chore(specs): gardener checkbox sync

[Dumbris]

17 ticks applied, 3 un-ticks proposed (not applied), 22 candidates examined-and-dropped as false alarms, run date 2026-09-21.

Scope of this run: the deterministic checker (scripts/check-spec-evidence.py) flagged 193 possibly_built tick candidates and 72 currently-ticked tasks with no resolvable artifact (67 UNRESOLVED + 5 REMOVED) across 75 specs. Every one of those 265 candidates was hand-verified against the actual code (reading the cited files, tracing wiring, and — for the applied batch — independently re-running the cited tests) before any checkbox changed. 36 additional RELOCATED findings were informational-only (work exists at a different path) and required no action.

Applied ticks

All 17 applied ticks are in specs/105-agent-scope-hardening/tasks.md, Phase 1 (Setup) and Phase 2 (PR A — scope-target-identity-producers). These tasks describe already-shipped, already-tested code that simply never got its checkbox flipped after merge. Each was independently re-verified by this run (not just trusted from the sub-review): the cited tests were re-run live and passed, and the cited symbols were re-grepped directly.

Task	file:line	Decisive evidence
T001	internal/server/scope_fixture_test.go:41,55	func agentCtx(allowed []string, perms []string, pin string) context.Context / func adminCtx() — present, used across the T00x test suite
T002	internal/server/scope_fixture_test.go:121	func startCountingUpstream(t *testing.T, proxy *MCPProxyServer, rt *runtime.Runtime, server string, tools ...toolSpec) *countingUpstream — called 48× across internal/server/*_test.go
T003	specs/105-agent-scope-hardening/spec.md:6,107,108,126,128,132,166,168	All six required spec-text amendments (FR-008 empty-raw-name, FR-003/004 zero-reach, SC-007 restatement, FR-009 unresolved-refuses-every-caller, FR-002 anonymous callers, SC-005 admin exceptions) present verbatim
T004	internal/runtime/tool_quarantine_identity_test.go + internal/server/mcp_call_tool_target_tier_test.go:1448-1466	TestCheckToolApprovals_NamespacedTool_PendingUnderRawName / TestCallToolRead_NamespacedTool_NoOwnRecord_IsPendingNotInherited — re-run live, PASS
T005	internal/runtime/lifecycle_identity_test.go:86,110 + internal/index/bleve_rawname_test.go	TestApplyDifferentialToolUpdate_ExactNameDisabledRecordSurvivesRerun and paired-raw-name docID tests — pass
T006	internal/server/mcp_direct_callability_test.go:255 + internal/server/preflight_glue_test.go:460	TestDirectDispatch_CollapsedOrAbsentApprovalIsPendingNotReady / TestPreflight_CollapsedPendingRecordIsPendingNotReady — re-run live, PASS
T007	internal/server/mcp_call_tool_target_tier_test.go:1495 + internal/server/mcp_code_execution_scope_test.go:84	TestCallToolRead_UnresolvedIdentityOnKnownServer_RefusedForEveryCaller (full-tier + admin refused, zero upstream) — re-run live, PASS
T008	internal/server/tool_gate_test.go:96,170	TestToolGate_NoApprovalRecordUnderActiveGate_IsPending / TestToolGate_QuarantineDisabled_NoRecordStaysCallable — pass
T009	internal/server/scope_target_tier_matrix_test.go:297,338,444,561	TestScopeTargetTier_RetrieveTable / _DirectTable / _NestedTable — generated 54-cell + direct + nested + paired-name tables, pass
T010	internal/server/scope_target_tier_matrix_test.go:338	TestScopeTargetTier_RetrieveTable_ReadDestructive — re-run live, PASS (all 18 subtests)
T011	internal/config/tool_identity.go:39	func RawToolName(tool *ToolMetadata) string prefers the RawName stamp — confirmed present, populated at internal/upstream/core/client.go:396
T012	internal/runtime/tool_quarantine.go:504 + internal/runtime/lifecycle.go:816,821	toolName := config.RawToolName(tool) / oldToolsMap[config.RawToolName(tool)] = tool — confirmed live
T013	internal/index/bleve.go:188,240	toolName := config.RawToolName(toolMeta) (docID) / RawName: strings.TrimPrefix(canonical, serverName+":") (read-side) — confirmed live
T014	internal/server/tool_gate.go:249 + internal/preflight/classify.go:116-120	lookupToolApproval exact-wins + pending-on-nil-under-gate; ClassifyTool consults the gate before Ready
T015	internal/server/mcp.go:2687-2689 + internal/jsruntime/runtime.go:146,612	const PermissionTierUnresolved = "unresolved"; retrieve and nested both refuse on it — re-run live, PASS
T016	docs/features/agent-tokens.md:152	### Target tool tier section replaces the old "destructive implies both" claim (confirmed absent via grep)
T017	internal/server/mcp_call_tool_target_tier_test.go:238-260	Ghost-tool cells inverted (comment documents the FR-009 inversion); extractToolName has zero remaining references in internal/server/*.go (confirmed via grep)

ROADMAP.md was regenerated (python3 scripts/gen-roadmap.py) in a separate commit after the checkbox commit, per the pre-commit hook requirement — spec 105's progress moved from 82/112 (73%) to 99/112 (88%). ROADMAP.md and roadmap.yaml were not hand-edited.

Proposed un-ticks (NOT applied)

These are currently - [x] but no artifact proving the promised behavior could be found. Flagged for human review only — never un-ticked by this run.

Task	Claim	Why it looks false
102-schema-deferred T026	Regression test for R14 (a servers.changed event published immediately after NewServer returns still reaches the direct rebuild)	The production fix is real (SubscribeEvents hoisted before StartBackgroundInitialization, internal/server/server.go:380-395), but no test constructs a Server and asserts a servers.changed fired immediately after construction is not dropped. The existing mcp_direct_init_test.go covers the related-but-distinct T024 (D15 initial-rebuild) claim, not this one.
044-diagnostics-taxonomy T071	macOS tray "Fix Issues (N)" submenu	No FixIssuesMenu.swift or any "Fix Issues" UI exists anywhere in native/macos/. The backing state property serversWithDiagnostic (State/AppState.swift:330) carries its own doc comment: "Nothing consumes this today, which is exactly why the drift would have gone unnoticed until something did." First-party confirmation the submenu was never built.
044-diagnostics-taxonomy T080	CLI test asserting doctor --server <name> table/JSON/YAML output formatting	cmd/mcpproxy/doctor_cmd_test.go's 17 test functions all cover pre-existing general doctor output formatting; none exercise the --server flag (which does exist, doctor_cmd.go:79) or the new per-server diagnostics REST response format.

Dropped by verification

Every other candidate the deterministic checker surfaced was examined and dropped. Grouped by why:

Tick candidates rejected (176 of 193) — task genuinely not built despite a matching filename/keyword hit:

• 058-mcp-2026-upgrade: all 40 rejected — Phase 3 onward (protocol-era-aware work: session statelessness, IsModernRequest gating, era-split tests, header validation, input_required detection, trace propagation, cache hints) genuinely has not landed; the evidence script matched on file existence, not the described behavior. Notably, this run also found the Phase-1 checkpoint note in tasks.md ("fails only TestProfile_SetProfileSessionScoped and TestProfile_SetProfileUnknown") no longer holds — both tests currently pass, because the client-facing protocol pin (T041, still unticked) hasn't been lifted. Not a checkbox issue, flagged for whoever picks up Phase 3.
• 009-proactive-oauth-refresh: all 21 rejected — missing frontend fields/computeds (oauthExpired, isAuthenticated, expiry badges), missing CLI --all logout loop, missing logout contract tests, missing OAS coverage (scripts/verify-oas-coverage.sh currently fails at 74.3%).
• 042-telemetry-tier2: all 12 rejected — real, wired production code (surface classifiers, error-category recording, startup-outcome tracking) consistently lacking the specific unit test the task promises; T057 also found ErrCatOAuthTokenExpired is defined but never recorded anywhere.
• 044-diagnostics-taxonomy: all 9 rejected — no go:generate codegen for internal/diagnostics (T004/T203), REST-level assertions and new-endpoint docs missing (T162/T202), e2e script never exercises the new endpoints (T034/T083).
• 001-code-execution: all 13 rejected — sandbox error-propagation, execution-ID, and code exec CLI-flag tests all absent; only success-path coverage exists.
• 004-management-health-refactor: all 9 rejected — named helper functions (logHTTPRequest, redactToken, sanitizeAuthHeader, monitorDockerLogsWithContext) don't exist at all; CLI E2E tests are unit-level formatting tests only.
• 006-oauth-extra-params: 6 of 7 rejected — auth-status output is missing masking, redirect-URI display, and last-refresh display; only T045 (full auth URL printed on login) confirmed.
• 017-activity-cli-commands: all 8 rejected — cited tests check unrelated things (cobra flag defaults, HTTP status codes) rather than the CLI behavior the task names; two are unverifiable "ran the linter/E2E suite" process claims.
• 001-oas-endpoint-documentation: all 6 rejected — three new REST endpoint families (/secrets/*, /code/exec, /events) have no swagger annotations and are absent from oas/swagger.yaml.
• 001-update-version-display, 008-oauth-token-refresh, 007-oauth-e2e-testing, 028-agent-tokens, 040-server-ux, 003-tool-annotations-webui, 026-pii-detection, 077-scanner-simplification, and 18 small specs: remaining rejections follow the same pattern — real underlying feature code with the specific test, doc section, or UI wiring the task promises still missing. Full per-task reasoning was captured during review; omitted here for length but available on request.
• A recurring category worth naming: several rejected tasks (017 T059/T060, 077 T040/T041, 083 T041, 096 T016, 097 T014, 098 T032) are "run the full verification gate and confirm green" process tasks where the only cited evidence was the pre-existing, repo-wide .github/.golangci.yml — that file existing proves nothing about whether this spec's gate was actually run. Treated as unverifiable, left unticked.

Un-tick candidates dropped (69 of 72) — ticked correctly, artifact just relocated or renamed, not missing:
The dominant pattern across 026-pii-detection (26), 107-server-edition-sso-hardening (11), 004-management-health-refactor (6), 001-oas-endpoint-documentation (5), 001-update-version-display (5), 044-retention-telemetry-v3 (6), and the rest: tasks.md cites a per-domain filename (e.g. internal/contracts/server.go, patterns/files.go, commands/activity.go) that was consolidated into a single file (internal/contracts/types.go, internal/security/paths.go, cmd/mcpproxy/activity_cmd.go) during refactors, or a Swift/native path was abbreviated with ... in the task text. In every one of these 69 cases the actual behavior and its test were located, read, and confirmed to match the task's claim. Two (107 T015/T016) are intentional deletion tasks, confirmed as correctly executed (the named symbols are genuinely gone, guarded by a regression test asserting their absence). One soft spot noted for a human, not a checkbox action: 107 T036's cache-TTL-clamp sub-clause is implemented with correct constants but has no dedicated unit test asserting the clamp behavior by name — everything else in that compound task is solidly tested.

Notes

• Verification was performed by 9 parallel code-reading passes (one per spec cluster), each independently applying the tick test (behavior over keyword-matching, real vs. stub/unwired, adversarial "argue the opposite" pass) before this run cross-checked a sample of the applied-tick batch directly (re-ran 5 of the 17 cited tests live, re-grepped 6 of the cited symbols) rather than trusting the sub-review verbatim.
• Cap: 17 of 40 allowed applied ticks used this run.
• Previous PR for this branch (chore(specs): gardener checkbox sync #1277) had already been merged; this run reset claude/spec-gardener to main before starting (only already-merged history was discarded, confirmed via git rebase dropping both prior commits as "patch already upstream").

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