /api/v1/workspaces/{id}/projects)
+func (_ Unimplemented) ListWorkspaceProjects(w http.ResponseWriter, r *http.Request, id string) {
 	w.WriteHeader(http.StatusNotImplemented)
 }
 
-// Attach an already-indexed project to a workspace
-// (POST /api/v1/workspaces/{id}/repos/link)
-func (_ Unimplemented) LinkExistingProject(w http.ResponseWriter, r *http.Request, id string) {
+// Link an existing project into this workspace
+// (POST /api/v1/workspaces/{id}/projects)
+func (_ Unimplemented) LinkProjectToWorkspace(w http.ResponseWriter, r *http.Request, id string) {
 	w.WriteHeader(http.StatusNotImplemented)
 }
 
-// Detach a repository from a workspace
-// (DELETE /api/v1/workspaces/{id}/repos/{repo_id})
-func (_ Unimplemented) DeleteWorkspaceRepo(w http.ResponseWriter, r *http.Request, id string, repoId string) {
-	w.WriteHeader(http.StatusNotImplemented)
-}
-
-// Manually re-trigger the clone + index pipeline
-// (POST /api/v1/workspaces/{id}/repos/{repo_id}/reindex)
-func (_ Unimplemented) ReindexWorkspaceRepo(w http.ResponseWriter, r *http.Request, id string, repoId string) {
-	w.WriteHeader(http.StatusNotImplemented)
-}
-
-// Get the webhook URL + secret for manual GitHub setup
-// (GET /api/v1/workspaces/{id}/repos/{repo_id}/webhook-info)
-func (_ Unimplemented) GetWorkspaceRepoWebhookInfo(w http.ResponseWriter, r *http.Request, id string, repoId string) {
+// Remove a project from this workspace (does not delete the project)
+// (DELETE /api/v1/workspaces/{id}/projects/{hash})
+func (_ Unimplemented) UnlinkProjectFromWorkspace(w http.ResponseWriter, r *http.Request, id string, hash string) {
 	w.WriteHeader(http.StatusNotImplemented)
 }
 
@@ -2902,6 +2825,26 @@ func (siw *ServerInterfaceWrapper) DeleteMySession(w http.ResponseWriter, r *htt
 	handler.ServeHTTP(w, r)
 }
 
+// AddGitRepo operation middleware
+func (siw *ServerInterfaceWrapper) AddGitRepo(w http.ResponseWriter, r *http.Request) {
+
+	ctx := r.Context()
+
+	ctx = context.WithValue(ctx, BearerAuthScopes, []string{})
+
+	r = r.WithContext(ctx)
+
+	handler := http.Handler(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+		siw.Handler.AddGitRepo(w, r)
+	}))
+
+	for _, middleware := range siw.HandlerMiddlewares {
+		handler = middleware(handler)
+	}
+
+	handler.ServeHTTP(w, r)
+}
+
 // ListGithubTokens operation middleware
 func (siw *ServerInterfaceWrapper) ListGithubTokens(w http.ResponseWriter, r *http.Request) {
 
@@ -3185,6 +3128,102 @@ func (siw *ServerInterfaceWrapper) CreateProject(w http.ResponseWriter, r *http.
 	handler.ServeHTTP(w, r)
 }
 
+// GetProjectGitRepo operation middleware
+func (siw *ServerInterfaceWrapper) GetProjectGitRepo(w http.ResponseWriter, r *http.Request) {
+
+	var err error
+	_ = err
+
+	// ------------- Path parameter "hash" -------------
+	var hash string
+
+	err = runtime.BindStyledParameterWithOptions("simple", "hash", chi.URLParam(r, "hash"), &hash, runtime.BindStyledParameterOptions{ParamLocation: runtime.ParamLocationPath, Explode: false, Required: true, Type: "string", Format: ""})
+	if err != nil {
+		siw.ErrorHandlerFunc(w, r, &InvalidParamFormatError{ParamName: "hash", Err: err})
+		return
+	}
+
+	ctx := r.Context()
+
+	ctx = context.WithValue(ctx, BearerAuthScopes, []string{})
+
+	r = r.WithContext(ctx)
+
+	handler := http.Handler(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+		siw.Handler.GetProjectGitRepo(w, r, hash)
+	}))
+
+	for _, middleware := range siw.HandlerMiddlewares {
+		handler = middleware(handler)
+	}
+
+	handler.ServeHTTP(w, r)
+}
+
+// ReindexProject operation middleware
+func (siw *ServerInterfaceWrapper) ReindexProject(w http.ResponseWriter, r *http.Request) {
+
+	var err error
+	_ = err
+
+	// ------------- Path parameter "hash" -------------
+	var hash string
+
+	err = runtime.BindStyledParameterWithOptions("simple", "hash", chi.URLParam(r, "hash"), &hash, runtime.BindStyledParameterOptions{ParamLocation: runtime.ParamLocationPath, Explode: false, Required: true, Type: "string", Format: ""})
+	if err != nil {
+		siw.ErrorHandlerFunc(w, r, &InvalidParamFormatError{ParamName: "hash", Err: err})
+		return
+	}
+
+	ctx := r.Context()
+
+	ctx = context.WithValue(ctx, BearerAuthScopes, []string{})
+
+	r = r.WithContext(ctx)
+
+	handler := http.Handler(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+		siw.Handler.ReindexProject(w, r, hash)
+	}))
+
+	for _, middleware := range siw.HandlerMiddlewares {
+		handler = middleware(handler)
+	}
+
+	handler.ServeHTTP(w, r)
+}
+
+// GetProjectWebhookInfo operation middleware
+func (siw *ServerInterfaceWrapper) GetProjectWebhookInfo(w http.ResponseWriter, r *http.Request) {
+
+	var err error
+	_ = err
+
+	// ------------- Path parameter "hash" -------------
+	var hash string
+
+	err = runtime.BindStyledParameterWithOptions("simple", "hash", chi.URLParam(r, "hash"), &hash, runtime.BindStyledParameterOptions{ParamLocation: runtime.ParamLocationPath, Explode: false, Required: true, Type: "string", Format: ""})
+	if err != nil {
+		siw.ErrorHandlerFunc(w, r, &InvalidParamFormatError{ParamName: "hash", Err: err})
+		return
+	}
+
+	ctx := r.Context()
+
+	ctx = context.WithValue(ctx, BearerAuthScopes, []string{})
+
+	r = r.WithContext(ctx)
+
+	handler := http.Handler(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+		siw.Handler.GetProjectWebhookInfo(w, r, hash)
+	}))
+
+	for _, middleware := range siw.HandlerMiddlewares {
+		handler = middleware(handler)
+	}
+
+	handler.ServeHTTP(w, r)
+}
+
 // DeleteProject operation middleware
 func (siw *ServerInterfaceWrapper) DeleteProject(w http.ResponseWriter, r *http.Request) {
 
@@ -3715,12 +3754,12 @@ func (siw *ServerInterfaceWrapper) ReceiveGithubWebhook(w http.ResponseWriter, r
 	var err error
 	_ = err
 
-	// ------------- Path parameter "repo_id" -------------
-	var repoId string
+	// ------------- Path parameter "hash" -------------
+	var hash string
 
-	err = runtime.BindStyledParameterWithOptions("simple", "repo_id", chi.URLParam(r, "repo_id"), &repoId, runtime.BindStyledParameterOptions{ParamLocation: runtime.ParamLocationPath, Explode: false, Required: true, Type: "string", Format: ""})
+	err = runtime.BindStyledParameterWithOptions("simple", "hash", chi.URLParam(r, "hash"), &hash, runtime.BindStyledParameterOptions{ParamLocation: runtime.ParamLocationPath, Explode: false, Required: true, Type: "string", Format: ""})
 	if err != nil {
-		siw.ErrorHandlerFunc(w, r, &InvalidParamFormatError{ParamName: "repo_id", Err: err})
+		siw.ErrorHandlerFunc(w, r, &InvalidParamFormatError{ParamName: "hash", Err: err})
 		return
 	}
 
@@ -3768,7 +3807,7 @@ func (siw *ServerInterfaceWrapper) ReceiveGithubWebhook(w http.ResponseWriter, r
 	}
 
 	handler := http.Handler(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
-		siw.Handler.ReceiveGithubWebhook(w, r, repoId, params)
+		siw.Handler.ReceiveGithubWebhook(w, r, hash, params)
 	}))
 
 	for _, middleware := range siw.HandlerMiddlewares {
@@ -3914,104 +3953,8 @@ func (siw *ServerInterfaceWrapper) UpdateWorkspace(w http.ResponseWriter, r *htt
 	handler.ServeHTTP(w, r)
 }
 
-// ListWorkspaceRepos operation middleware
-func (siw *ServerInterfaceWrapper) ListWorkspaceRepos(w http.ResponseWriter, r *http.Request) {
-
-	var err error
-	_ = err
-
-	// ------------- Path parameter "id" -------------
-	var id string
-
-	err = runtime.BindStyledParameterWithOptions("simple", "id", chi.URLParam(r, "id"), &id, runtime.BindStyledParameterOptions{ParamLocation: runtime.ParamLocationPath, Explode: false, Required: true, Type: "string", Format: ""})
-	if err != nil {
-		siw.ErrorHandlerFunc(w, r, &InvalidParamFormatError{ParamName: "id", Err: err})
-		return
-	}
-
-	ctx := r.Context()
-
-	ctx = context.WithValue(ctx, BearerAuthScopes, []string{})
-
-	r = r.WithContext(ctx)
-
-	handler := http.Handler(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
-		siw.Handler.ListWorkspaceRepos(w, r, id)
-	}))
-
-	for _, middleware := range siw.HandlerMiddlewares {
-		handler = middleware(handler)
-	}
-
-	handler.ServeHTTP(w, r)
-}
-
-// AddWorkspaceRepo operation middleware
-func (siw *ServerInterfaceWrapper) AddWorkspaceRepo(w http.ResponseWriter, r *http.Request) {
-
-	var err error
-	_ = err
-
-	// ------------- Path parameter "id" -------------
-	var id string
-
-	err = runtime.BindStyledParameterWithOptions("simple", "id", chi.URLParam(r, "id"), &id, runtime.BindStyledParameterOptions{ParamLocation: runtime.ParamLocationPath, Explode: false, Required: true, Type: "string", Format: ""})
-	if err != nil {
-		siw.ErrorHandlerFunc(w, r, &InvalidParamFormatError{ParamName: "id", Err: err})
-		return
-	}
-
-	ctx := r.Context()
-
-	ctx = context.WithValue(ctx, BearerAuthScopes, []string{})
-
-	r = r.WithContext(ctx)
-
-	handler := http.Handler(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
-		siw.Handler.AddWorkspaceRepo(w, r, id)
-	}))
-
-	for _, middleware := range siw.HandlerMiddlewares {
-		handler = middleware(handler)
-	}
-
-	handler.ServeHTTP(w, r)
-}
-
-// LinkExistingProject operation middleware
-func (siw *ServerInterfaceWrapper) LinkExistingProject(w http.ResponseWriter, r *http.Request) {
-
-	var err error
-	_ = err
-
-	// ------------- Path parameter "id" -------------
-	var id string
-
-	err = runtime.BindStyledParameterWithOptions("simple", "id", chi.URLParam(r, "id"), &id, runtime.BindStyledParameterOptions{ParamLocation: runtime.ParamLocationPath, Explode: false, Required: true, Type: "string", Format: ""})
-	if err != nil {
-		siw.ErrorHandlerFunc(w, r, &InvalidParamFormatError{ParamName: "id", Err: err})
-		return
-	}
-
-	ctx := r.Context()
-
-	ctx = context.WithValue(ctx, BearerAuthScopes, []string{})
-
-	r = r.WithContext(ctx)
-
-	handler := http.Handler(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
-		siw.Handler.LinkExistingProject(w, r, id)
-	}))
-
-	for _, middleware := range siw.HandlerMiddlewares {
-		handler = middleware(handler)
-	}
-
-	handler.ServeHTTP(w, r)
-}
-
-// DeleteWorkspaceRepo operation middleware
-func (siw *ServerInterfaceWrapper) DeleteWorkspaceRepo(w http.ResponseWriter, r *http.Request) {
+// ListWorkspaceProjects operation middleware
+func (siw *ServerInterfaceWrapper) ListWorkspaceProjects(w http.ResponseWriter, r *http.Request) {
 
 	var err error
 	_ = err
@@ -4025,15 +3968,6 @@ func (siw *ServerInterfaceWrapper) DeleteWorkspaceRepo(w http.ResponseWriter, r
 		return
 	}
 
-	// ------------- Path parameter "repo_id" -------------
-	var repoId string
-
-	err = runtime.BindStyledParameterWithOptions("simple", "repo_id", chi.URLParam(r, "repo_id"), &repoId, runtime.BindStyledParameterOptions{ParamLocation: runtime.ParamLocationPath, Explode: false, Required: true, Type: "string", Format: ""})
-	if err != nil {
-		siw.ErrorHandlerFunc(w, r, &InvalidParamFormatError{ParamName: "repo_id", Err: err})
-		return
-	}
-
 	ctx := r.Context()
 
 	ctx = context.WithValue(ctx, BearerAuthScopes, []string{})
@@ -4041,7 +3975,7 @@ func (siw *ServerInterfaceWrapper) DeleteWorkspaceRepo(w http.ResponseWriter, r
 	r = r.WithContext(ctx)
 
 	handler := http.Handler(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
-		siw.Handler.DeleteWorkspaceRepo(w, r, id, repoId)
+		siw.Handler.ListWorkspaceProjects(w, r, id)
 	}))
 
 	for _, middleware := range siw.HandlerMiddlewares {
@@ -4051,8 +3985,8 @@ func (siw *ServerInterfaceWrapper) DeleteWorkspaceRepo(w http.ResponseWriter, r
 	handler.ServeHTTP(w, r)
 }
 
-// ReindexWorkspaceRepo operation middleware
-func (siw *ServerInterfaceWrapper) ReindexWorkspaceRepo(w http.ResponseWriter, r *http.Request) {
+// LinkProjectToWorkspace operation middleware
+func (siw *ServerInterfaceWrapper) LinkProjectToWorkspace(w http.ResponseWriter, r *http.Request) {
 
 	var err error
 	_ = err
@@ -4066,15 +4000,6 @@ func (siw *ServerInterfaceWrapper) ReindexWorkspaceRepo(w http.ResponseWriter, r
 		return
 	}
 
-	// ------------- Path parameter "repo_id" -------------
-	var repoId string
-
-	err = runtime.BindStyledParameterWithOptions("simple", "repo_id", chi.URLParam(r, "repo_id"), &repoId, runtime.BindStyledParameterOptions{ParamLocation: runtime.ParamLocationPath, Explode: false, Required: true, Type: "string", Format: ""})
-	if err != nil {
-		siw.ErrorHandlerFunc(w, r, &InvalidParamFormatError{ParamName: "repo_id", Err: err})
-		return
-	}
-
 	ctx := r.Context()
 
 	ctx = context.WithValue(ctx, BearerAuthScopes, []string{})
@@ -4082,7 +4007,7 @@ func (siw *ServerInterfaceWrapper) ReindexWorkspaceRepo(w http.ResponseWriter, r
 	r = r.WithContext(ctx)
 
 	handler := http.Handler(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
-		siw.Handler.ReindexWorkspaceRepo(w, r, id, repoId)
+		siw.Handler.LinkProjectToWorkspace(w, r, id)
 	}))
 
 	for _, middleware := range siw.HandlerMiddlewares {
@@ -4092,8 +4017,8 @@ func (siw *ServerInterfaceWrapper) ReindexWorkspaceRepo(w http.ResponseWriter, r
 	handler.ServeHTTP(w, r)
 }
 
-// GetWorkspaceRepoWebhookInfo operation middleware
-func (siw *ServerInterfaceWrapper) GetWorkspaceRepoWebhookInfo(w http.ResponseWriter, r *http.Request) {
+// UnlinkProjectFromWorkspace operation middleware
+func (siw *ServerInterfaceWrapper) UnlinkProjectFromWorkspace(w http.ResponseWriter, r *http.Request) {
 
 	var err error
 	_ = err
@@ -4107,12 +4032,12 @@ func (siw *ServerInterfaceWrapper) GetWorkspaceRepoWebhookInfo(w http.ResponseWr
 		return
 	}
 
-	// ------------- Path parameter "repo_id" -------------
-	var repoId string
+	// ------------- Path parameter "hash" -------------
+	var hash string
 
-	err = runtime.BindStyledParameterWithOptions("simple", "repo_id", chi.URLParam(r, "repo_id"), &repoId, runtime.BindStyledParameterOptions{ParamLocation: runtime.ParamLocationPath, Explode: false, Required: true, Type: "string", Format: ""})
+	err = runtime.BindStyledParameterWithOptions("simple", "hash", chi.URLParam(r, "hash"), &hash, runtime.BindStyledParameterOptions{ParamLocation: runtime.ParamLocationPath, Explode: false, Required: true, Type: "string", Format: ""})
 	if err != nil {
-		siw.ErrorHandlerFunc(w, r, &InvalidParamFormatError{ParamName: "repo_id", Err: err})
+		siw.ErrorHandlerFunc(w, r, &InvalidParamFormatError{ParamName: "hash", Err: err})
 		return
 	}
 
@@ -4123,7 +4048,7 @@ func (siw *ServerInterfaceWrapper) GetWorkspaceRepoWebhookInfo(w http.ResponseWr
 	r = r.WithContext(ctx)
 
 	handler := http.Handler(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
-		siw.Handler.GetWorkspaceRepoWebhookInfo(w, r, id, repoId)
+		siw.Handler.UnlinkProjectFromWorkspace(w, r, id, hash)
 	}))
 
 	for _, middleware := range siw.HandlerMiddlewares {
@@ -4404,6 +4329,9 @@ func HandlerWithOptions(si ServerInterface, options ChiServerOptions) http.Handl
 	r.Group(func(r chi.Router) {
 		r.Delete(options.BaseURL+"/api/v1/auth/sessions/{id}", wrapper.DeleteMySession)
 	})
+	r.Group(func(r chi.Router) {
+		r.Post(options.BaseURL+"/api/v1/git-repos", wrapper.AddGitRepo)
+	})
 	r.Group(func(r chi.Router) {
 		r.Get(options.BaseURL+"/api/v1/github-tokens", wrapper.ListGithubTokens)
 	})
@@ -4428,6 +4356,15 @@ func HandlerWithOptions(si ServerInterface, options ChiServerOptions) http.Handl
 	r.Group(func(r chi.Router) {
 		r.Post(options.BaseURL+"/api/v1/projects", wrapper.CreateProject)
 	})
+	r.Group(func(r chi.Router) {
+		r.Get(options.BaseURL+"/api/v1/projects/{hash}/git-repo", wrapper.GetProjectGitRepo)
+	})
+	r.Group(func(r chi.Router) {
+		r.Post(options.BaseURL+"/api/v1/projects/{hash}/reindex", wrapper.ReindexProject)
+	})
+	r.Group(func(r chi.Router) {
+		r.Get(options.BaseURL+"/api/v1/projects/{hash}/webhook-info", wrapper.GetProjectWebhookInfo)
+	})
 	r.Group(func(r chi.Router) {
 		r.Delete(options.BaseURL+"/api/v1/projects/{path}", wrapper.DeleteProject)
 	})
@@ -4477,7 +4414,7 @@ func HandlerWithOptions(si ServerInterface, options ChiServerOptions) http.Handl
 		r.Get(options.BaseURL+"/api/v1/status", wrapper.GetStatus)
 	})
 	r.Group(func(r chi.Router) {
-		r.Post(options.BaseURL+"/api/v1/webhooks/github/{repo_id}", wrapper.ReceiveGithubWebhook)
+		r.Post(options.BaseURL+"/api/v1/webhooks/github/{hash}", wrapper.ReceiveGithubWebhook)
 	})
 	r.Group(func(r chi.Router) {
 		r.Get(options.BaseURL+"/api/v1/workspaces", wrapper.ListWorkspaces)
@@ -4495,22 +4432,13 @@ func HandlerWithOptions(si ServerInterface, options ChiServerOptions) http.Handl
 		r.Patch(options.BaseURL+"/api/v1/workspaces/{id}", wrapper.UpdateWorkspace)
 	})
 	r.Group(func(r chi.Router) {
-		r.Get(options.BaseURL+"/api/v1/workspaces/{id}/repos", wrapper.ListWorkspaceRepos)
-	})
-	r.Group(func(r chi.Router) {
-		r.Post(options.BaseURL+"/api/v1/workspaces/{id}/repos", wrapper.AddWorkspaceRepo)
-	})
-	r.Group(func(r chi.Router) {
-		r.Post(options.BaseURL+"/api/v1/workspaces/{id}/repos/link", wrapper.LinkExistingProject)
-	})
-	r.Group(func(r chi.Router) {
-		r.Delete(options.BaseURL+"/api/v1/workspaces/{id}/repos/{repo_id}", wrapper.DeleteWorkspaceRepo)
+		r.Get(options.BaseURL+"/api/v1/workspaces/{id}/projects", wrapper.ListWorkspaceProjects)
 	})
 	r.Group(func(r chi.Router) {
-		r.Post(options.BaseURL+"/api/v1/workspaces/{id}/repos/{repo_id}/reindex", wrapper.ReindexWorkspaceRepo)
+		r.Post(options.BaseURL+"/api/v1/workspaces/{id}/projects", wrapper.LinkProjectToWorkspace)
 	})
 	r.Group(func(r chi.Router) {
-		r.Get(options.BaseURL+"/api/v1/workspaces/{id}/repos/{repo_id}/webhook-info", wrapper.GetWorkspaceRepoWebhookInfo)
+		r.Delete(options.BaseURL+"/api/v1/workspaces/{id}/projects/{hash}", wrapper.UnlinkProjectFromWorkspace)
 	})
 	r.Group(func(r chi.Router) {
 		r.Get(options.BaseURL+"/api/v1/workspaces/{id}/search", wrapper.WorkspaceSearch)
@@ -4527,352 +4455,350 @@ func HandlerWithOptions(si ServerInterface, options ChiServerOptions) http.Handl
 // const string: with thousands of chunks the chained `+` fold is several
 // times slower for the Go compiler than parsing a slice literal.
 var swaggerSpec = []string{
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+	"+9+ySqffHY5go+1R8sn3r0j38+n7V/2MXzHiYrjVvpVJneu3Wcc3770cwFma8E4eWpatjPKNQjobKdWj",
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+	"DINH3jzIk+ogTw52GKXOad9AeaIURNHFOpkPyAmS24hB/1Xoiq1YJOyttwThKca1ToVSV4faZPkDnLVe",
+	"zmbMKJ640vYaEWEipS8J1RIj/aE2NtzbSGCZbom1D2YF8FHsEAv3FW+g913BD/5NTHaHHC/fwM+hcx5U",
+	"nbPQVbWSZ++GCBNeMJZX29FnUkz6hvIMwMWskoQ9uKNOJfBmLzNAQjuFBZuRdwhFOUAjMePXLO2nckYB",
+	"qC94wFp7VIaa22a6OBg87XXGltWbzlFnnElqOhVKOazQyUGgE8wgeuAWcSsXeDOSBlDHVy+8vB/F8N1y",
+	"pHgKQuI71EQctftTh8ZnVtpwcSsfwz01VJwympnp1mjvCv6CvIo6X+Iyk9Ml1SRUOCR5p1nZO88FObS6",
+	"QCJFWsJkPjv43qHf1b9cCJzRElHAGNX2rhxFncFgEMbEUM2rlySHOijKM221B0h2cgImPq7ettgXjfrd",
+	"acmCe4e78YAXAEfYTPewl1wTtxP3XaF7kymE43CM7dVLUoiQq7i3MVfhlM+ZYKjpjphPTGhMtqt/5bfO",
+	"yKp5yh6h/ajlSEhhTe61Czpjfan4hAvI65P9lLmG084YY9A+wn4hBAZ1zmAmhco6R519KPpws1pLn4IN",
+	"QLvBJSjaaevy3uEyWs2rSoua7sn551d7tTdRh1h/GYsNepWq1F5ZK4NNIdCGXym9qnQ2xX+vf/pyqhjr",
+	"A8ZMmRuaK2lkApU3np14nI/1LxyfvSepTIoZEwZIsHwrlUnjclwDih62kN7P5EQWpkdyqvVCqtTB4vcC",
+	"FInrsuybMltSaJhHANjHxPQZFXTCZphL5l+1zzS8+17rApsGKTaXVwy7t/uGGaFFBgAwnL7fv3j1ox2j",
+	"8t2c9+0TDZ8upQMCCTQ21bUfXlEv6ic5iEQlb4a4tJmyDf06CjEwYMT/wGhaD/t9zGTKx8t6Zv2AnJ0f",
+	"EnT7WKoE9J7n5RSXrobAbmYvEj4JtheA081C9rWhkyDZQpppBq4lUWktZNUjawmxgDhTscnGDBO3MEkT",
+	"ObPb44oIXN9lt6lnTGnQ1Y6TxHIb6K2u7X74VNSmwUDTSzIpkPb53NpxzvwTKel64PVsuRcalNpH/T4M",
+	"yAXAwUeCiUQtc8PSPjV9NE45JcevL/pvTz6gqVi2ubesxxmehF3TxGTLSEiRgLPu7NPFJdrKULdQNX0V",
+	"AwzX2ubUey5/+fnL/xcAAP//",
 }
 
 // decodeSpec returns the embedded OpenAPI spec as raw JSON bytes,
diff --git a/server/internal/httpapi/project_workspaces.go b/server/internal/httpapi/project_workspaces.go
index 644d9e6..e87434f 100644
--- a/server/internal/httpapi/project_workspaces.go
+++ b/server/internal/httpapi/project_workspaces.go
@@ -4,39 +4,28 @@ import (
 	"database/sql"
 	"errors"
 	"net/http"
+	"time"
 
 	"github.com/dvcdsys/code-index/server/internal/httpapi/openapi"
 	"github.com/dvcdsys/code-index/server/internal/projects"
 )
 
 // projectWorkspaceEntryPayload is the wire shape for one membership.
-// Kept JSON-tagged here rather than reusing the generated type so the
-// handler can set fields by name without aligning to openapi-codegen's
-// nullability quirks for the embedded enums.
 type projectWorkspaceEntryPayload struct {
-	WorkspaceID   string `json:"workspace_id"`
-	WorkspaceName string `json:"workspace_name"`
-	RepoID        string `json:"repo_id"`
-	Branch        string `json:"branch"`
-	Status        string `json:"status"`
-	IsLinked      bool   `json:"is_linked"`
+	WorkspaceID   string    `json:"workspace_id"`
+	WorkspaceName string    `json:"workspace_name"`
+	AddedAt       time.Time `json:"added_at"`
 }
 
 // ListProjectWorkspaces — GET /api/v1/projects/{path}/workspaces.
 //
-// Returns every workspace that has this project attached. Used by the
-// project detail page to render "Workspaces" chips linking to each
-// workspace. Empty list when the project isn't part of any workspace.
-//
-// The workspaces feature flag is NOT consulted here: even if workspaces
-// are disabled, returning an empty membership list is the right
-// response — the project page should still render cleanly.
+// Returns every workspace that this project is currently linked into.
+// Used by the project detail page to render "Workspaces" chips. Empty
+// list when the project is in no workspace (true for freshly-added
+// standalone projects). The workspaces feature flag is NOT consulted —
+// returning an empty list is fine even when the flag is off.
 func (s *Server) ListProjectWorkspaces(w http.ResponseWriter, r *http.Request, path openapi.ProjectHash) {
 	hash := string(path)
-
-	// Resolve the project first so 404 vs empty membership are clearly
-	// distinguishable: unknown hash → 404; known hash with zero
-	// memberships → 200 with workspaces=[].
 	proj, err := projects.GetByHash(r.Context(), s.Deps.DB, hash)
 	if err != nil {
 		if errors.Is(err, projects.ErrNotFound) {
@@ -48,10 +37,10 @@ func (s *Server) ListProjectWorkspaces(w http.ResponseWriter, r *http.Request, p
 	}
 
 	rows, err := s.Deps.DB.QueryContext(r.Context(), `
-		SELECT w.id, w.name, wr.id, wr.branch, wr.status, wr.is_linked
+		SELECT w.id, w.name, wp.added_at
 		  FROM workspaces w
-		  JOIN workspace_repos wr ON wr.workspace_id = w.id
-		 WHERE wr.project_path = ?
+		  JOIN workspace_projects wp ON wp.workspace_id = w.id
+		 WHERE wp.project_path = ?
 		 ORDER BY w.name`, proj.HostPath)
 	if err != nil {
 		writeError(w, http.StatusInternalServerError, "could not list workspaces: "+err.Error())
@@ -62,14 +51,14 @@ func (s *Server) ListProjectWorkspaces(w http.ResponseWriter, r *http.Request, p
 	entries := []projectWorkspaceEntryPayload{}
 	for rows.Next() {
 		var (
-			e        projectWorkspaceEntryPayload
-			isLinked int
+			e       projectWorkspaceEntryPayload
+			addedAt string
 		)
-		if scanErr := rows.Scan(&e.WorkspaceID, &e.WorkspaceName, &e.RepoID, &e.Branch, &e.Status, &isLinked); scanErr != nil {
+		if scanErr := rows.Scan(&e.WorkspaceID, &e.WorkspaceName, &addedAt); scanErr != nil {
 			writeError(w, http.StatusInternalServerError, "could not read row: "+scanErr.Error())
 			return
 		}
-		e.IsLinked = isLinked == 1
+		e.AddedAt, _ = time.Parse(time.RFC3339Nano, addedAt)
 		entries = append(entries, e)
 	}
 	if err := rows.Err(); err != nil && !errors.Is(err, sql.ErrNoRows) {
diff --git a/server/internal/httpapi/router.go b/server/internal/httpapi/router.go
index 444cf0b..6391a65 100644
--- a/server/internal/httpapi/router.go
+++ b/server/internal/httpapi/router.go
@@ -13,6 +13,7 @@ import (
 
 	"github.com/dvcdsys/code-index/server/internal/apikeys"
 	"github.com/dvcdsys/code-index/server/internal/embeddings"
+	"github.com/dvcdsys/code-index/server/internal/gitrepos"
 	"github.com/dvcdsys/code-index/server/internal/githubtokens"
 	"github.com/dvcdsys/code-index/server/internal/httpapi/openapi"
 	"github.com/dvcdsys/code-index/server/internal/indexer"
@@ -22,7 +23,7 @@ import (
 	"github.com/dvcdsys/code-index/server/internal/users"
 	"github.com/dvcdsys/code-index/server/internal/vectorstore"
 	"github.com/dvcdsys/code-index/server/internal/versioncheck"
-	"github.com/dvcdsys/code-index/server/internal/workspacerepos"
+	"github.com/dvcdsys/code-index/server/internal/workspaceprojects"
 	"github.com/dvcdsys/code-index/server/internal/workspaces"
 	"github.com/go-chi/chi/v5"
 	"github.com/go-chi/chi/v5/middleware"
@@ -86,9 +87,12 @@ type Deps struct {
 	WorkspacesEnabled bool
 	Workspaces        *workspaces.Service
 	GithubTokens      *githubtokens.Service
-	// PR2 additions — repo attachment + the persistent job queue.
-	WorkspaceRepos *workspacerepos.Service
-	Jobs           *jobs.Service
+	// GitRepos owns clone + webhook metadata for external projects;
+	// WorkspaceProjects owns the workspace ↔ project junction. Jobs is
+	// the persistent background queue.
+	GitRepos          *gitrepos.Service
+	WorkspaceProjects *workspaceprojects.Service
+	Jobs              *jobs.Service
 	// PublicBaseURL is the operator-set externally-reachable URL of the
 	// server. Used to build the webhook URL surfaced when adding a repo
 	// — when empty, handlers return the path-only form and rely on the
diff --git a/server/internal/httpapi/webhooks.go b/server/internal/httpapi/webhooks.go
index aa664a7..92cd123 100644
--- a/server/internal/httpapi/webhooks.go
+++ b/server/internal/httpapi/webhooks.go
@@ -10,73 +10,64 @@ import (
 	"net/http"
 	"strings"
 
+	"github.com/dvcdsys/code-index/server/internal/gitrepos"
 	"github.com/dvcdsys/code-index/server/internal/httpapi/openapi"
 	"github.com/dvcdsys/code-index/server/internal/jobs"
+	"github.com/dvcdsys/code-index/server/internal/projects"
 	"github.com/dvcdsys/code-index/server/internal/secrets"
 	"github.com/dvcdsys/code-index/server/internal/workspacejobs"
-	"github.com/dvcdsys/code-index/server/internal/workspacerepos"
 )
 
-// GetWorkspaceRepoWebhookInfo — GET /workspaces/{id}/repos/{repo_id}/webhook-info.
+// GetProjectWebhookInfo — GET /api/v1/projects/{hash}/webhook-info.
 //
 // Authenticated. Returns the publicly-reachable webhook URL + the HMAC
 // secret. Operators copy these into GitHub's webhook config when
-// auto_webhook=false.
-func (s *Server) GetWorkspaceRepoWebhookInfo(w http.ResponseWriter, r *http.Request, id, repoID string) {
-	if s.workspaceReposUnavailable(w) {
+// webhook_mode is not 'auto'. 404 when the project is local (no
+// git_repos row).
+func (s *Server) GetProjectWebhookInfo(w http.ResponseWriter, r *http.Request, hash openapi.ProjectHash) {
+	if s.gitReposUnavailable(w) {
 		return
 	}
-	if !s.requireWorkspace(w, r, id) {
-		return
-	}
-	wr, err := s.Deps.WorkspaceRepos.GetByID(r.Context(), repoID)
+	g, err := s.Deps.GitRepos.GetByHash(r.Context(), string(hash))
 	if err != nil {
-		if errors.Is(err, workspacerepos.ErrNotFound) {
-			writeError(w, http.StatusNotFound, "repo not found")
+		if errors.Is(err, gitrepos.ErrNotFound) {
+			writeError(w, http.StatusNotFound, "no git_repos row for this project (local projects have no webhook)")
 			return
 		}
-		writeError(w, http.StatusInternalServerError, "could not load repo")
-		return
-	}
-	if wr.WorkspaceID != id {
-		writeError(w, http.StatusNotFound, "repo not found")
+		writeError(w, http.StatusInternalServerError, "could not load git_repo: "+err.Error())
 		return
 	}
 	writeJSON(w, http.StatusOK, map[string]any{
-		"webhook_url":     s.buildWebhookURL(wr.ID),
-		"webhook_secret":  wr.WebhookSecret,
-		"auto_registered": wr.WebhookID != nil,
+		"webhook_url":     s.buildWebhookURL(g.PathHash),
+		"webhook_secret":  g.WebhookSecret,
+		"auto_registered": g.WebhookID != nil,
 	})
 }
 
 // pushEvent is the minimal subset of GitHub's push webhook body we care
-// about. We don't bind to go-github here because we only need two fields
-// — the ref and the head SHA — and pulling in the dependency for that
-// would be heavyweight.
+// about — the ref and the head SHA.
 type pushEvent struct {
-	Ref   string `json:"ref"`     // "refs/heads/main"
-	After string `json:"after"`   // post-push HEAD SHA
+	Ref   string `json:"ref"`   // "refs/heads/main"
+	After string `json:"after"` // post-push HEAD SHA
 }
 
-// ReceiveGithubWebhook — POST /api/v1/webhooks/github/{repo_id}.
+// ReceiveGithubWebhook — POST /api/v1/webhooks/github/{hash}.
 //
-// Public endpoint (added to publicPaths in middleware.go). Authenticated
-// per-row by HMAC-SHA256 over the body keyed by workspace_repos.webhook_secret.
-func (s *Server) ReceiveGithubWebhook(w http.ResponseWriter, r *http.Request, repoID string, params openapi.ReceiveGithubWebhookParams) {
-	if !s.Deps.WorkspacesEnabled || s.Deps.WorkspaceRepos == nil || s.Deps.Jobs == nil {
+// Public endpoint. Authenticated per-row by HMAC-SHA256 over the body
+// keyed by git_repos.webhook_secret (looked up via projects.path_hash).
+func (s *Server) ReceiveGithubWebhook(w http.ResponseWriter, r *http.Request, hash string, params openapi.ReceiveGithubWebhookParams) {
+	if !s.Deps.WorkspacesEnabled || s.Deps.GitRepos == nil || s.Deps.Jobs == nil {
 		writeError(w, http.StatusServiceUnavailable, "workspaces feature is disabled (set CIX_WORKSPACES_ENABLED=true and restart)")
 		return
 	}
 
-	// Read the raw body BEFORE any JSON parsing so we can compute HMAC
-	// against the exact byte sequence GitHub signed.
 	body, err := io.ReadAll(r.Body)
 	if err != nil {
 		writeError(w, http.StatusBadRequest, "could not read body")
 		return
 	}
 
-	wr, err := s.Deps.WorkspaceRepos.GetByID(r.Context(), repoID)
+	g, err := s.Deps.GitRepos.GetByHash(r.Context(), hash)
 	if err != nil {
 		// Don't leak existence — both unknown and bad-HMAC look like 404
 		// to a probing attacker.
@@ -89,12 +80,10 @@ func (s *Server) ReceiveGithubWebhook(w http.ResponseWriter, r *http.Request, re
 		sigHeader = *params.XHubSignature256
 	}
 	if sigHeader == "" {
-		// Fall back to direct header read in case oapi-codegen casing
-		// differs from what GitHub sends.
 		sigHeader = r.Header.Get("X-Hub-Signature-256")
 	}
-	if !validHMAC(body, []byte(wr.WebhookSecret), sigHeader) {
-		s.Deps.Logger.Warn("workspaces webhook: HMAC mismatch", "repo_id", repoID)
+	if !validHMAC(body, []byte(g.WebhookSecret), sigHeader) {
+		s.Deps.Logger.Warn("workspaces webhook: HMAC mismatch", "path_hash", hash)
 		writeError(w, http.StatusUnauthorized, "invalid signature")
 		return
 	}
@@ -109,17 +98,13 @@ func (s *Server) ReceiveGithubWebhook(w http.ResponseWriter, r *http.Request, re
 
 	switch event {
 	case "ping":
-		// GitHub sends ping on webhook creation — return 200 so the UI
-		// confirms the setup is wired.
 		writeJSON(w, http.StatusOK, map[string]any{"status": "ping"})
 		return
 	case "push":
 		// fall through
 	default:
-		// Unknown / unsupported events are ack'd quietly so GitHub stops
-		// retrying. We log so operators can see what arrived.
 		s.Deps.Logger.Info("workspaces webhook: ignored event",
-			"repo_id", repoID,
+			"path_hash", hash,
 			"event", event)
 		writeJSON(w, http.StatusOK, map[string]any{"status": "ignored"})
 		return
@@ -131,29 +116,36 @@ func (s *Server) ReceiveGithubWebhook(w http.ResponseWriter, r *http.Request, re
 		return
 	}
 
-	// Only react to pushes on the tracked branch. GitHub sends one delivery
-	// per ref; deletes have After=000…000 and we treat those as ignored.
-	wantRef := "refs/heads/" + wr.Branch
+	wantRef := "refs/heads/" + g.Branch
 	if p.Ref != wantRef {
 		writeJSON(w, http.StatusOK, map[string]any{"status": "ignored"})
 		return
 	}
 	if strings.Trim(p.After, "0") == "" {
-		// Branch deletion → ignore (cleanup story lives in PR4+).
 		writeJSON(w, http.StatusOK, map[string]any{"status": "ignored"})
 		return
 	}
 
+	// Sanity-check the projects row still exists so the job has
+	// something to work against. We don't require any particular
+	// status — re-clone is the normal recovery path.
+	if _, perr := projects.Get(r.Context(), s.Deps.DB, g.ProjectPath); perr != nil {
+		s.Deps.Logger.Error("webhook: project missing for git_repo",
+			"path_hash", hash, "project", g.ProjectPath, "err", perr)
+		writeError(w, http.StatusInternalServerError, "project row missing")
+		return
+	}
+
 	enqueued := true
 	if _, eerr := s.Deps.Jobs.Enqueue(r.Context(), jobs.EnqueueRequest{
 		Type:      workspacejobs.TypeCloneRepo,
-		DedupeKey: "clone:" + wr.ID,
-		Payload:   workspacejobs.ClonePayload{RepoID: wr.ID},
+		DedupeKey: "clone:" + g.PathHash,
+		Payload:   workspacejobs.ClonePayload{ProjectPath: g.ProjectPath},
 	}); eerr != nil {
 		if errors.Is(eerr, jobs.ErrDuplicate) {
 			enqueued = false
 		} else {
-			s.Deps.Logger.Error("workspaces webhook: enqueue failed", "repo_id", repoID, "err", eerr)
+			s.Deps.Logger.Error("workspaces webhook: enqueue failed", "path_hash", hash, "err", eerr)
 			writeError(w, http.StatusInternalServerError, "could not enqueue reindex")
 			return
 		}
@@ -162,13 +154,23 @@ func (s *Server) ReceiveGithubWebhook(w http.ResponseWriter, r *http.Request, re
 	if !enqueued {
 		status = "already_running"
 	}
-	writeJSON(w, http.StatusAccepted, map[string]any{"status": status, "repo_id": wr.ID})
+	writeJSON(w, http.StatusAccepted, map[string]any{"status": status, "path_hash": g.PathHash})
 }
 
 // validHMAC returns true when the given header matches HMAC-SHA256(body, secret).
-// Header format is "sha256=<hex>" per GitHub's spec. Constant-time compare
-// against the expected value to avoid leaking timing signals.
+// Header format is "sha256=<hex>" per GitHub's spec.
+//
+// An empty secret is rejected before any computation: HMAC keyed with the
+// empty string is a fixed, well-known value over any body (an attacker
+// who never saw our secret can forge a matching header). This case
+// should be unreachable — git_repos.webhook_secret is NOT NULL and the
+// add-repo handler always populates it with a random 32-byte secret —
+// but defending here makes the invariant explicit and removes the
+// "what if a future caller passes nil" footgun.
 func validHMAC(body, secret []byte, header string) bool {
+	if len(secret) == 0 {
+		return false
+	}
 	header = strings.TrimSpace(header)
 	const prefix = "sha256="
 	if !strings.HasPrefix(header, prefix) {
@@ -181,7 +183,5 @@ func validHMAC(body, secret []byte, header string) bool {
 	mac := hmac.New(sha256.New, secret)
 	mac.Write(body)
 	want := mac.Sum(nil)
-	// Use the secrets package's constant-time helper — same byte semantics
-	// as hmac.Equal, kept in one place across the codebase.
 	return secrets.ConstantTimeEqual(got, want)
 }
diff --git a/server/internal/httpapi/webhooks_test.go b/server/internal/httpapi/webhooks_test.go
index db16662..35173a7 100644
--- a/server/internal/httpapi/webhooks_test.go
+++ b/server/internal/httpapi/webhooks_test.go
@@ -9,55 +9,38 @@ import (
 	"encoding/json"
 	"net/http"
 	"net/http/httptest"
+	"strings"
 	"testing"
 	"time"
 
 	"github.com/dvcdsys/code-index/server/internal/githubtokens"
+	"github.com/dvcdsys/code-index/server/internal/gitrepos"
 	"github.com/dvcdsys/code-index/server/internal/jobs"
+	"github.com/dvcdsys/code-index/server/internal/projects"
 	"github.com/dvcdsys/code-index/server/internal/secrets"
-	"github.com/dvcdsys/code-index/server/internal/workspacerepos"
+	"github.com/dvcdsys/code-index/server/internal/workspaceprojects"
 	"github.com/dvcdsys/code-index/server/internal/workspaces"
 )
 
-// addRepo helper — creates a workspace + repo and returns the repo
-// payload so tests can lift webhook_secret/id directly.
-func addRepo(t *testing.T, router http.Handler, wsName, githubURL, branch string) workspaceRepoPayload {
+// addGitRepo helper — POSTs /git-repos and returns (path_hash, webhook_secret)
+// so individual webhook tests can post against the new URL shape.
+func addGitRepo(t *testing.T, router http.Handler, githubURL, branch string) (string, string) {
 	t.Helper()
-	wsID := createWS(t, router, wsName)
-	rr := doJSON(t, router, http.MethodPost, "/api/v1/workspaces/"+wsID+"/repos", map[string]any{
+	rr := doJSON(t, router, http.MethodPost, "/api/v1/git-repos", map[string]any{
 		"github_url": githubURL,
 		"branch":     branch,
 	})
 	if rr.Code != http.StatusCreated {
-		t.Fatalf("add repo: %d (%s)", rr.Code, rr.Body.String())
+		t.Fatalf("add git_repo: %d (%s)", rr.Code, rr.Body.String())
 	}
 	var got struct {
-		Repo          workspaceRepoPayload `json:"repo"`
-		WebhookSecret string               `json:"webhook_secret"`
+		GitRepo struct {
+			PathHash string `json:"path_hash"`
+		} `json:"git_repo"`
+		WebhookSecret string `json:"webhook_secret"`
 	}
 	_ = json.Unmarshal(rr.Body.Bytes(), &got)
-	// Stash the secret onto the payload via the URL — tests pluck it
-	// from the response body directly when needed; this helper just
-	// returns the repo. Test bodies that need the secret call addRepoWithSecret.
-	return got.Repo
-}
-
-func addRepoWithSecret(t *testing.T, router http.Handler, wsName, githubURL, branch string) (workspaceRepoPayload, string) {
-	t.Helper()
-	wsID := createWS(t, router, wsName)
-	rr := doJSON(t, router, http.MethodPost, "/api/v1/workspaces/"+wsID+"/repos", map[string]any{
-		"github_url": githubURL,
-		"branch":     branch,
-	})
-	if rr.Code != http.StatusCreated {
-		t.Fatalf("add repo: %d (%s)", rr.Code, rr.Body.String())
-	}
-	var got struct {
-		Repo          workspaceRepoPayload `json:"repo"`
-		WebhookSecret string               `json:"webhook_secret"`
-	}
-	_ = json.Unmarshal(rr.Body.Bytes(), &got)
-	return got.Repo, got.WebhookSecret
+	return got.GitRepo.PathHash, got.WebhookSecret
 }
 
 func signBody(body []byte, secret string) string {
@@ -66,9 +49,9 @@ func signBody(body []byte, secret string) string {
 	return "sha256=" + hex.EncodeToString(mac.Sum(nil))
 }
 
-func postWebhook(t *testing.T, router http.Handler, repoID string, body []byte, sig, event string) *httptest.ResponseRecorder {
+func postWebhook(t *testing.T, router http.Handler, hash string, body []byte, sig, event string) *httptest.ResponseRecorder {
 	t.Helper()
-	req := httptest.NewRequest(http.MethodPost, "/api/v1/webhooks/github/"+repoID, bytes.NewReader(body))
+	req := httptest.NewRequest(http.MethodPost, "/api/v1/webhooks/github/"+hash, bytes.NewReader(body))
 	req.Header.Set("Content-Type", "application/json")
 	if sig != "" {
 		req.Header.Set("X-Hub-Signature-256", sig)
@@ -83,9 +66,9 @@ func postWebhook(t *testing.T, router http.Handler, repoID string, body []byte,
 
 func TestWebhook_PingReturns200(t *testing.T) {
 	router, _ := reposRouter(t)
-	repo, secret := addRepoWithSecret(t, router, "platform", "https://github.com/x/y", "main")
+	hash, secret := addGitRepo(t, router, "https://github.com/x/y", "main")
 	body := []byte(`{"zen":"Speak like a human."}`)
-	rr := postWebhook(t, router, repo.ID, body, signBody(body, secret), "ping")
+	rr := postWebhook(t, router, hash, body, signBody(body, secret), "ping")
 	if rr.Code != http.StatusOK {
 		t.Fatalf("ping: expected 200, got %d (%s)", rr.Code, rr.Body.String())
 	}
@@ -93,10 +76,8 @@ func TestWebhook_PingReturns200(t *testing.T) {
 
 func TestWebhook_PushEnqueuesCloneJob(t *testing.T) {
 	router, jobsSvc := reposRouter(t)
-	repo, secret := addRepoWithSecret(t, router, "platform", "https://github.com/x/y", "main")
+	hash, secret := addGitRepo(t, router, "https://github.com/x/y", "main")
 
-	// Drain the initial clone job from the add-repo call so we can see the
-	// webhook's own dedupe behaviour clearly.
 	ctx := context.Background()
 	initial, _ := jobsSvc.List(ctx, jobs.StatusPending, "clone_repo", 10)
 	if len(initial) != 1 {
@@ -104,8 +85,7 @@ func TestWebhook_PushEnqueuesCloneJob(t *testing.T) {
 	}
 
 	body := []byte(`{"ref":"refs/heads/main","after":"abc123def456"}`)
-	rr := postWebhook(t, router, repo.ID, body, signBody(body, secret), "push")
-	// Dedupe with the in-flight initial clone → 202 already_running.
+	rr := postWebhook(t, router, hash, body, signBody(body, secret), "push")
 	if rr.Code != http.StatusAccepted {
 		t.Fatalf("push: expected 202, got %d (%s)", rr.Code, rr.Body.String())
 	}
@@ -120,9 +100,9 @@ func TestWebhook_PushEnqueuesCloneJob(t *testing.T) {
 
 func TestWebhook_PushOnDifferentBranchIgnored(t *testing.T) {
 	router, _ := reposRouter(t)
-	repo, secret := addRepoWithSecret(t, router, "platform", "https://github.com/x/y", "main")
+	hash, secret := addGitRepo(t, router, "https://github.com/x/y", "main")
 	body := []byte(`{"ref":"refs/heads/develop","after":"abc123"}`)
-	rr := postWebhook(t, router, repo.ID, body, signBody(body, secret), "push")
+	rr := postWebhook(t, router, hash, body, signBody(body, secret), "push")
 	if rr.Code != http.StatusOK {
 		t.Fatalf("ignored: expected 200, got %d", rr.Code)
 	}
@@ -137,10 +117,9 @@ func TestWebhook_PushOnDifferentBranchIgnored(t *testing.T) {
 
 func TestWebhook_BadSignatureRejected(t *testing.T) {
 	router, _ := reposRouter(t)
-	repo, _ := addRepoWithSecret(t, router, "platform", "https://github.com/x/y", "main")
+	hash, _ := addGitRepo(t, router, "https://github.com/x/y", "main")
 	body := []byte(`{"ref":"refs/heads/main","after":"abc"}`)
-	// Sign with the wrong secret.
-	rr := postWebhook(t, router, repo.ID, body, signBody(body, "wrong"), "push")
+	rr := postWebhook(t, router, hash, body, signBody(body, "wrong"), "push")
 	if rr.Code != http.StatusUnauthorized {
 		t.Fatalf("bad sig: expected 401, got %d (%s)", rr.Code, rr.Body.String())
 	}
@@ -148,28 +127,56 @@ func TestWebhook_BadSignatureRejected(t *testing.T) {
 
 func TestWebhook_MissingSignatureRejected(t *testing.T) {
 	router, _ := reposRouter(t)
-	repo, _ := addRepoWithSecret(t, router, "platform", "https://github.com/x/y", "main")
+	hash, _ := addGitRepo(t, router, "https://github.com/x/y", "main")
 	body := []byte(`{"ref":"refs/heads/main","after":"abc"}`)
-	rr := postWebhook(t, router, repo.ID, body, "", "push")
+	rr := postWebhook(t, router, hash, body, "", "push")
 	if rr.Code != http.StatusUnauthorized {
 		t.Fatalf("no sig: expected 401, got %d", rr.Code)
 	}
 }
 
-func TestWebhook_UnknownRepoReturns404(t *testing.T) {
+// TestValidHMAC_RejectsEmptySecret pins the empty-secret guard added in
+// Fix #13. HMAC keyed with the empty string returns a fixed, attacker-
+// computable digest for any body; if validHMAC accepted that case, a
+// caller who forgot to load the secret (or a future bug that passed
+// nil) would silently authenticate every delivery. We pre-compute the
+// "correct" HMAC with the empty key over a known body and assert the
+// function STILL rejects it — the empty-secret short-circuit must fire
+// before the constant-time compare, never after.
+func TestValidHMAC_RejectsEmptySecret(t *testing.T) {
+	body := []byte(`{"ref":"refs/heads/main"}`)
+	// Compute what the header WOULD be if we naively HMAC'd with "".
+	mac := hmac.New(sha256.New, []byte(""))
+	mac.Write(body)
+	forged := "sha256=" + hex.EncodeToString(mac.Sum(nil))
+
+	if validHMAC(body, nil, forged) {
+		t.Error("validHMAC accepted a nil-secret HMAC — guard missing")
+	}
+	if validHMAC(body, []byte(""), forged) {
+		t.Error("validHMAC accepted an empty-byte-slice secret HMAC — guard missing")
+	}
+
+	// Sanity: with a real secret + matching signature it still works.
+	real := []byte("real-secret")
+	mac2 := hmac.New(sha256.New, real)
+	mac2.Write(body)
+	good := "sha256=" + hex.EncodeToString(mac2.Sum(nil))
+	if !validHMAC(body, real, good) {
+		t.Error("validHMAC rejected a correctly-signed body with a real secret — guard over-broad")
+	}
+}
+
+func TestWebhook_UnknownHashReturns404(t *testing.T) {
 	router, _ := reposRouter(t)
 	body := []byte(`{}`)
-	// Use the right HMAC math but a bogus repo id — must still 404 (we
-	// short-circuit before HMAC since there's no secret to compare against).
-	rr := postWebhook(t, router, "no-such-repo", body, signBody(body, "anything"), "push")
+	rr := postWebhook(t, router, "0000000000000000", body, signBody(body, "anything"), "push")
 	if rr.Code != http.StatusNotFound {
-		t.Fatalf("unknown repo: expected 404, got %d", rr.Code)
+		t.Fatalf("unknown hash: expected 404, got %d", rr.Code)
 	}
 }
 
 func TestWebhook_PathIsPublic(t *testing.T) {
-	// Spin up a router with auth ENABLED (not the test-default) to verify
-	// the webhook path is reachable without credentials.
 	d, err := dbOpenMemory(t)
 	if err != nil {
 		t.Fatalf("open db: %v", err)
@@ -186,18 +193,12 @@ func TestWebhook_PathIsPublic(t *testing.T) {
 	rr := httptest.NewRecorder()
 	req := httptest.NewRequest(http.MethodPost, "/api/v1/webhooks/github/anything", bytes.NewReader([]byte(`{}`)))
 	router.ServeHTTP(rr, req)
-	// We expect either 503 (feature off) or 404, NOT 401 — the public-path
-	// gate should let us through the auth middleware.
 	if rr.Code == http.StatusUnauthorized {
 		t.Fatalf("webhook path leaked into auth-gated set, got 401")
 	}
 }
 
-func TestAddRepo_AutoRegisterFailsCleanlyWithoutPublicURL(t *testing.T) {
-	// reposRouter sets PublicBaseURL=https://cix.example.test, but the
-	// auto-register flow tries a real github.com call which the test
-	// can't allow. So skip when wired with a real URL — this test
-	// exercises the empty-URL branch by building a separate router.
+func TestAddGitRepo_AutoRegisterFailsCleanlyWithoutPublicURL(t *testing.T) {
 	d, err := dbOpenMemory(t)
 	if err != nil {
 		t.Fatalf("open db: %v", err)
@@ -210,7 +211,8 @@ func TestAddRepo_AutoRegisterFailsCleanlyWithoutPublicURL(t *testing.T) {
 	}
 	wsSvc := workspaces.New(d)
 	ghSvc := githubtokens.New(d, sec)
-	wrSvc := workspacerepos.New(d)
+	grSvc := gitrepos.New(d)
+	wpSvc := workspaceprojects.New(d)
 	jobsSvc := jobs.New(d, jobs.Options{Concurrency: 1, PollEvery: time.Hour})
 
 	router := NewRouter(Deps{
@@ -222,16 +224,16 @@ func TestAddRepo_AutoRegisterFailsCleanlyWithoutPublicURL(t *testing.T) {
 		WorkspacesEnabled: true,
 		Workspaces:        wsSvc,
 		GithubTokens:      ghSvc,
-		WorkspaceRepos:    wrSvc,
+		GitRepos:          grSvc,
+		WorkspaceProjects: wpSvc,
 		Jobs:              jobsSvc,
 		// PublicBaseURL deliberately unset.
 	})
 
-	wsID := createWS(t, router, "platform")
-	rr := doJSON(t, router, http.MethodPost, "/api/v1/workspaces/"+wsID+"/repos", map[string]any{
+	rr := doJSON(t, router, http.MethodPost, "/api/v1/git-repos", map[string]any{
 		"github_url":   "https://github.com/x/y",
 		"branch":       "main",
-		"auto_webhook": true,
+		"webhook_mode": "auto",
 	})
 	if rr.Code != http.StatusCreated {
 		t.Fatalf("create: %d (%s)", rr.Code, rr.Body.String())
@@ -249,25 +251,66 @@ func TestAddRepo_AutoRegisterFailsCleanlyWithoutPublicURL(t *testing.T) {
 	}
 }
 
+// TestGetProjectWebhookInfo_LocalProject_Returns404 verifies that the
+// webhook-info endpoint returns 404 when the project exists but has no
+// `git_repos` peer (i.e. it's a local-path project tracked only in the
+// `projects` table). Local projects don't go through the clone +
+// webhook lifecycle, so there's no URL or secret to surface. The
+// operation contract documented in doc/openapi.yaml requires callers
+// to disambiguate "project missing" vs "project local" by first
+// hitting GET /projects/{hash} — this test pins the local-project arm
+// of the 404 response so the contract doesn't drift.
+func TestGetProjectWebhookInfo_LocalProject_Returns404(t *testing.T) {
+	router, _, d := reposRouterDB(t)
+
+	// Seed a local project — absolute filesystem path, no git_repos peer.
+	hostPath := "/Users/x/local-proj"
+	hash := projects.HashPath(hostPath)
+	if _, err := d.Exec(`
+		INSERT INTO projects (host_path, container_path, languages, settings, stats,
+			status, created_at, updated_at, path_hash)
+		VALUES (?, ?, '[]', '{}', '{}', 'indexed', '2026-05-14T00:00:00Z', '2026-05-14T00:00:00Z', ?)`,
+		hostPath, hostPath, hash,
+	); err != nil {
+		t.Fatalf("seed local project: %v", err)
+	}
+
+	rr := doJSON(t, router, http.MethodGet, "/api/v1/projects/"+hash+"/webhook-info", nil)
+	if rr.Code != http.StatusNotFound {
+		t.Fatalf("expected 404 for local project webhook-info, got %d (%s)", rr.Code, rr.Body.String())
+	}
+	// Body should mention "local" or "no git_repos" so an operator
+	// reading the API response (or curl output) understands why this
+	// project doesn't have webhook coordinates.
+	body := rr.Body.String()
+	if !strings.Contains(body, "local") && !strings.Contains(body, "git_repos") {
+		t.Errorf("404 body should hint at the local-project cause, got: %s", body)
+	}
+}
+
 func TestWebhookInfo_ReturnsURLAndSecret(t *testing.T) {
 	router, _ := reposRouter(t)
-	wsID := createWS(t, router, "platform")
-	// Manual add — we want the wsID + repo for the URL construction.
-	rr := doJSON(t, router, http.MethodPost, "/api/v1/workspaces/"+wsID+"/repos", map[string]any{
+	// AddGitRepo includes the secret in the create response.
+	rr := doJSON(t, router, http.MethodPost, "/api/v1/git-repos", map[string]any{
 		"github_url": "https://github.com/a/b",
 		"branch":     "main",
 	})
 	if rr.Code != http.StatusCreated {
-		t.Fatalf("add: %d", rr.Code)
+		t.Fatalf("add: %d (%s)", rr.Code, rr.Body.String())
 	}
 	var created struct {
-		Repo          workspaceRepoPayload `json:"repo"`
-		WebhookSecret string               `json:"webhook_secret"`
+		GitRepo struct {
+			PathHash string `json:"path_hash"`
+		} `json:"git_repo"`
+		WebhookSecret string `json:"webhook_secret"`
 	}
 	_ = json.Unmarshal(rr.Body.Bytes(), &created)
 
-	rr = doJSON(t, router, http.MethodGet,
-		"/api/v1/workspaces/"+wsID+"/repos/"+created.Repo.ID+"/webhook-info", nil)
+	hash := projects.HashPath("github.com/a/b@main")
+	if hash != created.GitRepo.PathHash {
+		t.Fatalf("path_hash mismatch: %q vs %q", hash, created.GitRepo.PathHash)
+	}
+	rr = doJSON(t, router, http.MethodGet, "/api/v1/projects/"+hash+"/webhook-info", nil)
 	if rr.Code != http.StatusOK {
 		t.Fatalf("webhook-info: %d (%s)", rr.Code, rr.Body.String())
 	}
@@ -280,7 +323,7 @@ func TestWebhookInfo_ReturnsURLAndSecret(t *testing.T) {
 	if info.WebhookSecret != created.WebhookSecret {
 		t.Fatalf("secret mismatch between create and info")
 	}
-	if info.WebhookURL != "https://cix.example.test/api/v1/webhooks/github/"+created.Repo.ID {
+	if info.WebhookURL != "https://cix.example.test/api/v1/webhooks/github/"+hash {
 		t.Fatalf("URL wrong: %q", info.WebhookURL)
 	}
 	if info.AutoRegistered {
diff --git a/server/internal/httpapi/workspace_test_helpers_test.go b/server/internal/httpapi/workspace_test_helpers_test.go
new file mode 100644
index 0000000..3b2ea9d
--- /dev/null
+++ b/server/internal/httpapi/workspace_test_helpers_test.go
@@ -0,0 +1,117 @@
+package httpapi
+
+import (
+	"database/sql"
+	"encoding/json"
+	"net/http"
+	"testing"
+	"time"
+
+	"github.com/dvcdsys/code-index/server/internal/githubtokens"
+	"github.com/dvcdsys/code-index/server/internal/gitrepos"
+	"github.com/dvcdsys/code-index/server/internal/jobs"
+	"github.com/dvcdsys/code-index/server/internal/secrets"
+	"github.com/dvcdsys/code-index/server/internal/workspaceprojects"
+	"github.com/dvcdsys/code-index/server/internal/workspaces"
+)
+
+// reposRouter spins up a router with the full workspaces + git_repos +
+// workspace_projects surface wired against an in-memory DB. Auth is
+// disabled — the focus is the persistence + enqueue paths.
+//
+// The jobs worker pool is created but NOT started: tests only assert
+// jobs landed in the right state. End-to-end clone+index runs against
+// real git remotes — out of scope for unit tests.
+// reposRouterDB is the explicit form returning the DB handle too.
+// Tests that need to manipulate projects.status (a state normally owned
+// by the indexer) call this variant.
+func reposRouterDB(t *testing.T) (http.Handler, *jobs.Service, *sql.DB) {
+	t.Helper()
+	d, err := dbOpenMemory(t)
+	if err != nil {
+		t.Fatalf("open db: %v", err)
+	}
+	t.Setenv("CIX_SECRET_KEY", "")
+	t.Setenv("CIX_SECRET_KEYFILE", "")
+	sec, err := secrets.Open(secrets.OpenOptions{DataDir: t.TempDir(), AllowGenerate: true})
+	if err != nil {
+		t.Fatalf("open secrets: %v", err)
+	}
+	wsSvc := workspaces.New(d)
+	ghSvc := githubtokens.New(d, sec)
+	grSvc := gitrepos.New(d)
+	wpSvc := workspaceprojects.New(d)
+	jobsSvc := jobs.New(d, jobs.Options{Concurrency: 1, PollEvery: time.Hour})
+
+	router := NewRouter(Deps{
+		DB:                d,
+		ServerVersion:     "test",
+		APIVersion:        "v1",
+		Backend:           "go",
+		AuthDisabled:      true,
+		Users:             seedlessUsers(d),
+		Sessions:          seedlessSessions(d),
+		APIKeys:           seedlessAPIKeys(d),
+		WorkspacesEnabled: true,
+		Workspaces:        wsSvc,
+		GithubTokens:      ghSvc,
+		GitRepos:          grSvc,
+		WorkspaceProjects: wpSvc,
+		Jobs:              jobsSvc,
+		PublicBaseURL:     "https://cix.example.test",
+	})
+	return router, jobsSvc, d
+}
+
+func reposRouter(t *testing.T) (http.Handler, *jobs.Service) {
+	t.Helper()
+	d, err := dbOpenMemory(t)
+	if err != nil {
+		t.Fatalf("open db: %v", err)
+	}
+	t.Setenv("CIX_SECRET_KEY", "")
+	t.Setenv("CIX_SECRET_KEYFILE", "")
+	sec, err := secrets.Open(secrets.OpenOptions{DataDir: t.TempDir(), AllowGenerate: true})
+	if err != nil {
+		t.Fatalf("open secrets: %v", err)
+	}
+	wsSvc := workspaces.New(d)
+	ghSvc := githubtokens.New(d, sec)
+	grSvc := gitrepos.New(d)
+	wpSvc := workspaceprojects.New(d)
+	jobsSvc := jobs.New(d, jobs.Options{Concurrency: 1, PollEvery: time.Hour})
+
+	router := NewRouter(Deps{
+		DB:                d,
+		ServerVersion:     "test",
+		APIVersion:        "v1",
+		Backend:           "go",
+		AuthDisabled:      true,
+		Users:             seedlessUsers(d),
+		Sessions:          seedlessSessions(d),
+		APIKeys:           seedlessAPIKeys(d),
+		WorkspacesEnabled: true,
+		Workspaces:        wsSvc,
+		GithubTokens:      ghSvc,
+		GitRepos:          grSvc,
+		WorkspaceProjects: wpSvc,
+		Jobs:              jobsSvc,
+		PublicBaseURL:     "https://cix.example.test",
+	})
+	return router, jobsSvc
+}
+
+// createWS calls POST /api/v1/workspaces with the given name and returns
+// the new workspace id.
+func createWS(t *testing.T, router http.Handler, name string) string {
+	t.Helper()
+	rr := doJSON(t, router, http.MethodPost, "/api/v1/workspaces", map[string]any{
+		"name": name,
+	})
+	if rr.Code != http.StatusCreated {
+		t.Fatalf("create workspace: %d (%s)", rr.Code, rr.Body.String())
+	}
+	var got workspacePayload
+	_ = json.Unmarshal(rr.Body.Bytes(), &got)
+	return got.ID
+}
diff --git a/server/internal/httpapi/workspaceprojects.go b/server/internal/httpapi/workspaceprojects.go
new file mode 100644
index 0000000..96d81f6
--- /dev/null
+++ b/server/internal/httpapi/workspaceprojects.go
@@ -0,0 +1,151 @@
+package httpapi
+
+import (
+	"encoding/json"
+	"errors"
+	"net/http"
+
+	"github.com/dvcdsys/code-index/server/internal/httpapi/openapi"
+	"github.com/dvcdsys/code-index/server/internal/projects"
+	"github.com/dvcdsys/code-index/server/internal/workspaceprojects"
+	"github.com/dvcdsys/code-index/server/internal/workspaces"
+)
+
+// workspaceProjectsUnavailable returns 503 when the feature flag is
+// off OR any required service is nil.
+func (s *Server) workspaceProjectsUnavailable(w http.ResponseWriter) bool {
+	if !s.Deps.WorkspacesEnabled || s.Deps.WorkspaceProjects == nil || s.Deps.Workspaces == nil {
+		writeError(w, http.StatusServiceUnavailable, "workspaces feature is disabled (set CIX_WORKSPACES_ENABLED=true and restart)")
+		return true
+	}
+	return false
+}
+
+// requireWorkspace loads the parent workspace and returns 404 if missing.
+func (s *Server) requireWorkspace(w http.ResponseWriter, r *http.Request, workspaceID string) bool {
+	_, err := s.Deps.Workspaces.GetByID(r.Context(), workspaceID)
+	if err != nil {
+		if errors.Is(err, workspaces.ErrNotFound) {
+			writeError(w, http.StatusNotFound, "workspace not found")
+		} else {
+			writeError(w, http.StatusInternalServerError, "could not load workspace")
+		}
+		return false
+	}
+	return true
+}
+
+// ListWorkspaceProjects — GET /api/v1/workspaces/{id}/projects.
+func (s *Server) ListWorkspaceProjects(w http.ResponseWriter, r *http.Request, id string) {
+	if s.workspaceProjectsUnavailable(w) {
+		return
+	}
+	if !s.requireWorkspace(w, r, id) {
+		return
+	}
+	memberships, err := s.Deps.WorkspaceProjects.ListByWorkspace(r.Context(), id)
+	if err != nil {
+		writeError(w, http.StatusInternalServerError, "could not list workspace projects: "+err.Error())
+		return
+	}
+	out := make([]map[string]any, 0, len(memberships))
+	for _, m := range memberships {
+		proj, perr := projects.Get(r.Context(), s.Deps.DB, m.ProjectPath)
+		if perr != nil {
+			// The FK should prevent dangling rows, but if the project
+			// disappeared between SELECT and Get we just skip it.
+			s.Deps.Logger.Warn("workspaceprojects: project missing for membership",
+				"workspace_id", id, "project_path", m.ProjectPath, "err", perr)
+			continue
+		}
+		out = append(out, map[string]any{
+			"project":  projectToOpenAPI(proj),
+			"added_at": m.AddedAt,
+		})
+	}
+	writeJSON(w, http.StatusOK, map[string]any{
+		"projects": out,
+		"total":    len(out),
+	})
+}
+
+// LinkProjectToWorkspace — POST /api/v1/workspaces/{id}/projects.
+//
+// Adds an existing indexed project to a workspace. The project must be
+// in status='indexed'; pending/cloning projects return 422 so the
+// dashboard can prompt the user to wait.
+func (s *Server) LinkProjectToWorkspace(w http.ResponseWriter, r *http.Request, id string) {
+	if s.workspaceProjectsUnavailable(w) {
+		return
+	}
+	if !s.requireWorkspace(w, r, id) {
+		return
+	}
+	var body openapi.LinkProjectRequest
+	if err := json.NewDecoder(r.Body).Decode(&body); err != nil {
+		writeError(w, http.StatusUnprocessableEntity, "invalid JSON body")
+		return
+	}
+	proj, perr := projects.GetByHash(r.Context(), s.Deps.DB, body.ProjectHash)
+	if perr != nil {
+		if errors.Is(perr, projects.ErrNotFound) {
+			writeError(w, http.StatusNotFound, "project not found")
+			return
+		}
+		writeError(w, http.StatusInternalServerError, "could not load project: "+perr.Error())
+		return
+	}
+	m, err := s.Deps.WorkspaceProjects.Link(r.Context(), id, proj.HostPath)
+	if err != nil {
+		switch {
+		case errors.Is(err, workspaceprojects.ErrProjectNotIndexed):
+			writeError(w, http.StatusUnprocessableEntity,
+				"project is not yet indexed — wait for indexing to complete before linking")
+		case errors.Is(err, workspaceprojects.ErrProjectMissing):
+			writeError(w, http.StatusNotFound, "project not found")
+		case errors.Is(err, workspaceprojects.ErrWorkspaceMissing):
+			writeError(w, http.StatusNotFound, "workspace not found")
+		case errors.Is(err, workspaceprojects.ErrDuplicate):
+			writeError(w, http.StatusConflict, "project is already linked to this workspace")
+		default:
+			writeError(w, http.StatusInternalServerError, "could not link project: "+err.Error())
+		}
+		return
+	}
+	writeJSON(w, http.StatusCreated, map[string]any{
+		"workspace_id": m.WorkspaceID,
+		"project_path": m.ProjectPath,
+		"added_at":     m.AddedAt,
+	})
+}
+
+// UnlinkProjectFromWorkspace — DELETE /api/v1/workspaces/{id}/projects/{hash}.
+//
+// Removes the workspace_projects row. The project itself is untouched.
+// 204 on success, 404 when the project (or the membership) doesn't exist.
+func (s *Server) UnlinkProjectFromWorkspace(w http.ResponseWriter, r *http.Request, id string, hash openapi.ProjectHash) {
+	if s.workspaceProjectsUnavailable(w) {
+		return
+	}
+	if !s.requireWorkspace(w, r, id) {
+		return
+	}
+	proj, perr := projects.GetByHash(r.Context(), s.Deps.DB, string(hash))
+	if perr != nil {
+		if errors.Is(perr, projects.ErrNotFound) {
+			writeError(w, http.StatusNotFound, "project not found")
+			return
+		}
+		writeError(w, http.StatusInternalServerError, "could not load project: "+perr.Error())
+		return
+	}
+	if err := s.Deps.WorkspaceProjects.Unlink(r.Context(), id, proj.HostPath); err != nil {
+		if errors.Is(err, workspaceprojects.ErrNotFound) {
+			writeError(w, http.StatusNotFound, "project is not linked to this workspace")
+			return
+		}
+		writeError(w, http.StatusInternalServerError, "could not unlink project: "+err.Error())
+		return
+	}
+	w.WriteHeader(http.StatusNoContent)
+}
diff --git a/server/internal/httpapi/workspaceprojects_test.go b/server/internal/httpapi/workspaceprojects_test.go
new file mode 100644
index 0000000..07abb44
--- /dev/null
+++ b/server/internal/httpapi/workspaceprojects_test.go
@@ -0,0 +1,254 @@
+package httpapi
+
+import (
+	"database/sql"
+	"encoding/json"
+	"net/http"
+	"strings"
+	"testing"
+	"time"
+
+	"github.com/dvcdsys/code-index/server/internal/projects"
+)
+
+// markIndexed flips a project's status to 'indexed' so workspaceprojects.Link
+// passes its precondition. Production code does this through the indexer's
+// finish step (which also stamps last_indexed_at); tests don't run the
+// indexer so we mimic both writes here.
+//
+// The timestamp must be RFC3339Nano because projectToOpenAPI parses
+// last_indexed_at with time.RFC3339Nano — SQLite's `datetime('now')`
+// emits `2006-01-02 15:04:05` which fails that parse and silently
+// becomes NULL on the wire.
+func markIndexed(t *testing.T, d *sql.DB, hostPath string) {
+	t.Helper()
+	now := time.Now().UTC().Format(time.RFC3339Nano)
+	if _, err := d.Exec(
+		`UPDATE projects SET status = 'indexed', last_indexed_at = ? WHERE host_path = ?`,
+		now, hostPath,
+	); err != nil {
+		t.Fatalf("flip status to indexed for %s: %v", hostPath, err)
+	}
+}
+
+func TestLinkProjectToWorkspace_RejectsNotIndexed(t *testing.T) {
+	router, _ := reposRouter(t)
+	wsID := createWS(t, router, "platform")
+
+	rr := doJSON(t, router, http.MethodPost, "/api/v1/git-repos", map[string]any{
+		"github_url": "https://github.com/x/y",
+		"branch":     "main",
+	})
+	if rr.Code != http.StatusCreated {
+		t.Fatalf("add git_repo: %d (%s)", rr.Code, rr.Body.String())
+	}
+	hash := projects.HashPath("github.com/x/y@main")
+
+	rr = doJSON(t, router, http.MethodPost,
+		"/api/v1/workspaces/"+wsID+"/projects",
+		map[string]any{"project_hash": hash})
+	if rr.Code != http.StatusUnprocessableEntity {
+		t.Fatalf("link before indexed: expected 422, got %d (%s)", rr.Code, rr.Body.String())
+	}
+}
+
+func TestLinkProjectToWorkspace_AfterIndexed(t *testing.T) {
+	router, _, d := reposRouterDB(t)
+	wsID := createWS(t, router, "platform")
+	hostPath := "/Users/x/local-proj"
+	rr := doJSON(t, router, http.MethodPost, "/api/v1/projects", map[string]any{
+		"host_path": hostPath,
+	})
+	if rr.Code != http.StatusCreated {
+		t.Fatalf("create project: %d (%s)", rr.Code, rr.Body.String())
+	}
+	markIndexed(t, d, hostPath)
+	hash := projects.HashPath(hostPath)
+
+	rr = doJSON(t, router, http.MethodPost,
+		"/api/v1/workspaces/"+wsID+"/projects",
+		map[string]any{"project_hash": hash})
+	if rr.Code != http.StatusCreated {
+		t.Fatalf("link: %d (%s)", rr.Code, rr.Body.String())
+	}
+
+	rr = doJSON(t, router, http.MethodGet, "/api/v1/workspaces/"+wsID+"/projects", nil)
+	if rr.Code != http.StatusOK {
+		t.Fatalf("list: %d (%s)", rr.Code, rr.Body.String())
+	}
+	var list struct {
+		Projects []map[string]any `json:"projects"`
+		Total    int              `json:"total"`
+	}
+	_ = json.Unmarshal(rr.Body.Bytes(), &list)
+	if list.Total != 1 {
+		t.Fatalf("expected 1 project in workspace, got %d", list.Total)
+	}
+
+	// Wire-contract check — the CLI client (cli/internal/client/workspace.go)
+	// decodes this exact response into Project + WorkspaceProject + Wrapped
+	// list. Anyone breaking these field names breaks the CLI silently
+	// (which is how Fix #1 happened in the first place). Mirror the
+	// CLI's struct shape inline and assert every field the CLI reads.
+	type cliWire struct {
+		Projects []struct {
+			AddedAt time.Time `json:"added_at"`
+			Project struct {
+				PathHash      string     `json:"path_hash"`
+				HostPath      string     `json:"host_path"`
+				ContainerPath string     `json:"container_path"`
+				Status        string     `json:"status"`
+				LastIndexedAt *time.Time `json:"last_indexed_at"`
+				Languages     []string   `json:"languages"`
+			} `json:"project"`
+		} `json:"projects"`
+		Total int `json:"total"`
+	}
+	var wire cliWire
+	if err := json.Unmarshal(rr.Body.Bytes(), &wire); err != nil {
+		t.Fatalf("decode wire shape: %v", err)
+	}
+	if wire.Total != 1 || len(wire.Projects) != 1 {
+		t.Fatalf("expected wire to surface 1 project; got total=%d len=%d", wire.Total, len(wire.Projects))
+	}
+	got := wire.Projects[0]
+	if got.AddedAt.IsZero() {
+		t.Errorf("expected added_at to be a non-zero timestamp")
+	}
+	if got.Project.PathHash != hash {
+		t.Errorf("path_hash: want %q, got %q", hash, got.Project.PathHash)
+	}
+	if got.Project.HostPath != hostPath {
+		t.Errorf("host_path: want %q, got %q", hostPath, got.Project.HostPath)
+	}
+	if got.Project.Status != "indexed" {
+		t.Errorf("status: want \"indexed\", got %q", got.Project.Status)
+	}
+	if got.Project.LastIndexedAt == nil {
+		t.Errorf("last_indexed_at should be populated for an indexed project")
+	}
+	if got.Project.Languages == nil {
+		t.Errorf("languages should be [], not null — CLI iterates it without nil-check")
+	}
+}
+
+// TestListWorkspaceProjects_Empty pins the empty-membership response:
+// the handler MUST emit `"projects": []` (not `null`), so the CLI's
+// `for _, wp := range resp.Projects` loop is safe. A future refactor
+// that drops the `make([]map[string]any, 0, …)` initialisation would
+// regress to `null` and this test catches it at server CI.
+func TestListWorkspaceProjects_Empty(t *testing.T) {
+	router, _, _ := reposRouterDB(t)
+	wsID := createWS(t, router, "platform")
+
+	rr := doJSON(t, router, http.MethodGet, "/api/v1/workspaces/"+wsID+"/projects", nil)
+	if rr.Code != http.StatusOK {
+		t.Fatalf("expected 200, got %d (%s)", rr.Code, rr.Body.String())
+	}
+	body := rr.Body.String()
+	// `"projects":[]` (no whitespace; encoding/json produces compact JSON).
+	// Negative form `"projects":null` is the regression we're guarding.
+	if !strings.Contains(body, `"projects":[]`) {
+		t.Errorf("expected `\"projects\":[]` in body, got: %s", body)
+	}
+	var list struct {
+		Projects []map[string]any `json:"projects"`
+		Total    int              `json:"total"`
+	}
+	if err := json.Unmarshal(rr.Body.Bytes(), &list); err != nil {
+		t.Fatalf("decode: %v", err)
+	}
+	if list.Total != 0 {
+		t.Errorf("expected total=0, got %d", list.Total)
+	}
+	if list.Projects == nil {
+		t.Errorf("projects should be empty slice, not nil (CLI iterates it)")
+	}
+}
+
+// TestListWorkspaceProjects_WorkspaceMissing locks the "unknown id → 404"
+// contract for the new endpoint. The CLI surfaces this as a "workspace
+// %q not found" error to the user.
+func TestListWorkspaceProjects_WorkspaceMissing(t *testing.T) {
+	router, _, _ := reposRouterDB(t)
+	bogusID := "ws_does_not_exist_01J5"
+
+	rr := doJSON(t, router, http.MethodGet, "/api/v1/workspaces/"+bogusID+"/projects", nil)
+	if rr.Code != http.StatusNotFound {
+		t.Fatalf("expected 404, got %d (%s)", rr.Code, rr.Body.String())
+	}
+	if !strings.Contains(rr.Body.String(), "workspace not found") {
+		t.Errorf("expected 404 body to mention 'workspace not found', got: %s", rr.Body.String())
+	}
+}
+
+// TestListWorkspaceProjects_FeatureDisabled — when CIX_WORKSPACES_ENABLED
+// is false the handler must short-circuit with 503 *before* touching DB.
+// The CLI relies on this so `cix ws <name> list` against a disabled
+// server prints a useful "feature is disabled" hint, not a generic
+// failure.
+func TestListWorkspaceProjects_FeatureDisabled(t *testing.T) {
+	router := workspaceRouter(t, false)
+	// Any path id will do — 503 must come before the workspace lookup.
+	rr := doJSON(t, router, http.MethodGet, "/api/v1/workspaces/ws_any/projects", nil)
+	if rr.Code != http.StatusServiceUnavailable {
+		t.Fatalf("expected 503 with feature disabled, got %d (%s)", rr.Code, rr.Body.String())
+	}
+	if !strings.Contains(rr.Body.String(), "workspaces feature is disabled") {
+		t.Errorf("expected 503 body to mention 'workspaces feature is disabled', got: %s", rr.Body.String())
+	}
+}
+
+
+// TestLink_Duplicate confirms the workspace_projects PRIMARY KEY
+// catches a re-link as 409. Same project, same workspace, twice.
+func TestLink_Duplicate(t *testing.T) {
+	router, _, d := reposRouterDB(t)
+	wsID := createWS(t, router, "platform")
+	hostPath := "/Users/x/p"
+	_ = doJSON(t, router, http.MethodPost, "/api/v1/projects",
+		map[string]any{"host_path": hostPath})
+	markIndexed(t, d, hostPath)
+	hash := projects.HashPath(hostPath)
+
+	body := map[string]any{"project_hash": hash}
+	if rr := doJSON(t, router, http.MethodPost, "/api/v1/workspaces/"+wsID+"/projects", body); rr.Code != http.StatusCreated {
+		t.Fatalf("first link: %d", rr.Code)
+	}
+	if rr := doJSON(t, router, http.MethodPost, "/api/v1/workspaces/"+wsID+"/projects", body); rr.Code != http.StatusConflict {
+		t.Fatalf("second link should 409, got %d", rr.Code)
+	}
+}
+
+// TestUnlinkProject removes a membership without touching the project.
+func TestUnlinkProject(t *testing.T) {
+	router, _, d := reposRouterDB(t)
+	wsID := createWS(t, router, "platform")
+	hostPath := "/Users/x/local-proj"
+	_ = doJSON(t, router, http.MethodPost, "/api/v1/projects",
+		map[string]any{"host_path": hostPath})
+	markIndexed(t, d, hostPath)
+	hash := projects.HashPath(hostPath)
+
+	if rr := doJSON(t, router, http.MethodPost,
+		"/api/v1/workspaces/"+wsID+"/projects",
+		map[string]any{"project_hash": hash}); rr.Code != http.StatusCreated {
+		t.Fatalf("link: %d (%s)", rr.Code, rr.Body.String())
+	}
+
+	rr := doJSON(t, router, http.MethodDelete,
+		"/api/v1/workspaces/"+wsID+"/projects/"+hash, nil)
+	if rr.Code != http.StatusNoContent {
+		t.Fatalf("unlink: expected 204, got %d (%s)", rr.Code, rr.Body.String())
+	}
+	rr = doJSON(t, router, http.MethodDelete,
+		"/api/v1/workspaces/"+wsID+"/projects/"+hash, nil)
+	if rr.Code != http.StatusNotFound {
+		t.Fatalf("repeat unlink: expected 404, got %d", rr.Code)
+	}
+	// Project still exists.
+	rr = doJSON(t, router, http.MethodGet, "/api/v1/projects/"+hash, nil)
+	if rr.Code != http.StatusOK {
+		t.Fatalf("project should survive unlink, got %d", rr.Code)
+	}
+}
diff --git a/server/internal/httpapi/workspacerepos.go b/server/internal/httpapi/workspacerepos.go
deleted file mode 100644
index d135149..0000000
--- a/server/internal/httpapi/workspacerepos.go
+++ /dev/null
@@ -1,425 +0,0 @@
-package httpapi
-
-import (
-	"context"
-	"encoding/json"
-	"errors"
-	"net/http"
-	"strings"
-	"time"
-
-	"github.com/dvcdsys/code-index/server/internal/githubapi"
-	"github.com/dvcdsys/code-index/server/internal/githubtokens"
-	"github.com/dvcdsys/code-index/server/internal/httpapi/openapi"
-	"github.com/dvcdsys/code-index/server/internal/jobs"
-	"github.com/dvcdsys/code-index/server/internal/projects"
-	"github.com/dvcdsys/code-index/server/internal/workspacejobs"
-	"github.com/dvcdsys/code-index/server/internal/workspacerepos"
-	"github.com/dvcdsys/code-index/server/internal/workspaces"
-)
-
-type workspaceRepoPayload struct {
-	ID            string     `json:"id"`
-	WorkspaceID   string     `json:"workspace_id"`
-	GitHubURL     string     `json:"github_url"`
-	Branch        string     `json:"branch"`
-	ProjectPath   string     `json:"project_path"`
-	TokenID       *string    `json:"token_id"`
-	AutoWebhook   bool       `json:"auto_webhook"`
-	WebhookMode   string     `json:"webhook_mode"`
-	Status        string     `json:"status"`
-	LastSHA       *string    `json:"last_sha"`
-	LastError     *string    `json:"last_error"`
-	LastIndexedAt *time.Time `json:"last_indexed_at"`
-	IsLinked      bool       `json:"is_linked"`
-	CreatedAt     time.Time  `json:"created_at"`
-	UpdatedAt     time.Time  `json:"updated_at"`
-}
-
-func workspaceRepoToPayload(wr workspacerepos.WorkspaceRepo) workspaceRepoPayload {
-	var tokenID *string
-	if wr.TokenID != "" {
-		v := wr.TokenID
-		tokenID = &v
-	}
-	var lastSHA *string
-	if wr.LastSHA != "" {
-		v := wr.LastSHA
-		lastSHA = &v
-	}
-	var lastErr *string
-	if wr.LastError != "" {
-		v := wr.LastError
-		lastErr = &v
-	}
-	mode := wr.WebhookMode
-	if mode == "" {
-		mode = workspacerepos.WebhookModeManual
-	}
-	return workspaceRepoPayload{
-		ID:            wr.ID,
-		WorkspaceID:   wr.WorkspaceID,
-		GitHubURL:     wr.GitHubURL,
-		Branch:        wr.Branch,
-		ProjectPath:   wr.ProjectPath,
-		TokenID:       tokenID,
-		AutoWebhook:   wr.AutoWebhook,
-		WebhookMode:   mode,
-		Status:        wr.Status,
-		LastSHA:       lastSHA,
-		LastError:     lastErr,
-		LastIndexedAt: wr.LastIndexedAt,
-		IsLinked:      wr.IsLinked,
-		CreatedAt:     wr.CreatedAt,
-		UpdatedAt:     wr.UpdatedAt,
-	}
-}
-
-// workspaceReposUnavailable returns 503 when the feature flag is off OR
-// any required service is nil.
-func (s *Server) workspaceReposUnavailable(w http.ResponseWriter) bool {
-	if !s.Deps.WorkspacesEnabled || s.Deps.WorkspaceRepos == nil || s.Deps.Workspaces == nil || s.Deps.Jobs == nil {
-		writeError(w, http.StatusServiceUnavailable, "workspaces feature is disabled (set CIX_WORKSPACES_ENABLED=true and restart)")
-		return true
-	}
-	return false
-}
-
-// requireWorkspace loads the parent workspace and returns 404 if missing.
-// Used by every workspace-scoped endpoint to make "wrong workspace id"
-// vs "wrong repo id" distinguishable in error responses.
-func (s *Server) requireWorkspace(w http.ResponseWriter, r *http.Request, workspaceID string) bool {
-	_, err := s.Deps.Workspaces.GetByID(r.Context(), workspaceID)
-	if err != nil {
-		if errors.Is(err, workspaces.ErrNotFound) {
-			writeError(w, http.StatusNotFound, "workspace not found")
-		} else {
-			writeError(w, http.StatusInternalServerError, "could not load workspace")
-		}
-		return false
-	}
-	return true
-}
-
-// ListWorkspaceRepos — GET /api/v1/workspaces/{id}/repos.
-func (s *Server) ListWorkspaceRepos(w http.ResponseWriter, r *http.Request, id string) {
-	if s.workspaceReposUnavailable(w) {
-		return
-	}
-	if !s.requireWorkspace(w, r, id) {
-		return
-	}
-	list, err := s.Deps.WorkspaceRepos.ListByWorkspace(r.Context(), id)
-	if err != nil {
-		writeError(w, http.StatusInternalServerError, "could not list repos")
-		return
-	}
-	out := make([]workspaceRepoPayload, 0, len(list))
-	for _, wr := range list {
-		out = append(out, workspaceRepoToPayload(wr))
-	}
-	writeJSON(w, http.StatusOK, map[string]any{
-		"repos": out,
-		"total": len(out),
-	})
-}
-
-// AddWorkspaceRepo — POST /api/v1/workspaces/{id}/repos.
-//
-// Creates the workspace_repos row + enqueues the clone_repo job (which
-// chains to index_repo on success). Response carries the freshly-minted
-// webhook_secret + a constructed webhook_url so the operator can set up
-// the GitHub webhook manually (or wait for PR3's auto-register flow).
-func (s *Server) AddWorkspaceRepo(w http.ResponseWriter, r *http.Request, id string) {
-	if s.workspaceReposUnavailable(w) {
-		return
-	}
-	if !s.requireWorkspace(w, r, id) {
-		return
-	}
-	var body openapi.AddWorkspaceRepoRequest
-	if err := json.NewDecoder(r.Body).Decode(&body); err != nil {
-		writeError(w, http.StatusUnprocessableEntity, "invalid JSON body")
-		return
-	}
-	req := workspacerepos.CreateRequest{
-		WorkspaceID: id,
-		GitHubURL:   body.GithubUrl,
-		Branch:      body.Branch,
-	}
-	if body.TokenId != nil {
-		req.TokenID = *body.TokenId
-	}
-	if body.AutoWebhook != nil {
-		req.AutoWebhook = *body.AutoWebhook
-	}
-	if body.WebhookMode != nil {
-		req.WebhookMode = string(*body.WebhookMode)
-	}
-	wr, err := s.Deps.WorkspaceRepos.Create(r.Context(), req)
-	if err != nil {
-		switch {
-		case errors.Is(err, workspacerepos.ErrInvalidURL):
-			writeError(w, http.StatusUnprocessableEntity, "github_url must be an https://github.com/owner/repo URL")
-		case errors.Is(err, workspacerepos.ErrBranchEmpty):
-			writeError(w, http.StatusUnprocessableEntity, "branch is required")
-		case errors.Is(err, workspacerepos.ErrInvalidWebhookMode):
-			writeError(w, http.StatusUnprocessableEntity, "webhook_mode must be one of manual, auto, disabled")
-		case errors.Is(err, workspacerepos.ErrDuplicate):
-			writeError(w, http.StatusConflict, "this repo+branch is already attached to the workspace")
-		default:
-			writeError(w, http.StatusInternalServerError, "could not attach repo")
-		}
-		return
-	}
-
-	if err := workspacejobs.EnqueueClone(r.Context(), s.Deps.Jobs, wr.ID); err != nil {
-		// Row created, job not — surface the error but leave the row.
-		// A manual reindex will retry the clone.
-		writeError(w, http.StatusInternalServerError, "repo attached but clone could not be enqueued: "+err.Error())
-		return
-	}
-
-	webhookURL := s.buildWebhookURL(wr.ID)
-	autoRegistered := false
-	autoNote := ""
-	if wr.AutoWebhook {
-		ok, note := s.tryAutoRegisterWebhook(r.Context(), wr, webhookURL)
-		autoRegistered = ok
-		autoNote = note
-		if ok {
-			// Reload so the response reflects the persisted webhook_id.
-			if fresh, ferr := s.Deps.WorkspaceRepos.GetByID(r.Context(), wr.ID); ferr == nil {
-				wr = fresh
-			}
-		}
-	}
-
-	resp := map[string]any{
-		"repo":            workspaceRepoToPayload(wr),
-		"webhook_url":     webhookURL,
-		"webhook_secret":  wr.WebhookSecret,
-		"auto_registered": autoRegistered,
-	}
-	if autoNote != "" {
-		resp["auto_register_note"] = autoNote
-	}
-	writeJSON(w, http.StatusCreated, resp)
-}
-
-// tryAutoRegisterWebhook calls the GitHub API to register a push hook for
-// the given repo. Best-effort — failure does NOT roll back the
-// workspace_repos row; the operator can rerun manually via the
-// webhook-info endpoint. Returns (success, human-readable note).
-//
-// Public URL is required — without it GitHub would deliver to a path
-// that's not reachable. We refuse to attempt the call when PublicBaseURL
-// is empty and surface that as the note.
-func (s *Server) tryAutoRegisterWebhook(ctx context.Context, wr workspacerepos.WorkspaceRepo, deliveryURL string) (bool, string) {
-	logger := s.Deps.Logger
-	if !strings.HasPrefix(deliveryURL, "http") {
-		return false, "CIX_PUBLIC_URL is not set — register the webhook manually"
-	}
-	if wr.TokenID == "" {
-		return false, "auto_webhook=true requires a token_id with admin:repo_hook scope"
-	}
-	pat, err := s.Deps.GithubTokens.Reveal(ctx, wr.TokenID)
-	if err != nil {
-		if errors.Is(err, githubtokens.ErrNotFound) {
-			return false, "token_id not found"
-		}
-		return false, "could not decrypt the GitHub token"
-	}
-	_ = s.Deps.GithubTokens.Touch(ctx, wr.TokenID)
-
-	owner, repo, perr := githubapi.ParseOwnerRepo(wr.GitHubURL)
-	if perr != nil {
-		return false, "github_url is not a parseable owner/repo URL"
-	}
-	hr, herr := githubapi.New().CreateWebhook(ctx, githubapi.CreateWebhookOptions{
-		Owner:  owner,
-		Repo:   repo,
-		PAT:    pat,
-		URL:    deliveryURL,
-		Secret: wr.WebhookSecret,
-	})
-	if herr != nil {
-		if logger != nil {
-			logger.Warn("workspaces: auto-register webhook failed",
-				"repo_id", wr.ID, "owner", owner, "repo", repo, "err", herr)
-		}
-		if errors.Is(herr, githubapi.ErrUnauthorized) {
-			return false, "GitHub rejected the token — add admin:repo_hook scope or register manually"
-		}
-		return false, "GitHub API rejected the call: " + herr.Error()
-	}
-	if uerr := s.Deps.WorkspaceRepos.SetWebhookID(ctx, wr.ID, hr.ID); uerr != nil && logger != nil {
-		logger.Warn("workspaces: could not persist webhook id", "repo_id", wr.ID, "err", uerr)
-	}
-	return true, ""
-}
-
-// DeleteWorkspaceRepo — DELETE /api/v1/workspaces/{id}/repos/{repo_id}.
-func (s *Server) DeleteWorkspaceRepo(w http.ResponseWriter, r *http.Request, id, repoID string) {
-	if s.workspaceReposUnavailable(w) {
-		return
-	}
-	if !s.requireWorkspace(w, r, id) {
-		return
-	}
-	// Authorisation: a repo only belongs to its workspace, so we also
-	// require the repo's workspace_id to match. Otherwise users could
-	// detach repos across workspaces by guessing ids.
-	existing, err := s.Deps.WorkspaceRepos.GetByID(r.Context(), repoID)
-	if err != nil {
-		if errors.Is(err, workspacerepos.ErrNotFound) {
-			writeError(w, http.StatusNotFound, "repo not found")
-			return
-		}
-		writeError(w, http.StatusInternalServerError, "could not load repo")
-		return
-	}
-	if existing.WorkspaceID != id {
-		writeError(w, http.StatusNotFound, "repo not found")
-		return
-	}
-	if err := s.Deps.WorkspaceRepos.Delete(r.Context(), repoID); err != nil {
-		if errors.Is(err, workspacerepos.ErrNotFound) {
-			writeError(w, http.StatusNotFound, "repo not found")
-			return
-		}
-		writeError(w, http.StatusInternalServerError, "could not delete repo")
-		return
-	}
-	w.WriteHeader(http.StatusNoContent)
-}
-
-// ReindexWorkspaceRepo — POST /api/v1/workspaces/{id}/repos/{repo_id}/reindex.
-func (s *Server) ReindexWorkspaceRepo(w http.ResponseWriter, r *http.Request, id, repoID string) {
-	if s.workspaceReposUnavailable(w) {
-		return
-	}
-	if !s.requireWorkspace(w, r, id) {
-		return
-	}
-	wr, err := s.Deps.WorkspaceRepos.GetByID(r.Context(), repoID)
-	if err != nil {
-		if errors.Is(err, workspacerepos.ErrNotFound) {
-			writeError(w, http.StatusNotFound, "repo not found")
-			return
-		}
-		writeError(w, http.StatusInternalServerError, "could not load repo")
-		return
-	}
-	if wr.WorkspaceID != id {
-		writeError(w, http.StatusNotFound, "repo not found")
-		return
-	}
-
-	enqueued := true
-	if _, eerr := s.Deps.Jobs.Enqueue(r.Context(), jobs.EnqueueRequest{
-		Type:      workspacejobs.TypeCloneRepo,
-		DedupeKey: "clone:" + wr.ID,
-		Payload:   workspacejobs.ClonePayload{RepoID: wr.ID},
-	}); eerr != nil {
-		if errors.Is(eerr, jobs.ErrDuplicate) {
-			enqueued = false
-		} else {
-			writeError(w, http.StatusInternalServerError, "could not enqueue reindex")
-			return
-		}
-	}
-
-	status := "enqueued"
-	if !enqueued {
-		status = "already_running"
-	}
-	writeJSON(w, http.StatusAccepted, map[string]any{
-		"status": status,
-		"repo":   workspaceRepoToPayload(wr),
-	})
-}
-
-// buildWebhookURL constructs the publicly-reachable webhook delivery URL
-// for a workspace_repo. When PublicBaseURL is empty (no operator-set
-// origin), returns only the path so the dashboard can render it with a
-// helper note.
-func (s *Server) buildWebhookURL(repoID string) string {
-	path := "/api/v1/webhooks/github/" + repoID
-	base := strings.TrimRight(s.Deps.PublicBaseURL, "/")
-	if base == "" {
-		return path
-	}
-	return base + path
-}
-
-// LinkExistingProject — POST /api/v1/workspaces/{id}/repos/link.
-//
-// Attaches an already-indexed project to the workspace as a lightweight
-// linked row. No clone, no index job, no webhook. The response mirrors
-// AddWorkspaceRepo's shape so the dashboard can reuse the same refresh
-// pattern; webhook_url + webhook_secret are empty because linked rows
-// have no webhook to register.
-func (s *Server) LinkExistingProject(w http.ResponseWriter, r *http.Request, id string) {
-	if s.workspaceReposUnavailable(w) {
-		return
-	}
-	if !s.requireWorkspace(w, r, id) {
-		return
-	}
-	var body openapi.LinkExistingProjectRequest
-	if err := json.NewDecoder(r.Body).Decode(&body); err != nil {
-		writeError(w, http.StatusUnprocessableEntity, "invalid JSON body")
-		return
-	}
-	hash := strings.TrimSpace(body.ProjectHash)
-	if hash == "" {
-		writeError(w, http.StatusUnprocessableEntity, "project_hash is required")
-		return
-	}
-
-	// Resolve the project by hash so we can validate status + extract
-	// host_path. The same lookup is used by /projects/{path} so the
-	// behaviour is consistent — 404 for unknown hashes, 422 for known
-	// but not-yet-indexed projects.
-	proj, perr := projects.GetByHash(r.Context(), s.Deps.DB, hash)
-	if perr != nil {
-		if errors.Is(perr, projects.ErrNotFound) {
-			writeError(w, http.StatusNotFound, "project not found")
-			return
-		}
-		writeError(w, http.StatusInternalServerError, "could not load project")
-		return
-	}
-	if proj.Status != "indexed" {
-		writeError(w, http.StatusUnprocessableEntity,
-			"project is not yet indexed (status="+proj.Status+") — wait for indexing to complete before linking")
-		return
-	}
-
-	wr, err := s.Deps.WorkspaceRepos.CreateLink(r.Context(), id, proj.HostPath)
-	if err != nil {
-		switch {
-		case errors.Is(err, workspacerepos.ErrInvalidURL):
-			writeError(w, http.StatusUnprocessableEntity,
-				"project host_path is not a github.com/owner/repo@branch — local-path projects cannot be linked")
-		case errors.Is(err, workspacerepos.ErrBranchEmpty):
-			writeError(w, http.StatusUnprocessableEntity, "project host_path has no branch suffix")
-		case errors.Is(err, workspacerepos.ErrDuplicate):
-			writeError(w, http.StatusConflict, "this repo+branch is already attached to the workspace")
-		default:
-			writeError(w, http.StatusInternalServerError, "could not link project")
-		}
-		return
-	}
-
-	// Mirror AddWorkspaceRepo's envelope so the dashboard can decode one
-	// shape regardless of which create path it called. Linked rows have
-	// no webhook, so URL/secret are empty.
-	writeJSON(w, http.StatusCreated, map[string]any{
-		"repo":            workspaceRepoToPayload(wr),
-		"webhook_url":     "",
-		"webhook_secret":  "",
-		"auto_registered": false,
-	})
-}
diff --git a/server/internal/httpapi/workspacerepos_test.go b/server/internal/httpapi/workspacerepos_test.go
deleted file mode 100644
index cf137ee..0000000
--- a/server/internal/httpapi/workspacerepos_test.go
+++ /dev/null
@@ -1,558 +0,0 @@
-package httpapi
-
-import (
-	"context"
-	"database/sql"
-	"encoding/json"
-	"net/http"
-	"testing"
-	"time"
-
-	"github.com/dvcdsys/code-index/server/internal/githubtokens"
-	"github.com/dvcdsys/code-index/server/internal/jobs"
-	"github.com/dvcdsys/code-index/server/internal/projects"
-	"github.com/dvcdsys/code-index/server/internal/secrets"
-	"github.com/dvcdsys/code-index/server/internal/workspacerepos"
-	"github.com/dvcdsys/code-index/server/internal/workspaces"
-)
-
-// reposRouter spins up a router with the full workspaces+repos surface
-// wired against an in-memory DB. Auth is disabled — the focus here is
-// the persistence + enqueue paths.
-//
-// We deliberately do NOT start the jobs worker pool: we only assert the
-// job row landed in the right state. End-to-end clone+index runs against
-// real git remotes and the embeddings sidecar — out of scope for unit
-// tests.
-func reposRouter(t *testing.T) (http.Handler, *jobs.Service) {
-	t.Helper()
-	d, err := dbOpenMemory(t)
-	if err != nil {
-		t.Fatalf("open db: %v", err)
-	}
-
-	t.Setenv("CIX_SECRET_KEY", "")
-	t.Setenv("CIX_SECRET_KEYFILE", "")
-	sec, err := secrets.Open(secrets.OpenOptions{DataDir: t.TempDir(), AllowGenerate: true})
-	if err != nil {
-		t.Fatalf("open secrets: %v", err)
-	}
-	wsSvc := workspaces.New(d)
-	ghSvc := githubtokens.New(d, sec)
-	wrSvc := workspacerepos.New(d)
-	jobsSvc := jobs.New(d, jobs.Options{Concurrency: 1, PollEvery: time.Hour}) // never poll in tests
-
-	router := NewRouter(Deps{
-		DB:                d,
-		ServerVersion:     "test",
-		APIVersion:        "v1",
-		Backend:           "go",
-		AuthDisabled:      true,
-		Users:             seedlessUsers(d),
-		Sessions:          seedlessSessions(d),
-		APIKeys:           seedlessAPIKeys(d),
-		WorkspacesEnabled: true,
-		Workspaces:        wsSvc,
-		GithubTokens:      ghSvc,
-		WorkspaceRepos:    wrSvc,
-		Jobs:              jobsSvc,
-		PublicBaseURL:     "https://cix.example.test",
-	})
-	return router, jobsSvc
-}
-
-func createWS(t *testing.T, router http.Handler, name string) string {
-	t.Helper()
-	rr := doJSON(t, router, http.MethodPost, "/api/v1/workspaces", map[string]any{
-		"name": name,
-	})
-	if rr.Code != http.StatusCreated {
-		t.Fatalf("create workspace: %d (%s)", rr.Code, rr.Body.String())
-	}
-	var got workspacePayload
-	_ = json.Unmarshal(rr.Body.Bytes(), &got)
-	return got.ID
-}
-
-func TestRepos_AddEnqueuesCloneJob(t *testing.T) {
-	router, jobsSvc := reposRouter(t)
-	wsID := createWS(t, router, "platform")
-
-	rr := doJSON(t, router, http.MethodPost, "/api/v1/workspaces/"+wsID+"/repos", map[string]any{
-		"github_url": "https://github.com/spf13/cobra",
-		"branch":     "main",
-	})
-	if rr.Code != http.StatusCreated {
-		t.Fatalf("add repo: %d (%s)", rr.Code, rr.Body.String())
-	}
-	var resp struct {
-		Repo          workspaceRepoPayload `json:"repo"`
-		WebhookURL    string               `json:"webhook_url"`
-		WebhookSecret string               `json:"webhook_secret"`
-	}
-	if err := json.Unmarshal(rr.Body.Bytes(), &resp); err != nil {
-		t.Fatalf("decode: %v", err)
-	}
-	if resp.Repo.ProjectPath != "github.com/spf13/cobra@main" {
-		t.Fatalf("unexpected project_path %q", resp.Repo.ProjectPath)
-	}
-	if resp.Repo.Status != workspacerepos.StatusPending {
-		t.Fatalf("expected status=pending, got %q", resp.Repo.Status)
-	}
-	if resp.WebhookSecret == "" {
-		t.Fatalf("webhook secret should be present in response")
-	}
-	if resp.WebhookURL != "https://cix.example.test/api/v1/webhooks/github/"+resp.Repo.ID {
-		t.Fatalf("webhook URL wrong: %q", resp.WebhookURL)
-	}
-
-	// Verify the job landed on the queue.
-	jobList, err := jobsSvc.List(context.Background(), jobs.StatusPending, "clone_repo", 10)
-	if err != nil {
-		t.Fatalf("jobs list: %v", err)
-	}
-	if len(jobList) != 1 {
-		t.Fatalf("expected 1 pending clone_repo job, got %d", len(jobList))
-	}
-	if jobList[0].DedupeKey != "clone:"+resp.Repo.ID {
-		t.Fatalf("unexpected dedupe_key %q", jobList[0].DedupeKey)
-	}
-}
-
-func TestRepos_DuplicateRejected(t *testing.T) {
-	router, _ := reposRouter(t)
-	wsID := createWS(t, router, "platform")
-	body := map[string]any{
-		"github_url": "https://github.com/a/b",
-		"branch":     "main",
-	}
-	rr := doJSON(t, router, http.MethodPost, "/api/v1/workspaces/"+wsID+"/repos", body)
-	if rr.Code != http.StatusCreated {
-		t.Fatalf("first add: %d", rr.Code)
-	}
-	rr = doJSON(t, router, http.MethodPost, "/api/v1/workspaces/"+wsID+"/repos", body)
-	if rr.Code != http.StatusConflict {
-		t.Fatalf("duplicate should 409, got %d", rr.Code)
-	}
-}
-
-// TestRepos_WebhookModeStored covers the three-state webhook_mode
-// introduced for the add-repo UI. The DB column should round-trip the
-// chosen mode; the legacy auto_webhook bool is derived (true iff
-// mode == "auto") so old API clients keep behaving the same.
-func TestRepos_WebhookModeStored(t *testing.T) {
-	router, _ := reposRouter(t)
-	wsID := createWS(t, router, "platform")
-
-	cases := []struct {
-		name         string
-		body         map[string]any
-		wantMode     string
-		wantAutoBool bool
-	}{
-		{
-			name:         "manual explicit",
-			body:         map[string]any{"github_url": "https://github.com/a/manual", "branch": "main", "webhook_mode": "manual"},
-			wantMode:     "manual",
-			wantAutoBool: false,
-		},
-		{
-			name:         "auto explicit",
-			body:         map[string]any{"github_url": "https://github.com/a/auto", "branch": "main", "webhook_mode": "auto"},
-			wantMode:     "auto",
-			wantAutoBool: true,
-		},
-		{
-			name:         "disabled explicit",
-			body:         map[string]any{"github_url": "https://github.com/a/disabled", "branch": "main", "webhook_mode": "disabled"},
-			wantMode:     "disabled",
-			wantAutoBool: false,
-		},
-		{
-			name:         "legacy auto_webhook bool",
-			body:         map[string]any{"github_url": "https://github.com/a/legacy", "branch": "main", "auto_webhook": true},
-			wantMode:     "auto",
-			wantAutoBool: true,
-		},
-		{
-			name:         "default when omitted",
-			body:         map[string]any{"github_url": "https://github.com/a/default", "branch": "main"},
-			wantMode:     "manual",
-			wantAutoBool: false,
-		},
-	}
-	for _, tc := range cases {
-		t.Run(tc.name, func(t *testing.T) {
-			rr := doJSON(t, router, http.MethodPost, "/api/v1/workspaces/"+wsID+"/repos", tc.body)
-			if rr.Code != http.StatusCreated {
-				t.Fatalf("add: %d (%s)", rr.Code, rr.Body.String())
-			}
-			var resp struct {
-				Repo workspaceRepoPayload `json:"repo"`
-			}
-			_ = json.Unmarshal(rr.Body.Bytes(), &resp)
-			if resp.Repo.WebhookMode != tc.wantMode {
-				t.Fatalf("webhook_mode = %q, want %q", resp.Repo.WebhookMode, tc.wantMode)
-			}
-			if resp.Repo.AutoWebhook != tc.wantAutoBool {
-				t.Fatalf("auto_webhook = %v, want %v (for mode=%q)",
-					resp.Repo.AutoWebhook, tc.wantAutoBool, tc.wantMode)
-			}
-		})
-	}
-}
-
-// TestRepos_WebhookModeRejectsUnknown ensures the DB never receives an
-// unknown enum value — the dashboard's three radio buttons are the only
-// supported inputs.
-func TestRepos_WebhookModeRejectsUnknown(t *testing.T) {
-	router, _ := reposRouter(t)
-	wsID := createWS(t, router, "platform")
-	rr := doJSON(t, router, http.MethodPost, "/api/v1/workspaces/"+wsID+"/repos", map[string]any{
-		"github_url":   "https://github.com/a/b",
-		"branch":       "main",
-		"webhook_mode": "totally-bogus",
-	})
-	if rr.Code != http.StatusUnprocessableEntity {
-		t.Fatalf("expected 422 on unknown mode, got %d", rr.Code)
-	}
-}
-
-func TestRepos_BadURLRejected(t *testing.T) {
-	router, _ := reposRouter(t)
-	wsID := createWS(t, router, "platform")
-	rr := doJSON(t, router, http.MethodPost, "/api/v1/workspaces/"+wsID+"/repos", map[string]any{
-		"github_url": "https://gitlab.com/x/y",
-		"branch":     "main",
-	})
-	if rr.Code != http.StatusUnprocessableEntity {
-		t.Fatalf("expected 422 for non-github URL, got %d", rr.Code)
-	}
-}
-
-func TestRepos_DeleteCrossWorkspaceForbidden(t *testing.T) {
-	router, _ := reposRouter(t)
-	wsA := createWS(t, router, "alpha")
-	wsB := createWS(t, router, "bravo")
-
-	rr := doJSON(t, router, http.MethodPost, "/api/v1/workspaces/"+wsA+"/repos", map[string]any{
-		"github_url": "https://github.com/x/y",
-		"branch":     "main",
-	})
-	if rr.Code != http.StatusCreated {
-		t.Fatalf("add: %d", rr.Code)
-	}
-	var resp struct {
-		Repo workspaceRepoPayload `json:"repo"`
-	}
-	_ = json.Unmarshal(rr.Body.Bytes(), &resp)
-
-	// Try to delete repo from workspace B — must 404 (don't leak existence).
-	rr = doJSON(t, router, http.MethodDelete, "/api/v1/workspaces/"+wsB+"/repos/"+resp.Repo.ID, nil)
-	if rr.Code != http.StatusNotFound {
-		t.Fatalf("cross-workspace delete should 404, got %d", rr.Code)
-	}
-
-	// Correct workspace should succeed.
-	rr = doJSON(t, router, http.MethodDelete, "/api/v1/workspaces/"+wsA+"/repos/"+resp.Repo.ID, nil)
-	if rr.Code != http.StatusNoContent {
-		t.Fatalf("delete: %d", rr.Code)
-	}
-}
-
-func TestRepos_ReindexDedupeCollapsesInFlightJob(t *testing.T) {
-	router, jobsSvc := reposRouter(t)
-	wsID := createWS(t, router, "platform")
-
-	rr := doJSON(t, router, http.MethodPost, "/api/v1/workspaces/"+wsID+"/repos", map[string]any{
-		"github_url": "https://github.com/foo/bar",
-		"branch":     "main",
-	})
-	var created struct {
-		Repo workspaceRepoPayload `json:"repo"`
-	}
-	_ = json.Unmarshal(rr.Body.Bytes(), &created)
-
-	// Add-time already enqueued a clone_repo job — reindex should be
-	// dedup'd and return status="already_running".
-	rr = doJSON(t, router, http.MethodPost, "/api/v1/workspaces/"+wsID+"/repos/"+created.Repo.ID+"/reindex", nil)
-	if rr.Code != http.StatusAccepted {
-		t.Fatalf("reindex: %d (%s)", rr.Code, rr.Body.String())
-	}
-	var rresp struct {
-		Status string `json:"status"`
-	}
-	_ = json.Unmarshal(rr.Body.Bytes(), &rresp)
-	if rresp.Status != "already_running" {
-		t.Fatalf("expected already_running on dedupe, got %q", rresp.Status)
-	}
-
-	// Exactly one job on the queue still.
-	all, _ := jobsSvc.List(context.Background(), jobs.StatusPending, "clone_repo", 10)
-	if len(all) != 1 {
-		t.Fatalf("expected dedupe to collapse into 1 job, got %d", len(all))
-	}
-}
-
-func TestRepos_DisabledFeatureReturns503(t *testing.T) {
-	router := workspaceRouter(t, false)
-	rr := doJSON(t, router, http.MethodGet, "/api/v1/workspaces/any/repos", nil)
-	if rr.Code != http.StatusServiceUnavailable {
-		t.Fatalf("expected 503, got %d", rr.Code)
-	}
-}
-
-func TestJobs_ListEndpointFiltersByStatus(t *testing.T) {
-	router, jobsSvc := reposRouter(t)
-	ctx := context.Background()
-	if _, err := jobsSvc.Enqueue(ctx, jobs.EnqueueRequest{Type: "test_a"}); err != nil {
-		t.Fatalf("enqueue: %v", err)
-	}
-	if _, err := jobsSvc.Enqueue(ctx, jobs.EnqueueRequest{Type: "test_b"}); err != nil {
-		t.Fatalf("enqueue: %v", err)
-	}
-	rr := doJSON(t, router, http.MethodGet, "/api/v1/jobs", nil)
-	if rr.Code != http.StatusOK {
-		t.Fatalf("jobs list: %d", rr.Code)
-	}
-	var lr struct {
-		Jobs  []jobPayload `json:"jobs"`
-		Total int          `json:"total"`
-	}
-	_ = json.Unmarshal(rr.Body.Bytes(), &lr)
-	if lr.Total != 2 {
-		t.Fatalf("expected 2 jobs, got %d", lr.Total)
-	}
-	rr = doJSON(t, router, http.MethodGet, "/api/v1/jobs?type=test_a", nil)
-	if rr.Code != http.StatusOK {
-		t.Fatalf("typed list: %d", rr.Code)
-	}
-	_ = json.Unmarshal(rr.Body.Bytes(), &lr)
-	if lr.Total != 1 {
-		t.Fatalf("expected 1 typed job, got %d", lr.Total)
-	}
-}
-
-// reposRouterWithDB is the same router setup as reposRouter but also
-// returns the underlying *sql.DB so link-existing tests can seed
-// projects directly. We keep reposRouter signature unchanged so the
-// existing call sites in webhooks_test.go and elsewhere stay green.
-func reposRouterWithDB(t *testing.T) (http.Handler, *jobs.Service, *sql.DB) {
-	t.Helper()
-	d, err := dbOpenMemory(t)
-	if err != nil {
-		t.Fatalf("open db: %v", err)
-	}
-	t.Setenv("CIX_SECRET_KEY", "")
-	t.Setenv("CIX_SECRET_KEYFILE", "")
-	sec, err := secrets.Open(secrets.OpenOptions{DataDir: t.TempDir(), AllowGenerate: true})
-	if err != nil {
-		t.Fatalf("open secrets: %v", err)
-	}
-	wsSvc := workspaces.New(d)
-	ghSvc := githubtokens.New(d, sec)
-	wrSvc := workspacerepos.New(d)
-	jobsSvc := jobs.New(d, jobs.Options{Concurrency: 1, PollEvery: time.Hour})
-
-	router := NewRouter(Deps{
-		DB:                d,
-		ServerVersion:     "test",
-		APIVersion:        "v1",
-		Backend:           "go",
-		AuthDisabled:      true,
-		Users:             seedlessUsers(d),
-		Sessions:          seedlessSessions(d),
-		APIKeys:           seedlessAPIKeys(d),
-		WorkspacesEnabled: true,
-		Workspaces:        wsSvc,
-		GithubTokens:      ghSvc,
-		WorkspaceRepos:    wrSvc,
-		Jobs:              jobsSvc,
-		PublicBaseURL:     "https://cix.example.test",
-	})
-	return router, jobsSvc, d
-}
-
-// seedIndexedProject creates an indexed project row with the given
-// host_path and returns its path_hash. Used by the link-existing tests
-// so they don't need to invoke the real cloner+indexer.
-func seedIndexedProject(t *testing.T, db *sql.DB, hostPath string) string {
-	t.Helper()
-	if _, err := projects.Create(context.Background(), db, projects.CreateRequest{HostPath: hostPath}); err != nil {
-		t.Fatalf("seed project: %v", err)
-	}
-	if _, err := db.Exec(
-		`UPDATE projects SET status = 'indexed', last_indexed_at = ?, updated_at = ? WHERE host_path = ?`,
-		time.Now().UTC().Format(time.RFC3339Nano),
-		time.Now().UTC().Format(time.RFC3339Nano),
-		hostPath,
-	); err != nil {
-		t.Fatalf("mark indexed: %v", err)
-	}
-	return projects.HashPath(hostPath)
-}
-
-func TestLinkExistingProject_SkipsCloneJob(t *testing.T) {
-	router, jobsSvc, d := reposRouterWithDB(t)
-	wsID := createWS(t, router, "platform")
-	hash := seedIndexedProject(t, d, "github.com/spf13/cobra@main")
-
-	rr := doJSON(t, router, http.MethodPost,
-		"/api/v1/workspaces/"+wsID+"/repos/link",
-		map[string]any{"project_hash": hash})
-	if rr.Code != http.StatusCreated {
-		t.Fatalf("link: %d (%s)", rr.Code, rr.Body.String())
-	}
-	var resp struct {
-		Repo           workspaceRepoPayload `json:"repo"`
-		WebhookURL     string               `json:"webhook_url"`
-		WebhookSecret  string               `json:"webhook_secret"`
-		AutoRegistered bool                 `json:"auto_registered"`
-	}
-	if err := json.Unmarshal(rr.Body.Bytes(), &resp); err != nil {
-		t.Fatalf("decode: %v", err)
-	}
-	if !resp.Repo.IsLinked {
-		t.Fatalf("expected IsLinked=true, got %+v", resp.Repo)
-	}
-	if resp.Repo.Status != workspacerepos.StatusIndexed {
-		t.Fatalf("expected status=indexed, got %q", resp.Repo.Status)
-	}
-	if resp.Repo.WebhookMode != workspacerepos.WebhookModeDisabled {
-		t.Fatalf("expected webhook_mode=disabled, got %q", resp.Repo.WebhookMode)
-	}
-	if resp.WebhookURL != "" || resp.WebhookSecret != "" {
-		t.Fatalf("linked rows must not surface webhook info, got url=%q secret-len=%d",
-			resp.WebhookURL, len(resp.WebhookSecret))
-	}
-
-	// Critical: no clone_repo job should have been enqueued.
-	jobList, err := jobsSvc.List(context.Background(), jobs.StatusPending, "clone_repo", 10)
-	if err != nil {
-		t.Fatalf("jobs list: %v", err)
-	}
-	if len(jobList) != 0 {
-		t.Fatalf("expected 0 clone_repo jobs, got %d (linked rows must not clone)", len(jobList))
-	}
-}
-
-func TestLinkExistingProject_409OnDuplicate(t *testing.T) {
-	router, _, d := reposRouterWithDB(t)
-	wsID := createWS(t, router, "platform")
-	hash := seedIndexedProject(t, d, "github.com/foo/bar@main")
-
-	rr := doJSON(t, router, http.MethodPost,
-		"/api/v1/workspaces/"+wsID+"/repos/link",
-		map[string]any{"project_hash": hash})
-	if rr.Code != http.StatusCreated {
-		t.Fatalf("first link: %d (%s)", rr.Code, rr.Body.String())
-	}
-	rr = doJSON(t, router, http.MethodPost,
-		"/api/v1/workspaces/"+wsID+"/repos/link",
-		map[string]any{"project_hash": hash})
-	if rr.Code != http.StatusConflict {
-		t.Fatalf("expected 409 on duplicate link, got %d (%s)", rr.Code, rr.Body.String())
-	}
-}
-
-func TestLinkExistingProject_422IfProjectNotIndexed(t *testing.T) {
-	router, _, d := reposRouterWithDB(t)
-	wsID := createWS(t, router, "platform")
-	// Create the project but leave status=created (the default).
-	hostPath := "github.com/foo/bar@main"
-	if _, err := projects.Create(context.Background(), d,
-		projects.CreateRequest{HostPath: hostPath}); err != nil {
-		t.Fatalf("seed project: %v", err)
-	}
-	rr := doJSON(t, router, http.MethodPost,
-		"/api/v1/workspaces/"+wsID+"/repos/link",
-		map[string]any{"project_hash": projects.HashPath(hostPath)})
-	if rr.Code != http.StatusUnprocessableEntity {
-		t.Fatalf("expected 422, got %d (%s)", rr.Code, rr.Body.String())
-	}
-}
-
-func TestLinkExistingProject_404OnUnknownHash(t *testing.T) {
-	router, _ := reposRouter(t)
-	wsID := createWS(t, router, "platform")
-	rr := doJSON(t, router, http.MethodPost,
-		"/api/v1/workspaces/"+wsID+"/repos/link",
-		map[string]any{"project_hash": "0000000000000000"})
-	if rr.Code != http.StatusNotFound {
-		t.Fatalf("expected 404 for unknown project_hash, got %d (%s)", rr.Code, rr.Body.String())
-	}
-}
-
-func TestListProjectWorkspaces_ReturnsAllMemberships(t *testing.T) {
-	router, _, d := reposRouterWithDB(t)
-	hash := seedIndexedProject(t, d, "github.com/foo/bar@main")
-	wsA := createWS(t, router, "alpha")
-	wsB := createWS(t, router, "beta")
-
-	for _, ws := range []string{wsA, wsB} {
-		rr := doJSON(t, router, http.MethodPost,
-			"/api/v1/workspaces/"+ws+"/repos/link",
-			map[string]any{"project_hash": hash})
-		if rr.Code != http.StatusCreated {
-			t.Fatalf("link to %s: %d (%s)", ws, rr.Code, rr.Body.String())
-		}
-	}
-
-	rr := doJSON(t, router, http.MethodGet,
-		"/api/v1/projects/"+hash+"/workspaces", nil)
-	if rr.Code != http.StatusOK {
-		t.Fatalf("list workspaces: %d (%s)", rr.Code, rr.Body.String())
-	}
-	var resp struct {
-		Workspaces []struct {
-			WorkspaceID   string `json:"workspace_id"`
-			WorkspaceName string `json:"workspace_name"`
-			RepoID        string `json:"repo_id"`
-			IsLinked      bool   `json:"is_linked"`
-			Status        string `json:"status"`
-		} `json:"workspaces"`
-	}
-	if err := json.Unmarshal(rr.Body.Bytes(), &resp); err != nil {
-		t.Fatalf("decode: %v", err)
-	}
-	if len(resp.Workspaces) != 2 {
-		t.Fatalf("expected 2 memberships, got %d (%+v)", len(resp.Workspaces), resp.Workspaces)
-	}
-	for _, m := range resp.Workspaces {
-		if !m.IsLinked {
-			t.Fatalf("workspace %s membership should be linked", m.WorkspaceName)
-		}
-		if m.Status != workspacerepos.StatusIndexed {
-			t.Fatalf("status should be indexed, got %q", m.Status)
-		}
-	}
-}
-
-func TestListProjectWorkspaces_EmptyWhenUnused(t *testing.T) {
-	router, _, d := reposRouterWithDB(t)
-	hash := seedIndexedProject(t, d, "github.com/lonely/project@main")
-
-	rr := doJSON(t, router, http.MethodGet,
-		"/api/v1/projects/"+hash+"/workspaces", nil)
-	if rr.Code != http.StatusOK {
-		t.Fatalf("list workspaces: %d (%s)", rr.Code, rr.Body.String())
-	}
-	var resp struct {
-		Workspaces []any `json:"workspaces"`
-	}
-	if err := json.Unmarshal(rr.Body.Bytes(), &resp); err != nil {
-		t.Fatalf("decode: %v", err)
-	}
-	if len(resp.Workspaces) != 0 {
-		t.Fatalf("expected empty list, got %d", len(resp.Workspaces))
-	}
-}
-
-func TestListProjectWorkspaces_404OnUnknownHash(t *testing.T) {
-	router, _ := reposRouter(t)
-	rr := doJSON(t, router, http.MethodGet,
-		"/api/v1/projects/0000000000000000/workspaces", nil)
-	if rr.Code != http.StatusNotFound {
-		t.Fatalf("expected 404, got %d (%s)", rr.Code, rr.Body.String())
-	}
-}
diff --git a/server/internal/httpapi/workspacesearch.go b/server/internal/httpapi/workspacesearch.go
index 9a2518a..b5175c5 100644
--- a/server/internal/httpapi/workspacesearch.go
+++ b/server/internal/httpapi/workspacesearch.go
@@ -14,7 +14,6 @@ import (
 
 	"github.com/dvcdsys/code-index/server/internal/chunksfts"
 	"github.com/dvcdsys/code-index/server/internal/httpapi/openapi"
-	"github.com/dvcdsys/code-index/server/internal/workspacerepos"
 	"github.com/dvcdsys/code-index/server/internal/workspaces"
 )
 
@@ -137,7 +136,7 @@ type projectHits struct {
 // project threshold those repos drop out, restoring the cross-project
 // signal the user needs to scope an agent's follow-up search.
 func (s *Server) WorkspaceSearch(w http.ResponseWriter, r *http.Request, id string, params openapi.WorkspaceSearchParams) {
-	if s.workspaceReposUnavailable(w) {
+	if s.workspaceProjectsUnavailable(w) {
 		return
 	}
 	if s.Deps.VectorStore == nil || s.Deps.EmbeddingSvc == nil {
@@ -177,12 +176,39 @@ func (s *Server) WorkspaceSearch(w http.ResponseWriter, r *http.Request, id stri
 		return
 	}
 
-	repos, err := s.Deps.WorkspaceRepos.ListByWorkspace(r.Context(), id)
+	// Pull the workspace's project memberships joined with the projects
+	// table so we can split into indexed vs pending in one pass. The
+	// junction lives in workspace_projects; status lives on projects.
+	rows, err := s.Deps.DB.QueryContext(r.Context(), `
+		SELECT p.host_path, p.status
+		  FROM workspace_projects wp
+		  JOIN projects p ON p.host_path = wp.project_path
+		 WHERE wp.workspace_id = ?
+		 ORDER BY wp.added_at DESC`, id)
 	if err != nil {
-		writeError(w, http.StatusInternalServerError, "could not load workspace repos: "+err.Error())
+		writeError(w, http.StatusInternalServerError, "could not load workspace projects: "+err.Error())
 		return
 	}
-	if len(repos) == 0 {
+	type memberRow struct {
+		ProjectPath string
+		Status      string
+	}
+	var members []memberRow
+	for rows.Next() {
+		var m memberRow
+		if scanErr := rows.Scan(&m.ProjectPath, &m.Status); scanErr != nil {
+			rows.Close()
+			writeError(w, http.StatusInternalServerError, "scan workspace project row: "+scanErr.Error())
+			return
+		}
+		members = append(members, m)
+	}
+	rows.Close()
+	if err := rows.Err(); err != nil {
+		writeError(w, http.StatusInternalServerError, "iterate workspace projects: "+err.Error())
+		return
+	}
+	if len(members) == 0 {
 		writeJSON(w, http.StatusOK, workspaceSearchResponse(
 			"empty",
 			[]workspaceSearchProjectPayload{},
@@ -194,22 +220,22 @@ func (s *Server) WorkspaceSearch(w http.ResponseWriter, r *http.Request, id stri
 		return
 	}
 
-	seenProjects := make(map[string]struct{}, len(repos))
-	projectPaths := make([]string, 0, len(repos))
+	seenProjects := make(map[string]struct{}, len(members))
+	projectPaths := make([]string, 0, len(members))
 	pendingRepos := make([]workspaceSearchPendingRepoPayload, 0)
-	for _, rp := range repos {
-		if rp.Status != workspacerepos.StatusIndexed {
+	for _, m := range members {
+		if m.Status != "indexed" {
 			pendingRepos = append(pendingRepos, workspaceSearchPendingRepoPayload{
-				ProjectPath: rp.ProjectPath,
-				Status:      rp.Status,
+				ProjectPath: m.ProjectPath,
+				Status:      m.Status,
 			})
 			continue
 		}
-		if _, ok := seenProjects[rp.ProjectPath]; ok {
+		if _, ok := seenProjects[m.ProjectPath]; ok {
 			continue
 		}
-		seenProjects[rp.ProjectPath] = struct{}{}
-		projectPaths = append(projectPaths, rp.ProjectPath)
+		seenProjects[m.ProjectPath] = struct{}{}
+		projectPaths = append(projectPaths, m.ProjectPath)
 	}
 
 	if len(projectPaths) == 0 {
diff --git a/server/internal/httpapi/workspacesearch_test.go b/server/internal/httpapi/workspacesearch_test.go
index 4c74160..621de13 100644
--- a/server/internal/httpapi/workspacesearch_test.go
+++ b/server/internal/httpapi/workspacesearch_test.go
@@ -15,10 +15,12 @@ import (
 
 	"github.com/dvcdsys/code-index/server/internal/chunksfts"
 	"github.com/dvcdsys/code-index/server/internal/githubtokens"
+	"github.com/dvcdsys/code-index/server/internal/gitrepos"
 	"github.com/dvcdsys/code-index/server/internal/jobs"
+	"github.com/dvcdsys/code-index/server/internal/projects"
 	"github.com/dvcdsys/code-index/server/internal/secrets"
 	"github.com/dvcdsys/code-index/server/internal/vectorstore"
-	"github.com/dvcdsys/code-index/server/internal/workspacerepos"
+	"github.com/dvcdsys/code-index/server/internal/workspaceprojects"
 	"github.com/dvcdsys/code-index/server/internal/workspaces"
 )
 
@@ -36,8 +38,9 @@ func (e fixedEmbedder) EmbedQuery(_ context.Context, _ string) ([]float32, error
 func (e fixedEmbedder) Ready(_ context.Context) error { return nil }
 
 // newSearchRouter wires the minimum surface workspace search needs:
-// workspaces, workspace_repos, jobs (unused but in Deps), vectorstore
-// (real, on tmpdir), and a query embedder the caller controls.
+// workspaces, git_repos, workspace_projects, jobs (unused but in Deps),
+// vectorstore (real, on tmpdir), and a query embedder the caller
+// controls.
 func newSearchRouter(t *testing.T, d *sql.DB, vs *vectorstore.Store, emb fixedEmbedder) http.Handler {
 	t.Helper()
 	t.Setenv("CIX_SECRET_KEY", "")
@@ -55,18 +58,19 @@ func newSearchRouter(t *testing.T, d *sql.DB, vs *vectorstore.Store, emb fixedEm
 		WorkspacesEnabled: true,
 		Workspaces:        workspaces.New(d),
 		GithubTokens:      githubtokens.New(d, sec),
-		WorkspaceRepos:    workspacerepos.New(d),
+		GitRepos:          gitrepos.New(d),
+		WorkspaceProjects: workspaceprojects.New(d),
 		Jobs:              jobs.New(d, jobs.Options{Concurrency: 1, PollEvery: time.Hour}),
 		VectorStore:       vs,
 		EmbeddingSvc:      emb,
 	})
 }
 
-// seedRepoWithChunks inserts a projects + workspace_repos row for the
-// given project_path inside the workspace, then upserts the supplied
-// chunks into chromem so /search has something to retrieve. Bypasses
-// the clone+index job chain — those are exercised in workspacerepos
-// tests already.
+// seedRepoWithChunks inserts a projects row + workspace_projects
+// membership for the given project_path inside the workspace, then
+// upserts the supplied chunks into chromem so /search has something to
+// retrieve. Bypasses the clone+index job chain — those are exercised
+// in gitrepos tests already.
 func seedRepoWithChunks(
 	t *testing.T,
 	d *sql.DB,
@@ -79,19 +83,19 @@ func seedRepoWithChunks(
 	now := time.Now().UTC().Format(time.RFC3339Nano)
 	if _, err := d.Exec(
 		`INSERT INTO projects (host_path, container_path, languages, settings, stats, status, created_at, updated_at, path_hash)
-		 VALUES (?, ?, '[]', '{}', '{}', 'created', ?, ?, 'h')`,
-		projectPath, projectPath, now, now,
+		 VALUES (?, ?, '[]', '{}', '{}', 'indexed', ?, ?, ?)`,
+		projectPath, projectPath, now, now, projects.HashPath(projectPath),
 	); err != nil {
 		t.Fatalf("insert project %q: %v", projectPath, err)
 	}
 	if _, err := d.Exec(
-		`INSERT INTO workspace_repos
-		 (id, workspace_id, github_url, branch, project_path, webhook_secret, status, created_at, updated_at, last_indexed_at)
-		 VALUES (?, ?, ?, 'main', ?, 'sec', 'indexed', ?, ?, ?)`,
-		uuid.NewString(), wsID, "https://"+projectPath, projectPath, now, now, now,
+		`INSERT INTO workspace_projects (workspace_id, project_path, added_at)
+		 VALUES (?, ?, ?)`,
+		wsID, projectPath, now,
 	); err != nil {
-		t.Fatalf("insert workspace_repo %q: %v", projectPath, err)
+		t.Fatalf("insert workspace_project %q: %v", projectPath, err)
 	}
+	_ = uuid.NewString() // keep import in case future tests need it
 	if err := vs.UpsertChunks(context.Background(), projectPath, chunks, embeddings); err != nil {
 		t.Fatalf("upsert chunks for %q: %v", projectPath, err)
 	}
@@ -505,20 +509,19 @@ func TestWorkspaceSearch_FlagsStaleFTSRepos(t *testing.T) {
 	now := time.Now().UTC().Format(time.RFC3339Nano)
 	stalePath := "github.com/o/stale@main"
 	if _, err := d.Exec(
-		`INSERT INTO projects (host_path, container_path, languages, settings, stats, status, created_at, updated_at, path_hash)
-		 VALUES (?, ?, '[]', '{}', '{}', 'created', ?, ?, 'h')`,
-		stalePath, stalePath, now, now,
+		`INSERT INTO projects (host_path, container_path, languages, settings, stats, status, created_at, updated_at, last_indexed_at, path_hash)
+		 VALUES (?, ?, '[]', '{}', '{}', 'indexed', ?, ?, ?, ?)`,
+		stalePath, stalePath, now, now, now, projects.HashPath(stalePath),
 	); err != nil {
 		t.Fatalf("insert stale project: %v", err)
 	}
 	if _, err := d.Exec(
-		`INSERT INTO workspace_repos
-		 (id, workspace_id, github_url, branch, project_path, webhook_secret, status, created_at, updated_at, last_indexed_at)
-		 VALUES (?, ?, ?, 'main', ?, 'sec', 'indexed', ?, ?, ?)`,
-		uuid.NewString(), wsID, "https://"+stalePath, stalePath, now, now, now,
+		`INSERT INTO workspace_projects (workspace_id, project_path, added_at)
+		 VALUES (?, ?, ?)`, wsID, stalePath, now,
 	); err != nil {
-		t.Fatalf("insert stale workspace_repo: %v", err)
+		t.Fatalf("insert stale workspace_projects: %v", err)
 	}
+	_ = uuid.NewString()
 	if err := vs.UpsertChunks(context.Background(), stalePath,
 		[]vectorstore.Chunk{{Content: "stale chunk", FilePath: "s.go", StartLine: 1, EndLine: 9, Language: "go"}},
 		[][]float32{l2([]float32{0.9, 0.1, 0.0, 0.0})},
@@ -766,28 +769,36 @@ func TestWorkspaceSearch_Disabled(t *testing.T) {
 	}
 }
 
-// seedPendingRepo inserts a workspace_repos row with a non-`indexed`
-// status (no projects row, no chromem collection). Mirrors what the
-// DB looks like while clone/index jobs are still in flight.
+// seedPendingRepo inserts a projects row with a non-`indexed` status
+// AND a workspace_projects membership row. Mirrors what the DB looks
+// like while clone/index jobs are still in flight (project registered,
+// workspace_projects already attached, status not yet 'indexed').
 func seedPendingRepo(t *testing.T, d *sql.DB, wsID, projectPath, status string) {
 	t.Helper()
 	now := time.Now().UTC().Format(time.RFC3339Nano)
 	if _, err := d.Exec(
-		`INSERT INTO workspace_repos
-		 (id, workspace_id, github_url, branch, project_path, webhook_secret, status, created_at, updated_at)
-		 VALUES (?, ?, ?, 'main', ?, 'sec', ?, ?, ?)`,
-		uuid.NewString(), wsID, "https://"+projectPath, projectPath, status, now, now,
+		`INSERT INTO projects (
+			host_path, container_path, languages, settings, stats,
+			status, created_at, updated_at, path_hash
+		) VALUES (?, ?, '[]', '{}', '{}', ?, ?, ?, 'h')`,
+		projectPath, projectPath, status, now, now,
+	); err != nil {
+		t.Fatalf("insert pending project %q: %v", projectPath, err)
+	}
+	if _, err := d.Exec(
+		`INSERT INTO workspace_projects (workspace_id, project_path, added_at)
+		 VALUES (?, ?, ?)`, wsID, projectPath, now,
 	); err != nil {
-		t.Fatalf("insert pending workspace_repo %q: %v", projectPath, err)
+		t.Fatalf("insert workspace_projects %q: %v", projectPath, err)
 	}
+	_ = uuid.NewString()
 }
 
-// TestWorkspaceSearch_SurfacesPendingRepos verifies that repos whose
-// workspace_repos.status ≠ 'indexed' are reported back in
-// `pending_repos` instead of being silently dropped. The dashboard
-// uses this to render a "still indexing" banner — without it the
-// operator sees a partial result set with no hint that anything's
-// missing.
+// TestWorkspaceSearch_SurfacesPendingRepos verifies that projects whose
+// projects.status ≠ 'indexed' are reported back in `pending_repos`
+// instead of being silently dropped. The dashboard uses this to render
+// a "still indexing" banner — without it the operator sees a partial
+// result set with no hint that anything's missing.
 func TestWorkspaceSearch_SurfacesPendingRepos(t *testing.T) {
 	d, err := dbOpenMemory(t)
 	if err != nil {
@@ -808,8 +819,8 @@ func TestWorkspaceSearch_SurfacesPendingRepos(t *testing.T) {
 
 	// Two repos still in flight — different statuses to make sure
 	// every non-indexed value propagates verbatim.
-	seedPendingRepo(t, d, wsID, "github.com/o/cloning@main", workspacerepos.StatusCloning)
-	seedPendingRepo(t, d, wsID, "github.com/o/indexing@main", workspacerepos.StatusIndexing)
+	seedPendingRepo(t, d, wsID, "github.com/o/cloning@main", "cloning")
+	seedPendingRepo(t, d, wsID, "github.com/o/indexing@main", "indexing")
 
 	rr := doJSON(t, router, http.MethodGet, "/api/v1/workspaces/"+wsID+"/search?q=x", nil)
 	if rr.Code != http.StatusOK {
@@ -831,10 +842,10 @@ func TestWorkspaceSearch_SurfacesPendingRepos(t *testing.T) {
 	for _, p := range resp.PendingRepos {
 		gotStatuses[p.ProjectPath] = p.Status
 	}
-	if gotStatuses["github.com/o/cloning@main"] != workspacerepos.StatusCloning {
+	if gotStatuses["github.com/o/cloning@main"] != "cloning" {
 		t.Fatalf("cloning repo lost its status: %+v", resp.PendingRepos)
 	}
-	if gotStatuses["github.com/o/indexing@main"] != workspacerepos.StatusIndexing {
+	if gotStatuses["github.com/o/indexing@main"] != "indexing" {
 		t.Fatalf("indexing repo lost its status: %+v", resp.PendingRepos)
 	}
 }
@@ -853,8 +864,8 @@ func TestWorkspaceSearch_AllPendingReturnsEmpty(t *testing.T) {
 	router := newSearchRouter(t, d, vs, fixedEmbedder{q: l2([]float32{1, 0, 0, 0})})
 	wsID := createWS(t, router, "all-pending")
 
-	seedPendingRepo(t, d, wsID, "github.com/o/p1@main", workspacerepos.StatusPending)
-	seedPendingRepo(t, d, wsID, "github.com/o/p2@main", workspacerepos.StatusCloning)
+	seedPendingRepo(t, d, wsID, "github.com/o/p1@main", "pending")
+	seedPendingRepo(t, d, wsID, "github.com/o/p2@main", "cloning")
 
 	rr := doJSON(t, router, http.MethodGet, "/api/v1/workspaces/"+wsID+"/search?q=x", nil)
 	if rr.Code != http.StatusOK {
diff --git a/server/internal/repocloner/repocloner.go b/server/internal/repocloner/repocloner.go
index fef0bea..d8286c0 100644
--- a/server/internal/repocloner/repocloner.go
+++ b/server/internal/repocloner/repocloner.go
@@ -11,7 +11,7 @@
 //   - Fetch + reset to remote HEAD on subsequent runs
 //   - Report the current HEAD SHA (for last_sha bookkeeping)
 //   - Resolve a "github.com/owner/repo" + branch to a deterministic local
-//     directory under DataDir/repos/{repo_id}/
+//     directory under DataDir/repos/{path_hash}/
 //
 // Errors are deliberately coarse — the worker pool surfaces them in the
 // job row and the dashboard renders them verbatim. There's no point
@@ -62,8 +62,8 @@ type Result struct {
 // after the operation completes.
 //
 // The caller is responsible for choosing a LocalDir that won't collide
-// across repos — typically `<DataDir>/repos/<repo_id>/` keyed by the
-// workspace_repos row id (NOT the github URL, which can change with
+// across repos — typically `<DataDir>/repos/<path_hash>/` keyed by
+// projects.path_hash (NOT the github URL, which can change with
 // rename + redirect).
 func CloneOrFetch(ctx context.Context, opts CloneOptions) (Result, error) {
 	if strings.TrimSpace(opts.GitHubURL) == "" {
diff --git a/server/internal/workspacejobs/workspacejobs.go b/server/internal/workspacejobs/workspacejobs.go
index 7b7f2e2..8f2ab95 100644
--- a/server/internal/workspacejobs/workspacejobs.go
+++ b/server/internal/workspacejobs/workspacejobs.go
@@ -1,29 +1,27 @@
-// Package workspacejobs wires the workspaces feature's job handlers into
-// the generic internal/jobs queue. It owns nothing — just composes the
-// other workspaces packages (workspacerepos, githubtokens, repocloner,
-// repoindexer) behind a thin Register function called from main.
+// Package workspacejobs wires the workspaces feature's job handlers
+// into the generic internal/jobs queue. It owns nothing — just
+// composes gitrepos, githubtokens, repocloner, and repoindexer behind
+// a thin Register function called from main.
 //
-// Lifecycle for a repo:
+// Lifecycle for an external project:
 //
-//	1. POST /api/v1/workspaces/{id}/repos
-//	   - inserts a workspace_repos row (status=pending)
-//	   - enqueues clone_repo  job  (dedupe_key="clone:<repo_id>")
+//	1. POST /api/v1/git-repos
+//	   - inserts a projects row (status='pending') and a git_repos row
+//	   - enqueues clone_repo job (dedupe_key="clone:<path_hash>")
 //
 //	2. clone_repo handler
 //	   - reveals PAT via githubtokens.Reveal (if token_id set)
-//	   - calls repocloner.CloneOrFetch into DataDir/repos/<repo_id>/
-//	   - registers projects row (host_path = workspace_repos.project_path)
-//	   - flips status → indexing
-//	   - enqueues index_repo job (dedupe_key="index:<repo_id>")
+//	   - calls repocloner.CloneOrFetch into DataDir/repos/<path_hash>/
+//	   - flips projects.status → indexing
+//	   - enqueues index_repo job (dedupe_key="index:<path_hash>")
 //
 //	3. index_repo handler
-//	   - calls repoindexer.IndexDir with the workspace_repo.project_path
-//	   - flips status → indexed (or failed on error)
+//	   - calls repoindexer.IndexDir with the project_path
+//	   - flips projects.status → indexed (or 'error' on failure)
+//	   - writes last_indexed_at on the projects row
 //
-// Workspace-level search is served straight from the per-project
-// chromem collections via a weighted fan-out (see
-// internal/httpapi/workspacesearch.go) — there is no background
-// "build centroid index" step anymore.
+// Workspace-level search is served from per-project chromem
+// collections via a weighted fan-out (internal/httpapi/workspacesearch.go).
 package workspacejobs
 
 import (
@@ -33,52 +31,51 @@ import (
 	"errors"
 	"fmt"
 	"log/slog"
+	"strings"
 	"time"
 
 	"github.com/dvcdsys/code-index/server/internal/githubtokens"
+	"github.com/dvcdsys/code-index/server/internal/gitrepos"
 	"github.com/dvcdsys/code-index/server/internal/indexer"
 	"github.com/dvcdsys/code-index/server/internal/jobs"
 	"github.com/dvcdsys/code-index/server/internal/projects"
 	"github.com/dvcdsys/code-index/server/internal/repocloner"
 	"github.com/dvcdsys/code-index/server/internal/repoindexer"
 	"github.com/dvcdsys/code-index/server/internal/vectorstore"
-	"github.com/dvcdsys/code-index/server/internal/workspacerepos"
 )
 
-// Job type constants. Kept here so handlers and enqueue-sites share one
-// string — typos in job types are a notoriously easy source of "why isn't
-// this running?" bugs.
+// Job type constants.
 const (
 	TypeCloneRepo = "clone_repo"
 	TypeIndexRepo = "index_repo"
 )
 
-// ClonePayload is the JSON shape stored on a clone_repo job.
+// ClonePayload is the JSON shape stored on a clone_repo job. The
+// project_path doubles as the lookup key for the matching git_repos
+// row; path_hash is derived via db.HashHostPath when needed (e.g. as
+// the on-disk clone directory name).
 type ClonePayload struct {
-	RepoID string `json:"repo_id"`
+	ProjectPath string `json:"project_path"`
 }
 
-// IndexPayload is the JSON shape stored on an index_repo job.
+// IndexPayload mirrors ClonePayload.
 type IndexPayload struct {
-	RepoID string `json:"repo_id"`
+	ProjectPath string `json:"project_path"`
 }
 
-// Deps bundles everything the handlers need. Keeping it explicit makes
-// wiring obvious in main and means tests can swap any single piece for a
-// fake.
+// Deps bundles everything the handlers need.
 type Deps struct {
-	DB             *sql.DB
-	Jobs           *jobs.Service
-	WorkspaceRepos *workspacerepos.Service
-	GithubTokens   *githubtokens.Service
-	Indexer        *indexer.Service
-	VectorStore    *vectorstore.Store
-	DataDir        string // root for cloned repos: <DataDir>/repos/<id>/
-	Logger         *slog.Logger
+	DB           *sql.DB
+	Jobs         *jobs.Service
+	GitRepos     *gitrepos.Service
+	GithubTokens *githubtokens.Service
+	Indexer      *indexer.Service
+	VectorStore  *vectorstore.Store
+	DataDir      string // root for cloned repos: <DataDir>/repos/<path_hash>/
+	Logger       *slog.Logger
 }
 
-// Register hooks the workspaces job handlers into a jobs.Service. Call
-// once at startup, BEFORE jobs.Start.
+// Register hooks the workspaces job handlers into a jobs.Service.
 func Register(d Deps) {
 	if d.Logger == nil {
 		d.Logger = slog.Default()
@@ -93,11 +90,11 @@ func Register(d Deps) {
 
 // EnqueueClone inserts a clone_repo job. The index_repo job is chained
 // on successful clone — callers don't enqueue it directly.
-func EnqueueClone(ctx context.Context, j *jobs.Service, repoID string) error {
+func EnqueueClone(ctx context.Context, j *jobs.Service, projectPath string) error {
 	_, err := j.Enqueue(ctx, jobs.EnqueueRequest{
 		Type:      TypeCloneRepo,
-		DedupeKey: "clone:" + repoID,
-		Payload:   ClonePayload{RepoID: repoID},
+		DedupeKey: "clone:" + projects.HashPath(projectPath),
+		Payload:   ClonePayload{ProjectPath: projectPath},
 	})
 	if errors.Is(err, jobs.ErrDuplicate) {
 		// Already queued — soft no-op.
@@ -111,68 +108,65 @@ func handleClone(ctx context.Context, d Deps, job jobs.Job) error {
 	if err := jobs.UnmarshalPayload(job, &p); err != nil {
 		return fmt.Errorf("decode payload: %w", err)
 	}
-	if p.RepoID == "" {
-		return errors.New("empty repo_id")
+	if p.ProjectPath == "" {
+		return errors.New("empty project_path")
 	}
-	wr, err := d.WorkspaceRepos.GetByID(ctx, p.RepoID)
+	g, err := d.GitRepos.GetByPath(ctx, p.ProjectPath)
 	if err != nil {
-		return fmt.Errorf("load workspace_repo: %w", err)
+		return fmt.Errorf("load git_repo for %s: %w", p.ProjectPath, err)
 	}
+	hash := projects.HashPath(g.ProjectPath)
 
-	if err := d.WorkspaceRepos.SetStatus(ctx, wr.ID, workspacerepos.StatusCloning, "", "", nil); err != nil {
+	if err := setProjectStatus(ctx, d.DB, g.ProjectPath, "cloning"); err != nil {
 		return fmt.Errorf("mark cloning: %w", err)
 	}
 
 	pat := ""
-	if wr.TokenID != "" {
-		token, terr := d.GithubTokens.Reveal(ctx, wr.TokenID)
+	if g.TokenID != "" {
+		token, terr := d.GithubTokens.Reveal(ctx, g.TokenID)
 		if terr != nil {
-			d.recordFailure(ctx, wr.ID, fmt.Errorf("reveal token: %w", terr))
+			d.recordFailure(ctx, g, fmt.Errorf("reveal token: %w", terr))
 			return terr
 		}
 		pat = token
-		// Best-effort last_used bookkeeping; ignore errors.
-		_ = d.GithubTokens.Touch(ctx, wr.TokenID)
+		// Best-effort intent signal: rebind `pat` to a zero-filled string
+		// on function exit. Go strings are immutable, so this does NOT
+		// wipe the underlying bytes — the original allocation from
+		// Reveal/Decrypt may still be reachable from escape-analyzed
+		// copies (e.g. inside repocloner's HTTP basic-auth header). The
+		// gesture matters for readability + intent (PAT is sensitive,
+		// don't hold it longer than needed), not as a security control.
+		// Switching PAT to []byte with explicit wipe via crypto/subtle
+		// would be overkill for this code path.
+		defer func() { pat = strings.Repeat("\x00", len(pat)) }()
+		_ = d.GithubTokens.Touch(ctx, g.TokenID)
 	}
 
 	result, err := repocloner.CloneOrFetch(ctx, repocloner.CloneOptions{
-		GitHubURL: wr.GitHubURL,
-		Branch:    wr.Branch,
+		GitHubURL: g.GitHubURL,
+		Branch:    g.Branch,
 		PAT:       pat,
-		LocalDir:  repocloner.LocalDirFor(d.DataDir, wr.ID),
+		LocalDir:  repocloner.LocalDirFor(d.DataDir, hash),
 	})
 	if err != nil {
-		d.recordFailure(ctx, wr.ID, fmt.Errorf("clone: %w", err))
+		d.recordFailure(ctx, g, fmt.Errorf("clone: %w", err))
 		return err
 	}
 
-	// Register the project row (idempotent — Get-or-Create pattern). Two
-	// branches:
-	//   a) project already exists → leave it alone (incremental updates
-	//      happen via subsequent index runs)
-	//   b) project missing → create it with the project_path as host_path
-	if _, gerr := projects.Get(ctx, d.DB, wr.ProjectPath); gerr != nil {
-		if _, cerr := projects.Create(ctx, d.DB, projects.CreateRequest{
-			HostPath: wr.ProjectPath,
-		}); cerr != nil && !errors.Is(cerr, projects.ErrConflict) {
-			d.recordFailure(ctx, wr.ID, fmt.Errorf("register project: %w", cerr))
-			return cerr
-		}
+	if err := d.GitRepos.SetClone(ctx, g.ProjectPath, result.HeadSHA, ""); err != nil {
+		d.Logger.Warn("workspacejobs: set last_sha failed", "project", g.ProjectPath, "err", err)
 	}
 
-	if err := d.WorkspaceRepos.SetStatus(ctx, wr.ID, workspacerepos.StatusIndexing, result.HeadSHA, "", nil); err != nil {
-		// Non-fatal — still chain the index job.
-		d.Logger.Warn("workspacejobs: set status indexing failed", "repo_id", wr.ID, "err", err)
+	if err := setProjectStatus(ctx, d.DB, g.ProjectPath, "indexing"); err != nil {
+		d.Logger.Warn("workspacejobs: set status indexing failed", "project", g.ProjectPath, "err", err)
 	}
 
-	// Chain index_repo. Use the same dedupe pattern so a manual reindex
-	// fired by the user mid-clone collapses into the natural follow-up.
 	if _, eerr := d.Jobs.Enqueue(ctx, jobs.EnqueueRequest{
 		Type:      TypeIndexRepo,
-		DedupeKey: "index:" + wr.ID,
-		Payload:   IndexPayload{RepoID: wr.ID},
+		DedupeKey: "index:" + hash,
+		Payload:   IndexPayload{ProjectPath: g.ProjectPath},
 	}); eerr != nil && !errors.Is(eerr, jobs.ErrDuplicate) {
-		d.recordFailure(ctx, wr.ID, fmt.Errorf("enqueue index: %w", eerr))
+		d.recordFailure(ctx, g, fmt.Errorf("enqueue index: %w", eerr))
 		return eerr
 	}
 	return nil
@@ -183,47 +177,57 @@ func handleIndex(ctx context.Context, d Deps, job jobs.Job) error {
 	if err := jobs.UnmarshalPayload(job, &p); err != nil {
 		return fmt.Errorf("decode payload: %w", err)
 	}
-	if p.RepoID == "" {
-		return errors.New("empty repo_id")
+	if p.ProjectPath == "" {
+		return errors.New("empty project_path")
 	}
-	wr, err := d.WorkspaceRepos.GetByID(ctx, p.RepoID)
+	g, err := d.GitRepos.GetByPath(ctx, p.ProjectPath)
 	if err != nil {
-		return fmt.Errorf("load workspace_repo: %w", err)
+		return fmt.Errorf("load git_repo for %s: %w", p.ProjectPath, err)
 	}
-	cloneDir := repocloner.LocalDirFor(d.DataDir, wr.ID)
+	cloneDir := repocloner.LocalDirFor(d.DataDir, projects.HashPath(g.ProjectPath))
 
-	_, _, err = repoindexer.IndexDir(ctx, d.Indexer, wr.ProjectPath, cloneDir, repoindexer.DefaultFilter(), d.Logger)
+	_, _, err = repoindexer.IndexDir(ctx, d.Indexer, g.ProjectPath, cloneDir, repoindexer.DefaultFilter(), d.Logger)
 	if err != nil {
-		d.recordFailure(ctx, wr.ID, fmt.Errorf("index: %w", err))
+		d.recordFailure(ctx, g, fmt.Errorf("index: %w", err))
 		return err
 	}
 
-	now := time.Now().UTC()
-	if err := d.WorkspaceRepos.SetStatus(ctx, wr.ID, workspacerepos.StatusIndexed, "", "", &now); err != nil {
+	now := time.Now().UTC().Format(time.RFC3339Nano)
+	if _, err := d.DB.ExecContext(ctx,
+		`UPDATE projects SET status = 'indexed', last_indexed_at = ?, updated_at = ? WHERE host_path = ?`,
+		now, now, g.ProjectPath,
+	); err != nil {
 		return fmt.Errorf("mark indexed: %w", err)
 	}
 	return nil
 }
 
-// recordFailure flips the workspace_repo into status=failed with the
-// error message attached. Logs the error too (handler return value also
-// gets logged by the jobs service but at a different layer — duplicate
-// is fine).
-func (d Deps) recordFailure(ctx context.Context, repoID string, err error) {
+func setProjectStatus(ctx context.Context, db *sql.DB, projectPath, status string) error {
+	now := time.Now().UTC().Format(time.RFC3339Nano)
+	_, err := db.ExecContext(ctx,
+		`UPDATE projects SET status = ?, updated_at = ? WHERE host_path = ?`,
+		status, now, projectPath)
+	return err
+}
+
+func (d Deps) recordFailure(ctx context.Context, g gitrepos.GitRepo, err error) {
 	if err == nil {
 		return
 	}
-	d.Logger.Error("workspacejobs: repo failed", "repo_id", repoID, "err", err)
+	d.Logger.Error("workspacejobs: repo failed", "project", g.ProjectPath, "err", err)
 	msg := err.Error()
 	if len(msg) > 1024 {
 		msg = msg[:1024]
 	}
-	if uerr := d.WorkspaceRepos.SetStatus(ctx, repoID, workspacerepos.StatusFailed, "", msg, nil); uerr != nil {
-		d.Logger.Error("workspacejobs: could not write failed status", "repo_id", repoID, "err", uerr)
+	if uerr := d.GitRepos.SetClone(ctx, g.ProjectPath, "", msg); uerr != nil {
+		d.Logger.Error("workspacejobs: could not write last_error", "project", g.ProjectPath, "err", uerr)
+	}
+	if uerr := setProjectStatus(ctx, d.DB, g.ProjectPath, "error"); uerr != nil {
+		d.Logger.Error("workspacejobs: could not write status=error", "project", g.ProjectPath, "err", uerr)
 	}
 }
 
-// Compile-time guard: ClonePayload / IndexPayload encode cleanly.
+// Compile-time guard: payloads encode cleanly.
 var _ = func() (any, any) {
 	a, _ := json.Marshal(ClonePayload{})
 	b, _ := json.Marshal(IndexPayload{})
diff --git a/server/internal/workspaceprojects/workspaceprojects.go b/server/internal/workspaceprojects/workspaceprojects.go
new file mode 100644
index 0000000..95e7823
--- /dev/null
+++ b/server/internal/workspaceprojects/workspaceprojects.go
@@ -0,0 +1,191 @@
+// Package workspaceprojects is the service layer for the
+// workspace_projects junction table — the many-to-many mapping between
+// workspaces and projects. A row exists when a project is currently a
+// member of a workspace; Link adds one, Unlink removes one. The project
+// itself is unaffected by either operation (deletion happens through
+// the projects service, which cascades here via FK ON DELETE CASCADE).
+//
+// This is the only place in the codebase that knows how workspace
+// membership is represented. The gitrepos service knows about clone
+// metadata; the projects service knows about indexed content; this
+// service knows about "which workspace holds which project".
+package workspaceprojects
+
+import (
+	"context"
+	"database/sql"
+	"errors"
+	"fmt"
+	"strings"
+	"time"
+)
+
+// Errors.
+var (
+	ErrNotFound           = errors.New("workspace project membership not found")
+	ErrDuplicate          = errors.New("project is already linked to this workspace")
+	ErrProjectNotIndexed  = errors.New("project is not yet indexed — wait for indexing before linking")
+	ErrProjectMissing     = errors.New("project does not exist")
+	ErrWorkspaceMissing   = errors.New("workspace does not exist")
+)
+
+// Membership is the wire-friendly row shape.
+type Membership struct {
+	WorkspaceID string
+	ProjectPath string
+	AddedAt     time.Time
+}
+
+// Service wraps the workspace_projects table.
+type Service struct {
+	DB *sql.DB
+}
+
+func New(db *sql.DB) *Service { return &Service{DB: db} }
+
+// Link inserts (workspace_id, project_path) into workspace_projects.
+// The project must exist and be in status='indexed' so workspace search
+// has something to fan out to. Duplicates return ErrDuplicate; missing
+// targets return ErrWorkspaceMissing / ErrProjectMissing.
+//
+// Implementation: a single INSERT…SELECT WHERE EXISTS does the precondition
+// check and the write in one statement, eliminating the TOCTOU window
+// between separate SELECTs and the INSERT. If the insert produces 0 rows,
+// preconditions failed — diagnoseLinkFailure runs one SELECT with three
+// COUNT subqueries to map "0 rows" → a precise typed error for the API.
+func (s *Service) Link(ctx context.Context, workspaceID, projectPath string) (Membership, error) {
+	now := time.Now().UTC().Format(time.RFC3339Nano)
+	res, err := s.DB.ExecContext(ctx, `
+		INSERT INTO workspace_projects (workspace_id, project_path, added_at)
+		SELECT ?, ?, ?
+		 WHERE EXISTS (SELECT 1 FROM workspaces WHERE id = ?)
+		   AND EXISTS (SELECT 1 FROM projects   WHERE host_path = ? AND status = 'indexed')`,
+		workspaceID, projectPath, now, workspaceID, projectPath,
+	)
+	if err != nil {
+		if isUniqueConstraintViolation(err) {
+			return Membership{}, ErrDuplicate
+		}
+		return Membership{}, fmt.Errorf("insert workspace_project: %w", err)
+	}
+	n, _ := res.RowsAffected()
+	if n == 1 {
+		addedAt, _ := time.Parse(time.RFC3339Nano, now)
+		return Membership{
+			WorkspaceID: workspaceID,
+			ProjectPath: projectPath,
+			AddedAt:     addedAt,
+		}, nil
+	}
+	return Membership{}, s.diagnoseLinkFailure(ctx, workspaceID, projectPath)
+}
+
+// diagnoseLinkFailure runs after a 0-row INSERT to map the failure to a
+// typed error. One round-trip with three COUNT subqueries; cheaper than
+// separate queries and the values are mutually independent so subquery
+// ordering doesn't matter.
+//
+// TOCTOU edge case: if state flipped to "all preconditions met" between
+// the failed INSERT and this query (rare — would need a concurrent index
+// completing or a workspace being created in that window), all three
+// counts come back non-zero. We return a generic transient error so the
+// caller can retry — better than fabricating a misleading typed error.
+func (s *Service) diagnoseLinkFailure(ctx context.Context, workspaceID, projectPath string) error {
+	var wsExists, projExists, projIndexed int
+	if err := s.DB.QueryRowContext(ctx, `
+		SELECT
+		    (SELECT COUNT(*) FROM workspaces WHERE id = ?),
+		    (SELECT COUNT(*) FROM projects   WHERE host_path = ?),
+		    (SELECT COUNT(*) FROM projects   WHERE host_path = ? AND status = 'indexed')`,
+		workspaceID, projectPath, projectPath,
+	).Scan(&wsExists, &projExists, &projIndexed); err != nil {
+		return fmt.Errorf("diagnose link failure: %w", err)
+	}
+	switch {
+	case wsExists == 0:
+		return ErrWorkspaceMissing
+	case projExists == 0:
+		return ErrProjectMissing
+	case projIndexed == 0:
+		return ErrProjectNotIndexed
+	default:
+		return fmt.Errorf("link failed with no precondition violation (concurrent state change); retry")
+	}
+}
+
+// Unlink removes a (workspace_id, project_path) row. Returns ErrNotFound
+// when no such row exists so the handler can distinguish "deleted" from
+// "wasn't there" — both can become 204 in the API but tests need the
+// signal.
+func (s *Service) Unlink(ctx context.Context, workspaceID, projectPath string) error {
+	res, err := s.DB.ExecContext(ctx, `
+		DELETE FROM workspace_projects
+		 WHERE workspace_id = ? AND project_path = ?`,
+		workspaceID, projectPath)
+	if err != nil {
+		return fmt.Errorf("delete workspace_project: %w", err)
+	}
+	n, _ := res.RowsAffected()
+	if n == 0 {
+		return ErrNotFound
+	}
+	return nil
+}
+
+// ListByWorkspace returns every project_path attached to a workspace,
+// newest membership first.
+func (s *Service) ListByWorkspace(ctx context.Context, workspaceID string) ([]Membership, error) {
+	rows, err := s.DB.QueryContext(ctx, `
+		SELECT workspace_id, project_path, added_at
+		  FROM workspace_projects
+		 WHERE workspace_id = ?
+		 ORDER BY added_at DESC`, workspaceID)
+	if err != nil {
+		return nil, fmt.Errorf("list workspace_projects by workspace: %w", err)
+	}
+	defer rows.Close()
+	return scanRows(rows)
+}
+
+// ListByProject returns every workspace this project participates in.
+// Used by the project detail page to render "Workspaces" chips.
+func (s *Service) ListByProject(ctx context.Context, projectPath string) ([]Membership, error) {
+	rows, err := s.DB.QueryContext(ctx, `
+		SELECT wp.workspace_id, wp.project_path, wp.added_at
+		  FROM workspace_projects wp
+		 WHERE wp.project_path = ?
+		 ORDER BY wp.added_at DESC`, projectPath)
+	if err != nil {
+		return nil, fmt.Errorf("list workspace_projects by project: %w", err)
+	}
+	defer rows.Close()
+	return scanRows(rows)
+}
+
+// --- helpers ---
+
+func scanRows(rows *sql.Rows) ([]Membership, error) {
+	out := []Membership{}
+	for rows.Next() {
+		var (
+			m         Membership
+			addedAt   string
+		)
+		if err := rows.Scan(&m.WorkspaceID, &m.ProjectPath, &addedAt); err != nil {
+			return nil, fmt.Errorf("scan workspace_project: %w", err)
+		}
+		m.AddedAt, _ = time.Parse(time.RFC3339Nano, addedAt)
+		out = append(out, m)
+	}
+	return out, rows.Err()
+}
+
+func isUniqueConstraintViolation(err error) bool {
+	if err == nil {
+		return false
+	}
+	msg := err.Error()
+	return strings.Contains(msg, "UNIQUE constraint failed") ||
+		strings.Contains(msg, "constraint failed: UNIQUE") ||
+		strings.Contains(msg, "constraint failed: PRIMARY KEY")
+}
diff --git a/server/internal/workspaceprojects/workspaceprojects_test.go b/server/internal/workspaceprojects/workspaceprojects_test.go
new file mode 100644
index 0000000..b1053f4
--- /dev/null
+++ b/server/internal/workspaceprojects/workspaceprojects_test.go
@@ -0,0 +1,307 @@
+package workspaceprojects
+
+import (
+	"context"
+	"database/sql"
+	"errors"
+	"sync"
+	"testing"
+	"time"
+
+	"github.com/dvcdsys/code-index/server/internal/db"
+	"github.com/dvcdsys/code-index/server/internal/workspaces"
+)
+
+func mustOpen(t *testing.T) (*sql.DB, *Service) {
+	t.Helper()
+	d, err := db.Open(":memory:")
+	if err != nil {
+		t.Fatalf("open: %v", err)
+	}
+	t.Cleanup(func() { _ = d.Close() })
+	return d, New(d)
+}
+
+// seedIndexedProject inserts the project row in status='indexed' so
+// Link() satisfies its precondition. Avoids the full projects service
+// import to keep the test focused on this package.
+func seedIndexedProject(t *testing.T, d *sql.DB, hostPath string) {
+	t.Helper()
+	now := time.Now().UTC().Format(time.RFC3339Nano)
+	if _, err := d.Exec(`
+		INSERT INTO projects (
+			host_path, container_path, languages, settings, stats,
+			status, created_at, updated_at, path_hash
+		) VALUES (?, ?, '[]', '{}', '{}', 'indexed', ?, ?, ?)`,
+		hostPath, hostPath, now, now, db.HashHostPath(hostPath),
+	); err != nil {
+		t.Fatalf("seed project %s: %v", hostPath, err)
+	}
+}
+
+func seedWorkspace(t *testing.T, d *sql.DB, name string) string {
+	t.Helper()
+	ws, err := workspaces.New(d).Create(context.Background(), name, "")
+	if err != nil {
+		t.Fatalf("seed workspace %s: %v", name, err)
+	}
+	return ws.ID
+}
+
+func TestLink_HappyPath(t *testing.T) {
+	d, svc := mustOpen(t)
+	ctx := context.Background()
+	wsID := seedWorkspace(t, d, "platform")
+	seedIndexedProject(t, d, "github.com/x/y@main")
+
+	m, err := svc.Link(ctx, wsID, "github.com/x/y@main")
+	if err != nil {
+		t.Fatalf("Link: %v", err)
+	}
+	if m.WorkspaceID != wsID || m.ProjectPath != "github.com/x/y@main" {
+		t.Fatalf("Link returned wrong row: %+v", m)
+	}
+	if m.AddedAt.IsZero() {
+		t.Error("AddedAt was not populated")
+	}
+}
+
+func TestLink_DuplicateRejected(t *testing.T) {
+	d, svc := mustOpen(t)
+	ctx := context.Background()
+	wsID := seedWorkspace(t, d, "platform")
+	seedIndexedProject(t, d, "github.com/x/y@main")
+
+	if _, err := svc.Link(ctx, wsID, "github.com/x/y@main"); err != nil {
+		t.Fatalf("first Link: %v", err)
+	}
+	if _, err := svc.Link(ctx, wsID, "github.com/x/y@main"); !errors.Is(err, ErrDuplicate) {
+		t.Fatalf("second Link: got %v, want ErrDuplicate", err)
+	}
+}
+
+func TestLink_RejectsNonIndexed(t *testing.T) {
+	d, svc := mustOpen(t)
+	ctx := context.Background()
+	wsID := seedWorkspace(t, d, "platform")
+	// Seed without forcing status=indexed — default is 'pending'.
+	now := time.Now().UTC().Format(time.RFC3339Nano)
+	if _, err := d.Exec(`
+		INSERT INTO projects (
+			host_path, container_path, languages, settings, stats,
+			status, created_at, updated_at, path_hash
+		) VALUES (?, ?, '[]', '{}', '{}', 'pending', ?, ?, ?)`,
+		"github.com/x/y@main", "github.com/x/y@main", now, now,
+		db.HashHostPath("github.com/x/y@main"),
+	); err != nil {
+		t.Fatalf("seed pending project: %v", err)
+	}
+
+	if _, err := svc.Link(ctx, wsID, "github.com/x/y@main"); !errors.Is(err, ErrProjectNotIndexed) {
+		t.Fatalf("got %v, want ErrProjectNotIndexed", err)
+	}
+}
+
+func TestLink_RejectsMissingTargets(t *testing.T) {
+	d, svc := mustOpen(t)
+	ctx := context.Background()
+
+	// Unknown workspace.
+	if _, err := svc.Link(ctx, "no-such-ws", "github.com/x/y@main"); !errors.Is(err, ErrWorkspaceMissing) {
+		t.Fatalf("missing workspace: got %v, want ErrWorkspaceMissing", err)
+	}
+
+	wsID := seedWorkspace(t, d, "platform")
+	// Workspace exists but project doesn't.
+	if _, err := svc.Link(ctx, wsID, "github.com/missing/proj@main"); !errors.Is(err, ErrProjectMissing) {
+		t.Fatalf("missing project: got %v, want ErrProjectMissing", err)
+	}
+}
+
+func TestUnlink(t *testing.T) {
+	d, svc := mustOpen(t)
+	ctx := context.Background()
+	wsID := seedWorkspace(t, d, "platform")
+	seedIndexedProject(t, d, "github.com/x/y@main")
+	if _, err := svc.Link(ctx, wsID, "github.com/x/y@main"); err != nil {
+		t.Fatalf("Link: %v", err)
+	}
+
+	if err := svc.Unlink(ctx, wsID, "github.com/x/y@main"); err != nil {
+		t.Fatalf("Unlink: %v", err)
+	}
+	if err := svc.Unlink(ctx, wsID, "github.com/x/y@main"); !errors.Is(err, ErrNotFound) {
+		t.Fatalf("second Unlink: got %v, want ErrNotFound", err)
+	}
+}
+
+// TestListByWorkspace exercises the "newest first" ordering — the
+// dashboard uses this to show the most recently linked project at the
+// top of the workspace detail page.
+func TestListByWorkspace(t *testing.T) {
+	d, svc := mustOpen(t)
+	ctx := context.Background()
+	wsID := seedWorkspace(t, d, "platform")
+	seedIndexedProject(t, d, "github.com/a/older@main")
+	seedIndexedProject(t, d, "github.com/b/newer@main")
+
+	// Link older first, sleep enough for distinct ISO seconds, link newer.
+	if _, err := svc.Link(ctx, wsID, "github.com/a/older@main"); err != nil {
+		t.Fatalf("first Link: %v", err)
+	}
+	time.Sleep(2 * time.Millisecond)
+	if _, err := svc.Link(ctx, wsID, "github.com/b/newer@main"); err != nil {
+		t.Fatalf("second Link: %v", err)
+	}
+
+	list, err := svc.ListByWorkspace(ctx, wsID)
+	if err != nil {
+		t.Fatalf("ListByWorkspace: %v", err)
+	}
+	if len(list) != 2 {
+		t.Fatalf("expected 2 memberships, got %d", len(list))
+	}
+	if list[0].ProjectPath != "github.com/b/newer@main" {
+		t.Errorf("newest-first ordering broken: %+v", list)
+	}
+}
+
+// TestListByProject covers the reverse lookup — which workspaces
+// contain a given project. Used by the project detail page chips.
+func TestListByProject(t *testing.T) {
+	d, svc := mustOpen(t)
+	ctx := context.Background()
+	wsA := seedWorkspace(t, d, "alpha")
+	wsB := seedWorkspace(t, d, "beta")
+	seedIndexedProject(t, d, "github.com/x/y@main")
+
+	for _, ws := range []string{wsA, wsB} {
+		if _, err := svc.Link(ctx, ws, "github.com/x/y@main"); err != nil {
+			t.Fatalf("Link %s: %v", ws, err)
+		}
+	}
+	list, err := svc.ListByProject(ctx, "github.com/x/y@main")
+	if err != nil {
+		t.Fatalf("ListByProject: %v", err)
+	}
+	if len(list) != 2 {
+		t.Fatalf("expected 2 memberships, got %d", len(list))
+	}
+}
+
+// TestLink_ConcurrentDistinctWorkspaces — two goroutines link the same
+// indexed project to TWO different workspaces in parallel. Both inserts
+// hit different primary-key tuples, so the expected outcome is 2 ✓ Link
+// returns / 0 spurious errors. Acceptance criterion for Fix #6
+// (one-statement atomic precondition + insert).
+func TestLink_ConcurrentDistinctWorkspaces(t *testing.T) {
+	d, svc := mustOpen(t)
+	ctx := context.Background()
+	wsA := seedWorkspace(t, d, "alpha")
+	wsB := seedWorkspace(t, d, "beta")
+	seedIndexedProject(t, d, "github.com/x/y@main")
+
+	var (
+		wg       sync.WaitGroup
+		errs     [2]error
+		members  [2]Membership
+	)
+	wg.Add(2)
+	go func() {
+		defer wg.Done()
+		members[0], errs[0] = svc.Link(ctx, wsA, "github.com/x/y@main")
+	}()
+	go func() {
+		defer wg.Done()
+		members[1], errs[1] = svc.Link(ctx, wsB, "github.com/x/y@main")
+	}()
+	wg.Wait()
+
+	for i, e := range errs {
+		if e != nil {
+			t.Errorf("goroutine %d: unexpected error: %v", i, e)
+		}
+		if members[i].AddedAt.IsZero() {
+			t.Errorf("goroutine %d: AddedAt not populated", i)
+		}
+	}
+	// Sanity: both rows landed in the DB.
+	var n int
+	if err := d.QueryRowContext(ctx,
+		`SELECT COUNT(*) FROM workspace_projects WHERE project_path = ?`,
+		"github.com/x/y@main",
+	).Scan(&n); err != nil {
+		t.Fatalf("count: %v", err)
+	}
+	if n != 2 {
+		t.Errorf("expected 2 rows in workspace_projects, got %d", n)
+	}
+}
+
+// TestLink_ConcurrentSameWorkspace — two goroutines race to link the
+// SAME project to the SAME workspace. Exactly one must win (returns
+// ErrDuplicate from the loser) — never 2 successes (would violate PK)
+// and never a spurious error mapped to ErrWorkspaceMissing /
+// ErrProjectMissing. Pins the diagnostic path's correctness under
+// genuine PK contention.
+func TestLink_ConcurrentSameWorkspace(t *testing.T) {
+	d, svc := mustOpen(t)
+	ctx := context.Background()
+	wsID := seedWorkspace(t, d, "platform")
+	seedIndexedProject(t, d, "github.com/x/y@main")
+
+	var (
+		wg   sync.WaitGroup
+		errs [2]error
+	)
+	wg.Add(2)
+	for i := range errs {
+		go func() {
+			defer wg.Done()
+			_, errs[i] = svc.Link(ctx, wsID, "github.com/x/y@main")
+		}()
+	}
+	wg.Wait()
+
+	successes, duplicates := 0, 0
+	for _, e := range errs {
+		switch {
+		case e == nil:
+			successes++
+		case errors.Is(e, ErrDuplicate):
+			duplicates++
+		default:
+			t.Errorf("unexpected error %v (want nil or ErrDuplicate)", e)
+		}
+	}
+	if successes != 1 || duplicates != 1 {
+		t.Errorf("expected 1 success + 1 ErrDuplicate, got %d / %d", successes, duplicates)
+	}
+}
+
+// TestDeletingProject_CascadesMembership confirms the schema's FK
+// ON DELETE CASCADE actually fires: removing the projects row drops
+// every workspace_projects row referencing it.
+func TestDeletingProject_CascadesMembership(t *testing.T) {
+	d, svc := mustOpen(t)
+	ctx := context.Background()
+	wsA := seedWorkspace(t, d, "alpha")
+	wsB := seedWorkspace(t, d, "beta")
+	seedIndexedProject(t, d, "github.com/x/y@main")
+	for _, ws := range []string{wsA, wsB} {
+		if _, err := svc.Link(ctx, ws, "github.com/x/y@main"); err != nil {
+			t.Fatalf("Link: %v", err)
+		}
+	}
+
+	if _, err := d.ExecContext(ctx, `DELETE FROM projects WHERE host_path = ?`, "github.com/x/y@main"); err != nil {
+		t.Fatalf("delete project: %v", err)
+	}
+	memberships, err := svc.ListByProject(ctx, "github.com/x/y@main")
+	if err != nil {
+		t.Fatalf("ListByProject: %v", err)
+	}
+	if len(memberships) != 0 {
+		t.Fatalf("expected memberships cascaded to 0, got %d", len(memberships))
+	}
+}
diff --git a/server/internal/workspacerepos/workspacerepos.go b/server/internal/workspacerepos/workspacerepos.go
deleted file mode 100644
index f235fa1..0000000
--- a/server/internal/workspacerepos/workspacerepos.go
+++ /dev/null
@@ -1,466 +0,0 @@
-// Package workspacerepos is the service layer for the workspace_repos
-// table — one row per (workspace, github_url, branch). Each row maps 1:1
-// to an indexed project (host_path = "github.com/owner/repo@branch").
-//
-// Lifecycle (PR2):
-//
-//	create row (status=pending) → enqueue clone_repo job → worker clones
-//	→ enqueue index_repo job → worker indexes → status=indexed
-//
-// PR3 adds webhook delivery → enqueue fetch_repo on push; PR4+ feeds
-// call-graph + community recompute. This package stays small — handlers
-// own service composition; we just persist rows.
-package workspacerepos
-
-import (
-	"context"
-	"crypto/rand"
-	"database/sql"
-	"encoding/base64"
-	"errors"
-	"fmt"
-	"net/url"
-	"strings"
-	"time"
-
-	"github.com/google/uuid"
-)
-
-// Status values. Kept as bare strings since they map straight to the DB
-// column and the JSON wire format.
-const (
-	StatusPending  = "pending"  // row created, work not yet scheduled
-	StatusCloning  = "cloning"  // clone_repo job running
-	StatusIndexing = "indexing" // index_repo job running
-	StatusIndexed  = "indexed"  // happy path
-	StatusFailed   = "failed"   // last attempt errored (see LastError)
-)
-
-// Webhook modes. The legacy AutoWebhook bool stays in the struct for
-// backwards compatibility with old API consumers, but new code should
-// consult WebhookMode — it carries the operator's stated intent (auto
-// vs manual-pending vs deliberately disabled).
-const (
-	WebhookModeManual   = "manual"
-	WebhookModeAuto     = "auto"
-	WebhookModeDisabled = "disabled"
-)
-
-// NormaliseWebhookMode rejects unknown values up front so the database
-// only ever stores one of the three documented states. Empty input maps
-// to the default ('manual'), so old API clients that omit the field
-// keep working unchanged.
-func NormaliseWebhookMode(s string) (string, error) {
-	switch strings.ToLower(strings.TrimSpace(s)) {
-	case "":
-		return WebhookModeManual, nil
-	case WebhookModeManual:
-		return WebhookModeManual, nil
-	case WebhookModeAuto:
-		return WebhookModeAuto, nil
-	case WebhookModeDisabled:
-		return WebhookModeDisabled, nil
-	default:
-		return "", ErrInvalidWebhookMode
-	}
-}
-
-// Errors.
-var (
-	ErrNotFound           = errors.New("workspace repo not found")
-	ErrDuplicate          = errors.New("repo is already in this workspace on that branch")
-	ErrInvalidURL         = errors.New("github_url must be an https://github.com/owner/repo URL")
-	ErrBranchEmpty        = errors.New("branch is required")
-	ErrInvalidWebhookMode = errors.New("webhook_mode must be one of manual, auto, disabled")
-)
-
-// WorkspaceRepo is the wire view. Tokens themselves are referenced by
-// id — Reveal happens server-side via internal/githubtokens.
-type WorkspaceRepo struct {
-	ID             string
-	WorkspaceID    string
-	GitHubURL      string
-	Branch         string
-	ProjectPath    string
-	TokenID        string // empty when no PAT is associated (public repo)
-	WebhookSecret  string
-	WebhookID      *int64 // GitHub hook id (set by PR3 auto-register)
-	AutoWebhook    bool
-	WebhookMode    string // 'manual' | 'auto' | 'disabled'
-	Status         string
-	LastSHA        string
-	LastError      string
-	LastIndexedAt  *time.Time
-	IsLinked       bool // true for lightweight references to projects owned by another workspace_repo
-	CreatedAt      time.Time
-	UpdatedAt      time.Time
-}
-
-// Service wraps the workspace_repos table.
-type Service struct {
-	DB *sql.DB
-}
-
-// New returns a Service.
-func New(db *sql.DB) *Service { return &Service{DB: db} }
-
-// CreateRequest is what handlers pass in.
-type CreateRequest struct {
-	WorkspaceID string
-	GitHubURL   string
-	Branch      string
-	TokenID     string // optional
-	AutoWebhook bool   // legacy: kept for old clients; new code uses WebhookMode
-	WebhookMode string // 'manual' | 'auto' | 'disabled'; empty = manual
-}
-
-// Create inserts a workspace_repo and generates a webhook secret. The
-// resulting ProjectPath is "github.com/owner/repo@branch" — the canonical
-// id for downstream tables (projects.host_path).
-func (s *Service) Create(ctx context.Context, req CreateRequest) (WorkspaceRepo, error) {
-	owner, repo, err := parseGitHubURL(req.GitHubURL)
-	if err != nil {
-		return WorkspaceRepo{}, err
-	}
-	if strings.TrimSpace(req.Branch) == "" {
-		return WorkspaceRepo{}, ErrBranchEmpty
-	}
-	projectPath := fmt.Sprintf("github.com/%s/%s@%s", owner, repo, req.Branch)
-
-	secret, err := generateWebhookSecret()
-	if err != nil {
-		return WorkspaceRepo{}, fmt.Errorf("generate webhook secret: %w", err)
-	}
-
-	id := uuid.NewString()
-	now := time.Now().UTC().Format(time.RFC3339Nano)
-	githubURL := canonicaliseURL(req.GitHubURL)
-
-	// WebhookMode is the source of truth in the DB; AutoWebhook stays
-	// derived so the legacy SELECT path keeps working until removed.
-	mode, merr := NormaliseWebhookMode(req.WebhookMode)
-	if merr != nil {
-		return WorkspaceRepo{}, merr
-	}
-	// If the caller used the legacy bool but left WebhookMode empty,
-	// honour the bool — otherwise mode wins.
-	if req.WebhookMode == "" && req.AutoWebhook {
-		mode = WebhookModeAuto
-	}
-	auto := 0
-	if mode == WebhookModeAuto {
-		auto = 1
-	}
-	tokenID := nullableString(req.TokenID)
-
-	_, err = s.DB.ExecContext(ctx,
-		`INSERT INTO workspace_repos (
-		   id, workspace_id, github_url, branch, project_path,
-		   token_id, webhook_secret, auto_webhook, webhook_mode, status,
-		   created_at, updated_at
-		 ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)`,
-		id, req.WorkspaceID, githubURL, req.Branch, projectPath,
-		tokenID, secret, auto, mode, StatusPending,
-		now, now,
-	)
-	if err != nil {
-		if isUniqueConstraintViolation(err) {
-			return WorkspaceRepo{}, ErrDuplicate
-		}
-		return WorkspaceRepo{}, fmt.Errorf("insert workspace_repo: %w", err)
-	}
-	return s.GetByID(ctx, id)
-}
-
-// CreateLink inserts a workspace_repo with is_linked=1: a lightweight
-// pointer to an already-indexed project. Unlike Create, there is no
-// clone job, no webhook, no PAT — the row exists only so the project
-// participates in workspace-level features (search, communities,
-// the repo list UI). The canonical project must already exist in the
-// projects table; the caller (HTTP handler) is responsible for that
-// check + the status='indexed' precondition before calling here.
-//
-// projectPath must be the same canonical form Create produces, i.e.
-// "github.com/owner/repo@branch" — we round-trip through parseProjectPath
-// so the resulting (workspace_id, github_url, branch) triple matches
-// what an owned row would produce. This is what makes the
-// UNIQUE(workspace_id, github_url, branch) constraint catch an attempt
-// to link the same project that's already attached as owned.
-//
-// webhook_secret is generated but never used — the column is NOT NULL.
-// webhook_mode is set to 'disabled' so the dashboard hides the webhook
-// UI for linked rows.
-func (s *Service) CreateLink(ctx context.Context, workspaceID, projectPath string) (WorkspaceRepo, error) {
-	githubURL, branch, err := parseProjectPath(projectPath)
-	if err != nil {
-		return WorkspaceRepo{}, err
-	}
-
-	secret, err := generateWebhookSecret()
-	if err != nil {
-		return WorkspaceRepo{}, fmt.Errorf("generate webhook secret: %w", err)
-	}
-
-	id := uuid.NewString()
-	now := time.Now().UTC().Format(time.RFC3339Nano)
-
-	_, err = s.DB.ExecContext(ctx,
-		`INSERT INTO workspace_repos (
-		   id, workspace_id, github_url, branch, project_path,
-		   token_id, webhook_secret, auto_webhook, webhook_mode, status,
-		   is_linked, created_at, updated_at
-		 ) VALUES (?, ?, ?, ?, ?, NULL, ?, 0, ?, ?, 1, ?, ?)`,
-		id, workspaceID, githubURL, branch, projectPath,
-		secret, WebhookModeDisabled, StatusIndexed,
-		now, now,
-	)
-	if err != nil {
-		if isUniqueConstraintViolation(err) {
-			return WorkspaceRepo{}, ErrDuplicate
-		}
-		return WorkspaceRepo{}, fmt.Errorf("insert linked workspace_repo: %w", err)
-	}
-	return s.GetByID(ctx, id)
-}
-
-// GetByID returns one row.
-func (s *Service) GetByID(ctx context.Context, id string) (WorkspaceRepo, error) {
-	row := s.DB.QueryRowContext(ctx, selectColumns+` WHERE id = ?`, id)
-	return scanRow(row)
-}
-
-// ListByWorkspace returns every repo in a workspace, newest first.
-func (s *Service) ListByWorkspace(ctx context.Context, workspaceID string) ([]WorkspaceRepo, error) {
-	rows, err := s.DB.QueryContext(ctx,
-		selectColumns+` WHERE workspace_id = ? ORDER BY created_at DESC`, workspaceID)
-	if err != nil {
-		return nil, fmt.Errorf("list repos: %w", err)
-	}
-	defer rows.Close()
-	return scanRows(rows)
-}
-
-// SetStatus is the workhorse called from job handlers. lastSHA / lastError
-// / lastIndexedAt are optional — pass empty / nil / nil to leave them
-// unchanged.
-func (s *Service) SetStatus(ctx context.Context, id, status string, lastSHA, lastError string, indexed *time.Time) error {
-	now := time.Now().UTC().Format(time.RFC3339Nano)
-	// We use a single UPDATE with COALESCE to keep optional fields atomic.
-	var indexedStr any
-	if indexed != nil {
-		indexedStr = indexed.UTC().Format(time.RFC3339Nano)
-	} else {
-		indexedStr = nil
-	}
-	res, err := s.DB.ExecContext(ctx, `
-		UPDATE workspace_repos
-		   SET status         = ?,
-		       last_sha       = COALESCE(NULLIF(?, ''), last_sha),
-		       last_error     = CASE WHEN ? = '' THEN NULL ELSE ? END,
-		       last_indexed_at = COALESCE(?, last_indexed_at),
-		       updated_at     = ?
-		 WHERE id = ?`,
-		status, lastSHA, lastError, lastError, indexedStr, now, id,
-	)
-	if err != nil {
-		return fmt.Errorf("set status: %w", err)
-	}
-	n, _ := res.RowsAffected()
-	if n == 0 {
-		return ErrNotFound
-	}
-	return nil
-}
-
-// SetWebhookID persists the GitHub-side hook id returned by the
-// auto-register flow. ErrNotFound when the row is gone (race with
-// concurrent delete — caller can ignore).
-func (s *Service) SetWebhookID(ctx context.Context, id string, hookID int64) error {
-	res, err := s.DB.ExecContext(ctx,
-		`UPDATE workspace_repos SET webhook_id = ?, updated_at = ? WHERE id = ?`,
-		hookID, time.Now().UTC().Format(time.RFC3339Nano), id)
-	if err != nil {
-		return fmt.Errorf("set webhook_id: %w", err)
-	}
-	n, _ := res.RowsAffected()
-	if n == 0 {
-		return ErrNotFound
-	}
-	return nil
-}
-
-// Delete removes a workspace_repo. The on-disk clone, indexed project, and
-// associated rows are NOT cleaned up here — handlers should enqueue a
-// cleanup job (PR3+) or accept the orphan for now.
-func (s *Service) Delete(ctx context.Context, id string) error {
-	res, err := s.DB.ExecContext(ctx, `DELETE FROM workspace_repos WHERE id = ?`, id)
-	if err != nil {
-		return fmt.Errorf("delete workspace_repo: %w", err)
-	}
-	n, err := res.RowsAffected()
-	if err != nil {
-		return fmt.Errorf("rows affected: %w", err)
-	}
-	if n == 0 {
-		return ErrNotFound
-	}
-	return nil
-}
-
-// --- helpers ---
-
-const selectColumns = `
-	SELECT id, workspace_id, github_url, branch, project_path,
-	       token_id, webhook_secret, webhook_id, auto_webhook,
-	       webhook_mode, status, last_sha, last_error, last_indexed_at,
-	       is_linked, created_at, updated_at
-	  FROM workspace_repos`
-
-func scanRow(r interface{ Scan(dest ...any) error }) (WorkspaceRepo, error) {
-	var (
-		wr            WorkspaceRepo
-		tokenID       sql.NullString
-		webhookID     sql.NullInt64
-		autoWebhook   int
-		webhookMode   string
-		lastSHA       sql.NullString
-		lastError     sql.NullString
-		lastIndexed   sql.NullString
-		isLinked      int
-		createdAt     string
-		updatedAt     string
-	)
-	err := r.Scan(&wr.ID, &wr.WorkspaceID, &wr.GitHubURL, &wr.Branch, &wr.ProjectPath,
-		&tokenID, &wr.WebhookSecret, &webhookID, &autoWebhook,
-		&webhookMode, &wr.Status, &lastSHA, &lastError, &lastIndexed,
-		&isLinked, &createdAt, &updatedAt)
-	if err != nil {
-		if errors.Is(err, sql.ErrNoRows) {
-			return WorkspaceRepo{}, ErrNotFound
-		}
-		return WorkspaceRepo{}, fmt.Errorf("scan workspace_repo: %w", err)
-	}
-	wr.TokenID = tokenID.String
-	if webhookID.Valid {
-		v := webhookID.Int64
-		wr.WebhookID = &v
-	}
-	wr.AutoWebhook = autoWebhook == 1
-	wr.WebhookMode = webhookMode
-	if wr.WebhookMode == "" {
-		wr.WebhookMode = WebhookModeManual
-	}
-	wr.LastSHA = lastSHA.String
-	wr.LastError = lastError.String
-	if lastIndexed.Valid {
-		t, _ := time.Parse(time.RFC3339Nano, lastIndexed.String)
-		wr.LastIndexedAt = &t
-	}
-	wr.IsLinked = isLinked == 1
-	wr.CreatedAt, _ = time.Parse(time.RFC3339Nano, createdAt)
-	wr.UpdatedAt, _ = time.Parse(time.RFC3339Nano, updatedAt)
-	return wr, nil
-}
-
-func scanRows(rows *sql.Rows) ([]WorkspaceRepo, error) {
-	out := []WorkspaceRepo{}
-	for rows.Next() {
-		wr, err := scanRow(rows)
-		if err != nil {
-			return nil, err
-		}
-		out = append(out, wr)
-	}
-	return out, rows.Err()
-}
-
-// parseGitHubURL extracts owner + repo from an HTTPS GitHub URL. Accepts
-// trailing slash and ".git" suffix. Rejects anything not on github.com so
-// we don't accidentally try to clone arbitrary forge URLs (each forge has
-// its own quirks — supporting them is out of scope).
-func parseGitHubURL(s string) (owner, repo string, err error) {
-	s = strings.TrimSpace(s)
-	if s == "" {
-		return "", "", ErrInvalidURL
-	}
-	u, perr := url.Parse(s)
-	if perr != nil {
-		return "", "", ErrInvalidURL
-	}
-	if !strings.EqualFold(u.Host, "github.com") {
-		return "", "", ErrInvalidURL
-	}
-	path := strings.Trim(u.Path, "/")
-	path = strings.TrimSuffix(path, ".git")
-	parts := strings.Split(path, "/")
-	if len(parts) != 2 || parts[0] == "" || parts[1] == "" {
-		return "", "", ErrInvalidURL
-	}
-	return parts[0], parts[1], nil
-}
-
-// parseProjectPath splits a canonical project_path of the form
-// "github.com/owner/repo@branch" back into (github_url, branch) so we
-// can reuse the per-workspace uniqueness key when creating a linked
-// row from a project hash. Inverse of the Sprintf at Create().
-//
-// Errors:
-//   - empty input or missing "@" → ErrInvalidURL
-//   - prefix not "github.com/" → ErrInvalidURL (linked rows only make
-//     sense for GitHub-derived projects; local paths can't map to a
-//     workspace_repo since the schema requires github_url + branch)
-//   - branch portion empty → ErrBranchEmpty
-func parseProjectPath(projectPath string) (githubURL, branch string, err error) {
-	s := strings.TrimSpace(projectPath)
-	at := strings.LastIndex(s, "@")
-	if at <= 0 {
-		return "", "", ErrInvalidURL
-	}
-	left, right := s[:at], s[at+1:]
-	if right == "" {
-		return "", "", ErrBranchEmpty
-	}
-	const prefix = "github.com/"
-	if !strings.HasPrefix(left, prefix) {
-		return "", "", ErrInvalidURL
-	}
-	ownerRepo := strings.Trim(left[len(prefix):], "/")
-	parts := strings.Split(ownerRepo, "/")
-	if len(parts) != 2 || parts[0] == "" || parts[1] == "" {
-		return "", "", ErrInvalidURL
-	}
-	return "https://github.com/" + parts[0] + "/" + parts[1], right, nil
-}
-
-// canonicaliseURL strips trailing slash + ".git" so two forms of the same
-// URL aren't treated as distinct repos.
-func canonicaliseURL(s string) string {
-	s = strings.TrimSpace(s)
-	s = strings.TrimSuffix(s, "/")
-	s = strings.TrimSuffix(s, ".git")
-	return s
-}
-
-func generateWebhookSecret() (string, error) {
-	var buf [32]byte
-	if _, err := rand.Read(buf[:]); err != nil {
-		return "", err
-	}
-	return base64.RawURLEncoding.EncodeToString(buf[:]), nil
-}
-
-func nullableString(s string) any {
-	if s == "" {
-		return nil
-	}
-	return s
-}
-
-func isUniqueConstraintViolation(err error) bool {
-	if err == nil {
-		return false
-	}
-	msg := err.Error()
-	return strings.Contains(msg, "UNIQUE constraint failed") ||
-		strings.Contains(msg, "constraint failed: UNIQUE")
-}
diff --git a/server/internal/workspacerepos/workspacerepos_test.go b/server/internal/workspacerepos/workspacerepos_test.go
deleted file mode 100644
index aa5437c..0000000
--- a/server/internal/workspacerepos/workspacerepos_test.go
+++ /dev/null
@@ -1,244 +0,0 @@
-package workspacerepos
-
-import (
-	"context"
-	"errors"
-	"testing"
-	"time"
-
-	"github.com/dvcdsys/code-index/server/internal/db"
-	"github.com/dvcdsys/code-index/server/internal/workspaces"
-)
-
-// withWorkspace creates a workspaces row and returns its id. Tests need a
-// real FK target since workspace_repos.workspace_id has ON DELETE CASCADE.
-func withWorkspace(t *testing.T) (*Service, string) {
-	t.Helper()
-	d, err := db.Open(":memory:")
-	if err != nil {
-		t.Fatalf("open: %v", err)
-	}
-	t.Cleanup(func() { _ = d.Close() })
-	ws, err := workspaces.New(d).Create(context.Background(), "ws", "")
-	if err != nil {
-		t.Fatalf("seed workspace: %v", err)
-	}
-	return New(d), ws.ID
-}
-
-func TestCreateAndGet(t *testing.T) {
-	svc, wsID := withWorkspace(t)
-	ctx := context.Background()
-	wr, err := svc.Create(ctx, CreateRequest{
-		WorkspaceID: wsID,
-		GitHubURL:   "https://github.com/spf13/cobra",
-		Branch:      "main",
-	})
-	if err != nil {
-		t.Fatalf("Create: %v", err)
-	}
-	if wr.ProjectPath != "github.com/spf13/cobra@main" {
-		t.Fatalf("unexpected project_path %q", wr.ProjectPath)
-	}
-	if wr.WebhookSecret == "" {
-		t.Fatalf("webhook secret should be auto-generated")
-	}
-	if wr.Status != StatusPending {
-		t.Fatalf("expected pending status, got %q", wr.Status)
-	}
-
-	got, err := svc.GetByID(ctx, wr.ID)
-	if err != nil {
-		t.Fatalf("GetByID: %v", err)
-	}
-	if got.ProjectPath != wr.ProjectPath {
-		t.Fatalf("get/create mismatch")
-	}
-}
-
-func TestURLNormalisation(t *testing.T) {
-	svc, wsID := withWorkspace(t)
-	ctx := context.Background()
-	// trailing slash + .git suffix should be collapsed.
-	wr, err := svc.Create(ctx, CreateRequest{
-		WorkspaceID: wsID,
-		GitHubURL:   "https://github.com/spf13/cobra.git/",
-		Branch:      "main",
-	})
-	if err != nil {
-		t.Fatalf("Create: %v", err)
-	}
-	if wr.GitHubURL != "https://github.com/spf13/cobra" {
-		t.Fatalf("URL not canonicalised, got %q", wr.GitHubURL)
-	}
-	if wr.ProjectPath != "github.com/spf13/cobra@main" {
-		t.Fatalf("project_path wrong: %q", wr.ProjectPath)
-	}
-}
-
-func TestDuplicateRejected(t *testing.T) {
-	svc, wsID := withWorkspace(t)
-	ctx := context.Background()
-	if _, err := svc.Create(ctx, CreateRequest{
-		WorkspaceID: wsID, GitHubURL: "https://github.com/x/y", Branch: "main",
-	}); err != nil {
-		t.Fatalf("first: %v", err)
-	}
-	if _, err := svc.Create(ctx, CreateRequest{
-		WorkspaceID: wsID, GitHubURL: "https://github.com/x/y", Branch: "main",
-	}); !errors.Is(err, ErrDuplicate) {
-		t.Fatalf("expected ErrDuplicate, got %v", err)
-	}
-	// Different branch should succeed.
-	if _, err := svc.Create(ctx, CreateRequest{
-		WorkspaceID: wsID, GitHubURL: "https://github.com/x/y", Branch: "develop",
-	}); err != nil {
-		t.Fatalf("different branch should succeed: %v", err)
-	}
-}
-
-func TestInvalidURL(t *testing.T) {
-	svc, wsID := withWorkspace(t)
-	cases := []string{
-		"",
-		"not a url",
-		"https://gitlab.com/x/y",
-		"https://github.com",
-		"https://github.com/onlyowner",
-	}
-	for _, c := range cases {
-		_, err := svc.Create(context.Background(), CreateRequest{
-			WorkspaceID: wsID, GitHubURL: c, Branch: "main",
-		})
-		if !errors.Is(err, ErrInvalidURL) {
-			t.Fatalf("URL %q: expected ErrInvalidURL, got %v", c, err)
-		}
-	}
-}
-
-func TestSetStatus(t *testing.T) {
-	svc, wsID := withWorkspace(t)
-	ctx := context.Background()
-	wr, _ := svc.Create(ctx, CreateRequest{
-		WorkspaceID: wsID, GitHubURL: "https://github.com/x/y", Branch: "main",
-	})
-	now := time.Now().UTC()
-	if err := svc.SetStatus(ctx, wr.ID, StatusIndexed, "abc123", "", &now); err != nil {
-		t.Fatalf("SetStatus: %v", err)
-	}
-	got, _ := svc.GetByID(ctx, wr.ID)
-	if got.Status != StatusIndexed || got.LastSHA != "abc123" {
-		t.Fatalf("status/sha not persisted: %+v", got)
-	}
-	if got.LastIndexedAt == nil {
-		t.Fatalf("LastIndexedAt should be set")
-	}
-}
-
-func TestDeleteCascade(t *testing.T) {
-	svc, wsID := withWorkspace(t)
-	ctx := context.Background()
-	wr, _ := svc.Create(ctx, CreateRequest{
-		WorkspaceID: wsID, GitHubURL: "https://github.com/a/b", Branch: "main",
-	})
-	if err := svc.Delete(ctx, wr.ID); err != nil {
-		t.Fatalf("Delete: %v", err)
-	}
-	if err := svc.Delete(ctx, wr.ID); !errors.Is(err, ErrNotFound) {
-		t.Fatalf("expected ErrNotFound, got %v", err)
-	}
-}
-
-func TestCreateLink_HappyPath(t *testing.T) {
-	svc, wsID := withWorkspace(t)
-	ctx := context.Background()
-	wr, err := svc.CreateLink(ctx, wsID, "github.com/spf13/cobra@main")
-	if err != nil {
-		t.Fatalf("CreateLink: %v", err)
-	}
-	if !wr.IsLinked {
-		t.Fatalf("expected IsLinked=true, got %v", wr.IsLinked)
-	}
-	if wr.Status != StatusIndexed {
-		t.Fatalf("expected status=indexed, got %q", wr.Status)
-	}
-	if wr.WebhookMode != WebhookModeDisabled {
-		t.Fatalf("expected webhook_mode=disabled, got %q", wr.WebhookMode)
-	}
-	if wr.TokenID != "" {
-		t.Fatalf("linked rows must have empty token_id, got %q", wr.TokenID)
-	}
-	if wr.GitHubURL != "https://github.com/spf13/cobra" {
-		t.Fatalf("github_url derived wrong: %q", wr.GitHubURL)
-	}
-	if wr.Branch != "main" {
-		t.Fatalf("branch derived wrong: %q", wr.Branch)
-	}
-	if wr.ProjectPath != "github.com/spf13/cobra@main" {
-		t.Fatalf("project_path mismatch: %q", wr.ProjectPath)
-	}
-}
-
-func TestCreateLink_DuplicateInSameWorkspace(t *testing.T) {
-	svc, wsID := withWorkspace(t)
-	ctx := context.Background()
-	if _, err := svc.CreateLink(ctx, wsID, "github.com/foo/bar@main"); err != nil {
-		t.Fatalf("first: %v", err)
-	}
-	// Second link with the same (workspace, repo, branch) → ErrDuplicate.
-	if _, err := svc.CreateLink(ctx, wsID, "github.com/foo/bar@main"); !errors.Is(err, ErrDuplicate) {
-		t.Fatalf("expected ErrDuplicate, got %v", err)
-	}
-	// An owned row in the same workspace conflicts with the linked one too —
-	// both share the same UNIQUE(workspace_id, github_url, branch) key.
-	if _, err := svc.Create(ctx, CreateRequest{
-		WorkspaceID: wsID, GitHubURL: "https://github.com/foo/bar", Branch: "main",
-	}); !errors.Is(err, ErrDuplicate) {
-		t.Fatalf("owned-after-linked: expected ErrDuplicate, got %v", err)
-	}
-}
-
-func TestCreateLink_AllowedAcrossWorkspaces(t *testing.T) {
-	svcA, wsA := withWorkspace(t)
-	// Reuse the same underlying DB — withWorkspace gives us a Service
-	// bound to a fresh DB; for a cross-workspace test we need two
-	// workspaces on one DB. Seed a second workspace explicitly.
-	wsB, err := workspaces.New(svcA.DB).Create(context.Background(), "ws-b", "")
-	if err != nil {
-		t.Fatalf("seed second workspace: %v", err)
-	}
-	ctx := context.Background()
-	// Same canonical project_path attaches as owned in A, then linked
-	// in B without tripping the legacy global UNIQUE.
-	if _, err := svcA.Create(ctx, CreateRequest{
-		WorkspaceID: wsA, GitHubURL: "https://github.com/x/y", Branch: "main",
-	}); err != nil {
-		t.Fatalf("owned in A: %v", err)
-	}
-	if _, err := svcA.CreateLink(ctx, wsB.ID, "github.com/x/y@main"); err != nil {
-		t.Fatalf("linked in B (same project): %v", err)
-	}
-}
-
-func TestCreateLink_InvalidProjectPath(t *testing.T) {
-	svc, wsID := withWorkspace(t)
-	ctx := context.Background()
-	cases := []struct {
-		name string
-		path string
-		want error
-	}{
-		{"empty", "", ErrInvalidURL},
-		{"no at", "github.com/foo/bar", ErrInvalidURL},
-		{"empty branch", "github.com/foo/bar@", ErrBranchEmpty},
-		{"non-github", "gitlab.com/foo/bar@main", ErrInvalidURL},
-		{"missing repo", "github.com/foo@main", ErrInvalidURL},
-	}
-	for _, c := range cases {
-		t.Run(c.name, func(t *testing.T) {
-			if _, err := svc.CreateLink(ctx, wsID, c.path); !errors.Is(err, c.want) {
-				t.Fatalf("path=%q: expected %v, got %v", c.path, c.want, err)
-			}
-		})
-	}
-}
diff --git a/server/internal/workspaces/workspaces.go b/server/internal/workspaces/workspaces.go
index efb7cf7..38f5a8a 100644
--- a/server/internal/workspaces/workspaces.go
+++ b/server/internal/workspaces/workspaces.go
@@ -1,12 +1,15 @@
 // Package workspaces is the service layer for the workspaces table — the
 // top-level entity of the workspaces feature. A workspace groups one or
-// more GitHub repos for cross-project semantic search powered by
-// community-detection on the call graph (PRs 2–7 of the feature branch).
+// more projects (each backed by an indexed `projects` row, optionally
+// with a `git_repos` peer for GitHub-cloned projects) for cross-project
+// semantic search powered by hybrid BM25 + dense fan-out across the
+// memberships in `workspace_projects`.
 //
-// PR1 scope: bare CRUD. workspace_repos / call_edges / communities land in
-// later PRs. Visibility model is server-wide shared: every authenticated
-// user can list/create/modify any workspace. The decision is captured in
-// the workspaces.md plan; revisit if a per-user ACL becomes necessary.
+// Scope of this package: bare workspace CRUD. Membership lives in
+// `workspaceprojects`; clone + webhook metadata lives in `gitrepos`.
+// Visibility model is server-wide shared: every authenticated user can
+// list/create/modify any workspace. The decision is captured in the
+// workspaces.md plan; revisit if a per-user ACL becomes necessary.
 package workspaces
 
 import (
diff --git a/skills/cix-workspace/SKILL.md b/skills/cix-workspace/SKILL.md
index b750f2a..276aa95 100644
--- a/skills/cix-workspace/SKILL.md
+++ b/skills/cix-workspace/SKILL.md
@@ -2,6 +2,7 @@
 name: cix-workspace
 description: Cross-project research workflow for cix workspaces. Manual-invocation skill — load explicitly via `/cix-workspace <task>` when a request spans multiple repos and you want the full workflow guidance (which repos? what code? what changes?) plus the trust rules for interpreting workspace search responses. Bundles the cix-workspace-investigator sub-agent for parallel per-repo fan-out. Do not auto-trigger.
 user-invocable: true
+allowed-tools: Bash(cix *), Agent
 ---
 
 # `cix workspace` — Cross-Project Research Workflow
@@ -491,8 +492,8 @@ fan-out — the same algorithm that produces the false-positive
 failure mode described in the worked example above.
 
 The response includes `stale_fts_repos` listing the affected
-project_paths. Fix: reindex each repo (dashboard → repo card →
-reindex button, or `POST /api/v1/workspaces/{id}/repos/{repo_id}/reindex`).
+project_paths. Fix: reindex each project (dashboard → project card →
+reindex button, or `POST /api/v1/projects/{hash}/reindex`).
 After reindex, BM25 populates incrementally per-file as chunks are
 written.
 
diff --git a/workspaces.md b/workspaces.md
index 4b26418..72e1ddd 100644
--- a/workspaces.md
+++ b/workspaces.md
@@ -104,18 +104,27 @@ A user creates a workspace, then attaches repositories to it. A workspace
 has no built-in access control beyond what the server's auth layer already
 provides — anyone authenticated can list and search workspaces today.
 
-### Workspace repo
-
-A row in `workspace_repos` that ties one GitHub repo+branch to a
-workspace. Two kinds:
-
-- **Owned** (`is_linked=0`): the server clones the repo to disk and runs
-  indexing. Status transitions: `pending → cloning → indexing → indexed`
-  (or `failed`). These are the "true" workspace repos.
-- **Linked** (`is_linked=1`): a lightweight pointer to an *already-indexed*
-  local project (one that's tracked in the `projects` table because you
-  `cix init`'d it). No clone, no separate index. Useful for including
-  your primary repo in a workspace without duplicating data.
+### Workspace project (membership)
+
+A row in `workspace_projects` that ties one indexed project to a
+workspace. Both the `projects` row and the workspace must already exist
+— linking is the act of declaring "this project participates in this
+workspace's cross-project search". Two underlying project kinds make it
+into a workspace:
+
+- **GitHub-cloned project** — backed by a row in the `git_repos` table.
+  The server cloned the repo to disk and indexed it. `host_path` looks
+  like `github.com/owner/repo@branch`. Its lifecycle (clone, index,
+  reindex, webhook) lives in the `projects` row's `status` column.
+- **Local-path project** — backed only by the `projects` row, no
+  `git_repos` peer. Created with `cix init` against an absolute filesystem
+  path, indexed by the local CLI / file watcher rather than the server's
+  clone pipeline. Useful for including your primary repo in a workspace
+  without duplicating data.
+
+Both kinds are linked into a workspace identically — there is no
+`is_linked` column anymore. The distinction is "does a `git_repos` row
+exist for this project?".
 
 ### GitHub token
 
@@ -178,13 +187,15 @@ must rotate.
 
 ### 4. Attach a repo
 
-Dashboard: open the workspace → **Add repository** → walk through the
-staged dialog (token → account/org → repo → branch → webhook mode).
+Dashboard: open the workspace → **Add GitHub repository** → walk through
+the staged dialog (token → account/org → repo → branch → webhook mode).
 
-Or:
+Or via the API — register the project + clone metadata, then link it
+into the workspace:
 
 ```bash
-curl -X POST http://localhost:21847/api/v1/workspaces/<workspace-id>/repos \
+# Step 1 — register the project + git_repos row (kicks off clone + index).
+curl -X POST http://localhost:21847/api/v1/git-repos \
   -H "Authorization: Bearer $CIX_API_KEY" \
   -d '{
     "github_url":"https://github.com/acme/api-server",
@@ -192,18 +203,23 @@ curl -X POST http://localhost:21847/api/v1/workspaces/<workspace-id>/repos \
     "token_id":"abc-123",
     "webhook_mode":"manual"
   }'
-# → {"id":"...","status":"pending","project_path":"github.com/acme/api-server@main",...}
+# → {"path_hash":"abc1234567890def","project_path":"github.com/acme/api-server@main","status":"created",...}
+
+# Step 2 — link the new path_hash into the workspace.
+curl -X POST http://localhost:21847/api/v1/workspaces/<workspace-id>/projects \
+  -H "Authorization: Bearer $CIX_API_KEY" \
+  -d '{"path_hash":"abc1234567890def"}'
 ```
 
-Status will transition through `cloning → indexing → indexed` over the
+Status will transition through `created → indexing → indexed` over the
 next minutes (depends on repo size + embedding throughput).
 
 ### 5. Watch the indexing progress
 
 ```bash
 curl -H "Authorization: Bearer $CIX_API_KEY" \
-  http://localhost:21847/api/v1/workspaces/<workspace-id>/repos
-# Look for `status: "indexed"` per repo.
+  http://localhost:21847/api/v1/workspaces/<workspace-id>/projects
+# Look for `project.status: "indexed"` per project.
 ```
 
 ### 6. Search
@@ -226,20 +242,25 @@ curl -G -H "Authorization: Bearer $CIX_API_KEY" \
 
 ## Adding repositories
 
-### Owned vs linked
+### GitHub-cloned vs local-path projects
 
-| | Owned repo (`is_linked=0`) | Linked project (`is_linked=1`) |
+| | GitHub-cloned project | Local-path project |
 |---|---|---|
 | Source | GitHub clone | Existing `cix init`'d local project |
-| Clone path | `<data-dir>/repos/<repo_id>/` | n/a (uses original) |
+| Clone path | `<data-dir>` → `repos` → `<path_hash>` | n/a (uses original) |
+| Backing tables | `projects` + `git_repos` | `projects` only |
 | Index lifecycle | Server-managed | Whatever the user runs locally |
 | Indexed by | Server's index pipeline | `cix init` / `cix watch` |
 | Webhooks | Supported | Not applicable |
-| API | `POST /workspaces/{id}/repos` | `POST /workspaces/{id}/repos/link` |
-| Dashboard | **Add repository** button | **Link existing project** button |
+| Created via | `POST /api/v1/git-repos` | `POST /api/v1/projects` (or `cix init` locally) |
+| Linked into workspace via | `POST /api/v1/workspaces/{id}/projects` | `POST /api/v1/workspaces/{id}/projects` |
+| Dashboard | **Add GitHub repository** button | **Link existing project** button |
 
-Use **linked** when the primary project you're working in should appear
-in the workspace search but you don't want a second clone.
+Both kinds are linked into a workspace through the same membership
+endpoint; the only difference is which table owns the project's
+clone-and-webhook metadata. Use a local-path project when the primary
+project you're working in should appear in the workspace search but you
+don't want a second clone.
 
 ### From the dashboard
 
@@ -255,13 +276,21 @@ The **Add repository** dialog is staged:
 5. **Pick a webhook mode** — `manual` / `auto` / `disabled`. See
    [Webhooks](#webhooks-auto-reindex-on-push).
 
-The dialog calls `POST /workspaces/{id}/repos` at the end. The clone +
-index job runs in the background.
+The dialog calls `POST /api/v1/git-repos` to register the project +
+clone metadata, then `POST /api/v1/workspaces/{id}/projects` to link
+the resulting `path_hash` into the workspace. The clone + index job
+runs in the background.
 
 ### From the API
 
+Registering a GitHub-cloned project is a two-step flow: create the
+project (with its `git_repos` peer) via `POST /git-repos`, then link
+the resulting `path_hash` into the workspace via
+`POST /workspaces/{id}/projects`.
+
 ```bash
-curl -X POST http://localhost:21847/api/v1/workspaces/<id>/repos \
+# 1. Register the project + git_repos row (kicks off clone + index).
+curl -X POST http://localhost:21847/api/v1/git-repos \
   -H "Authorization: Bearer $CIX_API_KEY" \
   -H "Content-Type: application/json" \
   -d '{
@@ -270,56 +299,83 @@ curl -X POST http://localhost:21847/api/v1/workspaces/<id>/repos \
     "token_id": "<token-uuid-or-null>",
     "webhook_mode": "manual"
   }'
+# → {"path_hash":"abc1234567890def","project_path":"github.com/owner/repo@main",...}
+
+# 2. Link the path_hash into the workspace.
+curl -X POST http://localhost:21847/api/v1/workspaces/<id>/projects \
+  -H "Authorization: Bearer $CIX_API_KEY" \
+  -H "Content-Type: application/json" \
+  -d '{"path_hash": "abc1234567890def"}'
 ```
 
-Response fields worth knowing:
+Response fields worth knowing on the `POST /git-repos` response:
 
-- `id` — workspace_repo UUID (use this for delete / reindex / webhook
-  endpoints)
-- `project_path` — `github.com/owner/repo@branch`, the search identifier
-- `status` — starts at `pending`, becomes `indexed` when the pipeline
-  finishes
+- `path_hash` — the 16-hex-char project identifier used by every
+  per-project endpoint (`/projects/{hash}/reindex`,
+  `/webhooks/github/{hash}`, etc.).
+- `project_path` — `github.com/owner/repo@branch`, the search
+  identifier the dashboard surfaces.
+- `status` — lives on the `projects` row; starts at `created`,
+  transitions through `indexing` to `indexed` once the pipeline
+  finishes.
 - `webhook_secret` — server-generated HMAC secret. Returned exactly
   once if you set `webhook_mode=manual`. Use it when you configure the
   webhook on GitHub manually.
 
 ### Cloning, indexing, and status transitions
 
-What happens when you add a repo:
-
-1. **`pending`** — row inserted in `workspace_repos`. Clone job queued.
-2. **`cloning`** — server fetches via `git clone` (or `git fetch +
-   checkout` if the repo is already on disk). Private repos use the
-   attached token. Result lands at `<CIX_WORKSPACES_DATA_DIR>/<repo_id>/`.
-3. **`indexing`** — indexer scans the clone with the standard pipeline
-   (tree-sitter chunking → embeddings → vector store + FTS5 mirror).
-4. **`indexed`** — `last_indexed_at` updated, repo is searchable.
-5. **`failed`** — clone or index errored out. `last_error` populated.
-   Common causes: invalid token, repo not found, branch doesn't exist,
-   embedder unavailable.
+`projects.status` tracks the per-project lifecycle. What happens after
+`POST /git-repos`:
+
+1. **`created`** — rows inserted in `projects` and `git_repos`. Clone
+   job queued.
+2. **`indexing`** — server fetches via `git clone` (or `git fetch +
+   checkout` if the repo is already on disk) into
+   `<CIX_WORKSPACES_DATA_DIR>/<path_hash>/`, then runs the indexer
+   pipeline (tree-sitter chunking → embeddings → vector store + FTS5
+   mirror). Private repos use the attached token.
+3. **`indexed`** — `last_indexed_at` updated, project is searchable.
+4. **`error`** — clone or index errored out. The dashboard surfaces
+   the underlying error from the job. Common causes: invalid token,
+   repo not found, branch doesn't exist, embedder unavailable.
 
 Clone + index parallelism: `CIX_WORKER_CONCURRENCY` (default `2`).
 Increase for fleet onboarding; lower if you saturate disk or GPU.
 
-### Reindexing a single repo
+### Reindexing a single project
+
+Per-project endpoint — the same call reindexes a GitHub-cloned project
+or a local-path project, no workspace context needed.
 
 ```bash
-curl -X POST http://localhost:21847/api/v1/workspaces/<wid>/repos/<rid>/reindex \
+curl -X POST http://localhost:21847/api/v1/projects/<path_hash>/reindex \
   -H "Authorization: Bearer $CIX_API_KEY"
 ```
 
 Use this after a manual content update, after the embedding model
 changes, or after the stale-FTS warning (see [Search algorithm](#search-algorithm)).
 
-### Removing a repo
+### Unlinking a project from a workspace
+
+Removes the membership row but leaves the underlying project (and any
+clone on disk) intact, so the same project can be re-linked or remain
+linked to other workspaces.
 
 ```bash
-curl -X DELETE http://localhost:21847/api/v1/workspaces/<wid>/repos/<rid> \
+curl -X DELETE http://localhost:21847/api/v1/workspaces/<wid>/projects/<path_hash> \
   -H "Authorization: Bearer $CIX_API_KEY"
 ```
 
-The clone is deleted from disk; the `projects` row is cleaned up if no
-other workspace_repo references it; vectors are removed from chromem.
+### Deleting a project entirely
+
+Removes the `projects` row along with its `git_repos` peer (if any),
+the on-disk clone, the vectors, and — via `ON DELETE CASCADE` — every
+workspace membership referencing it.
+
+```bash
+curl -X DELETE http://localhost:21847/api/v1/projects/<host_path-or-hash> \
+  -H "Authorization: Bearer $CIX_API_KEY"
+```
 
 ---
 
@@ -463,8 +519,8 @@ Response shape (abbreviated):
     },
     ...
   ],
-  "pending_repos":   [...],         // repos still cloning / indexing
-  "failed_repos":    [...],         // repos that errored out
+  "pending_repos":   [...],         // projects still in created / indexing
+  "failed_repos":    [...],         // projects in error status
   "stale_fts_repos": [...]          // pre-FTS-mirror repos — reindex
 }
 ```
@@ -565,7 +621,7 @@ BM25 will be permanently 0 for it. The response surfaces this via
 `stale_fts_repos: [{project_path: "..."}]`. Run a reindex on each:
 
 ```bash
-curl -X POST http://localhost:21847/api/v1/workspaces/<wid>/repos/<rid>/reindex \
+curl -X POST http://localhost:21847/api/v1/projects/<path_hash>/reindex \
   -H "Authorization: Bearer $CIX_API_KEY"
 ```
 
@@ -588,11 +644,13 @@ Each workspace repo has a `webhook_mode`:
 ### Delivery endpoint
 
 ```
-POST /api/v1/webhooks/github/{repo_id}
+POST /api/v1/webhooks/github/{path_hash}
 ```
 
-GitHub's payload is HMAC-SHA256-signed with `webhook_secret`; the
-server verifies via the `X-Hub-Signature-256` header.
+The `{path_hash}` segment is the same 16-hex-char value returned by
+`POST /git-repos` and surfaced on every per-project endpoint. GitHub's
+payload is HMAC-SHA256-signed with the matching `git_repos.webhook_secret`;
+the server verifies via the `X-Hub-Signature-256` header.
 
 Event handling:
 
@@ -609,7 +667,7 @@ When `webhook_mode=manual`, the add-repo response includes a
 `webhook_secret` (returned once) and a `webhook_url` (always
 returnable). Configure on GitHub:
 
-- **Payload URL:** `<CIX_PUBLIC_URL>/api/v1/webhooks/github/<repo_id>`
+- **Payload URL:** `<CIX_PUBLIC_URL>/api/v1/webhooks/github/<path_hash>`
 - **Content type:** `application/json`
 - **Secret:** the returned `webhook_secret`
 - **Events:** Just `push` (the server ignores everything else)
@@ -735,15 +793,22 @@ PATCH  /api/v1/workspaces/{id}                  rename / update description
 DELETE /api/v1/workspaces/{id}                  remove (cascades to repos + clones)
 ```
 
-### Workspace repos
+### Workspace project membership
+
+```
+GET    /api/v1/workspaces/{id}/projects                         list projects linked to this workspace
+POST   /api/v1/workspaces/{id}/projects                         link an existing indexed project (body: {path_hash})
+DELETE /api/v1/workspaces/{id}/projects/{hash}                  unlink (project + clone preserved)
+```
+
+### Projects (per-project, workspace-independent)
 
 ```
-GET    /api/v1/workspaces/{id}/repos                            list
-POST   /api/v1/workspaces/{id}/repos                            add (clones + indexes)
-POST   /api/v1/workspaces/{id}/repos/link                       link existing local project
-DELETE /api/v1/workspaces/{id}/repos/{repo_id}                  remove
-POST   /api/v1/workspaces/{id}/repos/{repo_id}/reindex          trigger fresh index
-GET    /api/v1/workspaces/{id}/repos/{repo_id}/webhook-info     dashboard helper
+POST   /api/v1/git-repos                                        register a new GitHub-cloned project (clones + indexes)
+GET    /api/v1/projects/{hash}/git-repo                         git_repos peer of a project (404 for local-path projects)
+POST   /api/v1/projects/{hash}/reindex                          trigger a fresh index
+GET    /api/v1/projects/{hash}/webhook-info                     dashboard helper — current webhook URL + secret
+DELETE /api/v1/projects/{path}                                  delete project + clone + memberships (CASCADE)
 ```
 
 ### Workspace search
@@ -767,7 +832,7 @@ DELETE /api/v1/github-tokens/{id}                               revoke (server-s
 ### Webhooks
 
 ```
-POST   /api/v1/webhooks/github/{repo_id}                        GitHub delivery endpoint
+POST   /api/v1/webhooks/github/{hash}                           GitHub delivery endpoint (HMAC-verified)
 ```
 
 Full OpenAPI: `doc/openapi.yaml` and `http://<host>:21847/docs`.
@@ -780,27 +845,27 @@ Full OpenAPI: `doc/openapi.yaml` and `http://<host>:21847/docs`.
 → `CIX_WORKSPACES_ENABLED=true` is missing or the server hasn't been
 restarted.
 
-**`status: "failed"` on a repo, `last_error: "authentication required"`**
+**`status: "error"` on a project, dashboard surfaces "authentication required"**
 → Private repo with no token, or token's scopes are insufficient.
 Re-create the token with `repo` scope (and `admin:repo_hook` if you
-want auto webhooks), then retry by deleting and re-adding the repo.
+want auto webhooks), then retry by deleting and re-adding the project.
 
-**`status: "failed"`, `last_error: "branch not found"`**
-→ Typo or the branch was deleted upstream. Delete the repo entry and
-re-add with the correct branch.
+**`status: "error"`, dashboard surfaces "branch not found"**
+→ Typo or the branch was deleted upstream. Delete the project and
+re-add it via `POST /git-repos` with the correct branch.
 
 **Search returns `empty` for a query that should match**
 → Three likely causes:
 1. Default `min_score=0.4` filtered everything. Retry with `min_score=0`.
-2. Repo is still indexing (`status: pending|cloning|indexing`). Check
-   `GET /workspaces/{id}/repos`.
+2. Project is still indexing (`status: created|indexing`). Check
+   `GET /workspaces/{id}/projects`.
 3. The literal terms genuinely don't appear in any repo AND dense
    similarity is below threshold. Re-phrase with the term the code
    actually uses.
 
 **`stale_fts_repos` populated on every search**
 → These repos were indexed pre-FTS5 mirror. Run
-`POST /workspaces/{id}/repos/{repo_id}/reindex` on each.
+`POST /api/v1/projects/{hash}/reindex` on each.
 
 **`status: "partial_failure"`**
 → At least one repo's dense search errored (corrupt chromem collection,
@@ -810,7 +875,7 @@ fastest fix is usually a reindex of the failed repo.
 **Webhook isn't triggering reindex**
 → Verify:
 1. GitHub's webhook deliveries page shows 200 OK.
-2. Push was to the *tracked* branch (the one in `workspace_repos.branch`).
+2. Push was to the *tracked* branch (the one in `git_repos.branch`).
 3. Server logs show signature verification succeeding.
 4. `CIX_PUBLIC_URL` is set and reachable from GitHub (for `auto` mode).