fix: automatic recognition of root

README.md

@@ -144,9 +144,11 @@ codegraph index .
 ### 4. Start the MCP server
 
 ```bash
-codegraph serve --repo-root .
+codegraph serve
 ```
 
+Repo root is auto-detected from git (or falls back to your current working directory).
+
 That's it. Your AI assistant now has deep structural code understanding.
 
 ---
@@ -169,7 +171,7 @@ codegraph install
   "mcpServers": {
     "codegraph": {
       "command": "codegraph",
-      "args": ["serve", "--repo-root", "."]
+      "args": ["serve"]
     }
   }
 }
@@ -184,7 +186,7 @@ codegraph install
   "mcpServers": {
     "codegraph": {
       "command": "codegraph",
-      "args": ["serve", "--repo-root", "."]
+      "args": ["serve"]
     }
   }
 }
@@ -197,7 +199,7 @@ codegraph install
 ```toml
 [mcp_servers.codegraph]
 command = "codegraph"
-args = ["serve", "--repo-root", "/path/to/repo"]
+args = ["serve"]
 startup_timeout_sec = 60
 ```
 </details>
@@ -278,7 +280,7 @@ codegraph watch <path>                    # Watch and auto-reindex
 codegraph clean <path>                    # Clean database
 
 # MCP Server
-codegraph serve --repo-root <path>        # Start MCP server
+codegraph serve [--repo-root <path>]      # Start MCP server (auto-detects repo root)
 
 # Query
 codegraph stats <path>                    # Graph statistics
@@ -292,7 +294,7 @@ codegraph impact <path> --symbol <name>   # Impact analysis
 codegraph affected-tests [--stdin] <files>  # Tests affected by changed files
 
 # Visualization & Export
-codegraph visualize --repo-root <path>      # Interactive D3.js graph
+codegraph visualize [--repo-root <path>]    # Interactive D3.js graph (auto-detects repo root)
 codegraph graph export <path> --format dot  # Export as Graphviz DOT
 codegraph graph export <path> --format json # Export as JSON
 
@@ -307,10 +309,12 @@ codegraph benchmark                         # Token savings benchmark
 git diff --name-only | codegraph affected-tests --stdin
 
 # CI integration
-TESTS=$(git diff --name-only HEAD~1 | codegraph affected-tests --stdin --repo-root .)
+TESTS=$(git diff --name-only HEAD~1 | codegraph affected-tests --stdin)
 go test $TESTS
 ```
 
+Replace `--repo-root .` with nothing if you are already in the repo you want to inspect.
+
 ---
 
 ## Optional: Embeddings & Agentic Mode
@@ -397,6 +401,16 @@ Created with `codegraph config init --repo .` at `.codegraph/config.json`:
 }
 ```
 
+### Repo Root Resolution
+
+When `--repo-root` (CLI) or `repo_root` (MCP tool parameter) is omitted, codegraph resolves the repo root using:
+
+1. Per-call `repo_root` MCP tool parameter
+2. `--repo-root` CLI flag (process-level default)
+3. `git rev-parse --show-toplevel` from the current working directory
+4. `os.Getwd()` (current working directory)
+5. Return error
+
 ### Ignore file
 
 Create `.codegraphignore` in the repo root (same syntax as `.gitignore`):

docs/ai-assistant-guidance.md

@@ -6,7 +6,7 @@ This repository ships `codegraph`, a local-first code context engine and MCP ser
 
 - Run `codegraph install` once to set up local configuration and optional editor/tool integration.
 - Run `codegraph index <repo>` to build the initial graph.
-- Use `codegraph serve --repo-root <repo>` for stdio MCP integration.
+- Use `codegraph serve` for stdio MCP integration (repo root auto-detected).
 - Prefer MCP tools for repository context instead of repeated shelling out.
 
 ## Guidance For Tool-Driven Work

docs/codegraph-roadmap.md

@@ -37,11 +37,11 @@ Observed in `internal/cli/app.go:Run` dispatch and `printUsage`:
 - `doctor`
 - `config <show|edit-path|validate|init>`
 - `benchmark`
-- `serve --repo-root <repo-path>`
+- `serve [--repo-root <repo-path>]`
 - `watch <repo-path>`
 - `graph export <repo-path> [--format json|dot] ...`
-- `affected-tests [--repo-root PATH] [--stdin] [--json] [--limit N] <file>...`
-- `visualize [--repo-root PATH] ...`
+- `affected-tests [--repo-root PATH] [--stdin] [--json] [--limit N] <file>...` (repo root auto-detects when omitted)
+- `visualize [--repo-root PATH] ...` (repo root auto-detects when omitted)
 - `clean [repo-path] [--vacuum]`
 
 Notes:

examples/README.md

@@ -13,7 +13,7 @@ This directory contains minimal `codegraph` MCP server configuration examples fo
 All examples start the same server command:
 
 ```text
-codegraph serve --repo-root /absolute/path/to/repo
+codegraph serve
 ```
 
 Replace `/absolute/path/to/repo` with the repository you want `codegraph` to serve.
@@ -23,7 +23,7 @@ Replace `/absolute/path/to/repo` with the repository you want `codegraph` to ser
 `codex-mcp.toml` includes:
 
 - `command = "codegraph"`
-- `args = ["serve", "--repo-root", "..."]`
+- `args = ["serve"]`
 - `startup_timeout_sec = 60`
 
 Keep `startup_timeout_sec = 60` so Codex allows enough time for the server to open or migrate the local SQLite database on startup.
@@ -33,7 +33,7 @@ Keep `startup_timeout_sec = 60` so Codex allows enough time for the server to op
 The JSON examples are intentionally minimal:
 
 - `command`: `codegraph`
-- `args`: `["serve", "--repo-root", "/absolute/path/to/repo"]`
+- `args`: `["serve"]`
 
 If `codegraph` is not on `PATH`, replace `command` and `args` with a form that launches it through `go run` from the repository checkout.
 

examples/claude-desktop-mcp.json

@@ -2,11 +2,9 @@
   "mcpServers": {
     "codegraph": {
       "command": "codegraph",
-      "args": [
-        "serve",
-        "--repo-root",
-        "/absolute/path/to/repo"
-      ]
+        "args": [
+          "serve"
+        ]
     }
   }
 }

examples/codex-mcp.toml

@@ -1,4 +1,4 @@
 [mcp_servers.codegraph]
 command = "codegraph"
-args = ["serve", "--repo-root", "/absolute/path/to/repo"]
+args = ["serve"]
 startup_timeout_sec = 60

examples/gemini-mcp.json

@@ -2,11 +2,9 @@
   "mcpServers": {
     "codegraph": {
       "command": "codegraph",
-      "args": [
-        "serve",
-        "--repo-root",
-        "/absolute/path/to/repo"
-      ]
+        "args": [
+          "serve"
+        ]
     }
   }
 }

internal/cli/app.go

@@ -155,11 +155,11 @@ func runDoctor(ctx context.Context, cfg config.Config, stdout io.Writer, args []
 	deep := fs.Bool("deep", false, "run deeper (potentially slow) diagnostics, including integrity_check")
 	repoRootFlag := fs.String("repo-root", "", "repository root to inspect (optional)")
 
-	defaultRepoRoot := ""
-	if config.IsRepoDBDir(cfg.DBDir) {
-		defaultRepoRoot = "."
+	repoRootCandidate, err := parseOptionalRepoRootArg(fs, args, repoRootFlag, "")
+	if err != nil {
+		return err
 	}
-	repoRoot, err := parseOptionalRepoRootArg(fs, args, repoRootFlag, defaultRepoRoot)
+	repoRoot, err := config.ResolveRepoRoot(repoRootCandidate, "")
 	if err != nil {
 		return err
 	}
@@ -601,8 +601,8 @@ func runInstall(stdout io.Writer) error {
 }`)
 
 	// Always print manual snippets as a fallback / reference.
-	codexSnippet := fmt.Sprintf("[mcp_servers.codegraph]\ncommand = %q\nargs = [\"serve\", \"--repo-root\", \"/absolute/path/to/repo\"]\nstartup_timeout_sec = 60", appname.BinaryName)
-	clientSnippet := fmt.Sprintf(`{"mcpServers":{"codegraph":{"command":%q,"args":["serve","--repo-root","/absolute/path/to/repo"]}}}`, appname.BinaryName)
+	codexSnippet := fmt.Sprintf("[mcp_servers.codegraph]\ncommand = %q\nargs = [\"serve\"]\nstartup_timeout_sec = 60", appname.BinaryName)
+	clientSnippet := fmt.Sprintf(`{"mcpServers":{"codegraph":{"command":%q,"args":["serve"]}}}`, appname.BinaryName)
 	fmt.Fprintln(stdout)
 	fmt.Fprintln(stdout, "Manual MCP snippets (if auto-configure did not apply):")
 	fmt.Fprintln(stdout)
@@ -639,9 +639,13 @@ func runIndex(ctx context.Context, cfg config.Config, stdout io.Writer, cmdName
 	if err := fs.Parse(filtered); err != nil {
 		return err
 	}
-	repoRoot := "."
+	repoRootCandidate := ""
 	if fs.NArg() > 0 {
-		repoRoot = fs.Arg(0)
+		repoRootCandidate = fs.Arg(0)
+	}
+	repoRoot, err := config.ResolveRepoRoot(repoRootCandidate, "")
+	if err != nil {
+		return err
 	}
 	app, repo, repoID, err := openApp(ctx, cfg, repoRoot)
 	if err != nil {
@@ -1150,11 +1154,13 @@ func runStats(ctx context.Context, cfg config.Config, stdout io.Writer, args []s
 	if err := fs.Parse(args); err != nil {
 		return err
 	}
-	repoRoot := "."
-	if *repoRootFlag != "" {
-		repoRoot = *repoRootFlag
-	} else if fs.NArg() > 0 {
-		repoRoot = fs.Arg(0)
+	repoRootCandidate := strings.TrimSpace(*repoRootFlag)
+	if repoRootCandidate == "" && fs.NArg() > 0 {
+		repoRootCandidate = fs.Arg(0)
+	}
+	repoRoot, err := config.ResolveRepoRoot(repoRootCandidate, "")
+	if err != nil {
+		return err
 	}
 	app, _, repoID, err := openApp(ctx, cfg, repoRoot)
 	if err != nil {
@@ -1185,15 +1191,12 @@ func runQueryCommand(ctx context.Context, cfg config.Config, stdout io.Writer, q
 		return err
 	}
 
-	repoRoot := "."
-	if *repoRootFlag != "" {
-		repoRoot = *repoRootFlag
-	}
+	repoRootCandidate := strings.TrimSpace(*repoRootFlag)
 	queryValue := *queryFlag
 	symbol := ""
 	rest := fs.Args()
-	if *repoRootFlag == "" && len(rest) > 0 {
-		repoRoot = rest[0]
+	if repoRootCandidate == "" && len(rest) > 0 {
+		repoRootCandidate = rest[0]
 		rest = rest[1:]
 	}
 	if queryValue == "" && len(rest) > 0 {
@@ -1209,6 +1212,10 @@ func runQueryCommand(ctx context.Context, cfg config.Config, stdout io.Writer, q
 		symbol = queryValue
 	}
 
+	repoRoot, err := config.ResolveRepoRoot(repoRootCandidate, "")
+	if err != nil {
+		return err
+	}
 	app, _, repoID, err := openApp(ctx, cfg, repoRoot)
 	if err != nil {
 		return err
@@ -1309,18 +1316,20 @@ func runServe(ctx context.Context, cfg config.Config, stdout, stderr io.Writer,
 	if err := fs.Parse(args); err != nil {
 		return err
 	}
-	repoRoot := "."
-	if *repoRootFlag != "" {
-		repoRoot = *repoRootFlag
-	} else if fs.NArg() > 0 {
-		repoRoot = fs.Arg(0)
+	repoRootCandidate := strings.TrimSpace(*repoRootFlag)
+	if repoRootCandidate == "" && fs.NArg() > 0 {
+		repoRootCandidate = fs.Arg(0)
+	}
+	repoRoot, err := config.ResolveRepoRoot(repoRootCandidate, "")
+	if err != nil {
+		return err
 	}
 	app, repo, repoID, err := openApp(ctx, cfg, repoRoot)
 	if err != nil {
 		return err
 	}
 	defer app.Close()
-	server := mcp.NewServer(repo.RootPath, repoID, app.Store, app.Indexer, app.Query, stderr)
+	server := mcp.NewServer(repoRootCandidate, repo.RootPath, repoID, app.Store, app.Indexer, app.Query, stderr)
 	if repoCfg, err := config.LoadRepo(repo.RootPath); err == nil {
 		if repoCfg.Agent.Enabled || repoCfg.Agent.BaseURL != "" || repoCfg.Agent.Model != "" {
 			server.SetAgentConfig(repoCfg.Agent.BaseURL, repoCfg.Agent.Model)
@@ -1337,11 +1346,13 @@ func runWatch(ctx context.Context, cfg config.Config, stdout io.Writer, args []s
 	if err := fs.Parse(args); err != nil {
 		return err
 	}
-	repoRoot := "."
-	if *repoRootFlag != "" {
-		repoRoot = *repoRootFlag
-	} else if fs.NArg() > 0 {
-		repoRoot = fs.Arg(0)
+	repoRootCandidate := strings.TrimSpace(*repoRootFlag)
+	if repoRootCandidate == "" && fs.NArg() > 0 {
+		repoRootCandidate = fs.Arg(0)
+	}
+	repoRoot, err := config.ResolveRepoRoot(repoRootCandidate, "")
+	if err != nil {
+		return err
 	}
 	app, repo, repoID, err := openApp(ctx, cfg, repoRoot)
 	if err != nil {
@@ -1498,18 +1509,24 @@ func runGraph(ctx context.Context, cfg config.Config, stdout io.Writer, args []s
 func runVisualize(ctx context.Context, cfg config.Config, stdout io.Writer, args []string) error {
 	fs := flag.NewFlagSet("visualize", flag.ContinueOnError)
 	fs.SetOutput(io.Discard)
-	repoRoot := fs.String("repo-root", ".", "repository root")
+	repoRootFlag := fs.String("repo-root", "", "repository root")
 	symbol := fs.String("symbol", "", "focus on a specific symbol")
 	output := fs.String("output", "", "write HTML to this file instead of opening a browser")
 	depth := fs.Int("depth", 2, "traversal depth from focus symbol")
 	if err := fs.Parse(args); err != nil {
 		return err
 	}
-	if fs.NArg() > 0 && *repoRoot == "." {
-		*repoRoot = fs.Arg(0)
+
+	repoRootCandidate := strings.TrimSpace(*repoRootFlag)
+	if repoRootCandidate == "" && fs.NArg() > 0 {
+		repoRootCandidate = fs.Arg(0)
+	}
+	repoRoot, err := config.ResolveRepoRoot(repoRootCandidate, "")
+	if err != nil {
+		return err
 	}
 
-	app, _, repoID, err := openApp(ctx, cfg, *repoRoot)
+	app, _, repoID, err := openApp(ctx, cfg, repoRoot)
 	if err != nil {
 		return err
 	}
@@ -1571,11 +1588,11 @@ func runClean(ctx context.Context, cfg config.Config, stdout io.Writer, args []s
 	incrementalVacuum := fs.Bool("incremental-vacuum", false, "run PRAGMA incremental_vacuum (requires auto_vacuum=INCREMENTAL)")
 	repoRootFlag := fs.String("repo-root", "", "repository root to clean")
 
-	defaultRepoRoot := ""
-	if config.IsRepoDBDir(cfg.DBDir) {
-		defaultRepoRoot = "."
+	repoRootCandidate, err := parseOptionalRepoRootArg(fs, args, repoRootFlag, "")
+	if err != nil {
+		return err
 	}
-	repoRoot, err := parseOptionalRepoRootArg(fs, args, repoRootFlag, defaultRepoRoot)
+	repoRoot, err := config.ResolveRepoRoot(repoRootCandidate, "")
 	if err != nil {
 		return err
 	}
@@ -1962,9 +1979,10 @@ func runAffectedTests(ctx context.Context, cfg config.Config, stdout io.Writer,
 		return err
 	}
 
-	repoRoot := "."
-	if *repoRootFlag != "" {
-		repoRoot = *repoRootFlag
+	repoRootCandidate := strings.TrimSpace(*repoRootFlag)
+	repoRoot, err := config.ResolveRepoRoot(repoRootCandidate, "")
+	if err != nil {
+		return err
 	}
 
 	var files []string
@@ -2049,7 +2067,7 @@ func printRootHelp(w io.Writer) {
 	fmt.Fprintf(w, "  %s index .\n", appname.BinaryName)
 	fmt.Fprintf(w, "  %s stats .\n", appname.BinaryName)
 	fmt.Fprintf(w, "  %s find_symbol . MySymbol\n", appname.BinaryName)
-	fmt.Fprintf(w, "  %s serve --repo-root .\n", appname.BinaryName)
+	fmt.Fprintf(w, "  %s serve\n", appname.BinaryName)
 }
 
 func formatCommandExample(ex string) string {