docs: close stale hook and script-count records

[BigSimmo]

Summary

• Removes the stale hard-coded script-file count from CLAUDE.md and points to the generated scripts index.
• Archives issue Overlap regression tests, dead mic removal, CSS layering (plan items 3-5) #143 because PR chore(docs): automate documentation synchronization #1442 placed both the shared pre-commit hook and its inventory script under version control with the fail-open linked-worktree behavior.
• Retains no root-directory gate implementation: PR fix: resolve bounded outstanding reliability tasks #1480 already landed the stronger tracked-root coverage gate, so duplicating that code here would add churn without coverage.

RAG impact: no retrieval behaviour change — this is documentation and issue-ledger maintenance only.

Verification

• npm run check:outstanding-issues — passed (146 rows, unique IDs, no merge driver).
• npm run check:branch-review-ledger — passed (205 live + 1206 archived records).
• npm run docs:check-index — passed (49 roots/modules/routes and schema tables indexed).
• npm run docs:check-links — passed (1413 references).
• npx prettier --check CLAUDE.md docs/outstanding-issues.md docs/branch-review-ledger.md — passed.
• git diff --check origin/main — passed.

Not run

No provider-backed, Supabase, OpenAI, browser, build, or deployment checks were run; this final diff is documentation-only.

Risk

Low. The issue-ledger table is temporarily re-padded by the repository formatter; PR #1479 is the separate queued change that removes that conflict-prone padding.

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Review details

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: CHILL

Plan: Pro

Run ID: cc9df437-beb9-43f0-8dbb-a6a70889d5b4

📥 Commits

Reviewing files that changed from the base of the PR and between b100657 and 3986601.

📒 Files selected for processing (3)

• CLAUDE.md
• docs/branch-review-ledger.md
• docs/outstanding-issues.md

📝 Walkthrough

Walkthrough

The coverage checker now includes tracked repository-root directories, validates their documentation, supports root-specific allowlisting, and has expanded tests. Related index, script-count, repository-layout, review-ledger, and issue-ledger documentation were updated.

Changes

Repository index coverage

Layer / File(s)	Summary
Root coverage discovery and gap reporting scripts/check-codebase-index-coverage.mjs	The checker discovers tracked root directories, adds root coverage candidates and section bounds, distinguishes root identifiers, and updates missing-coverage output.
Root coverage test coverage tests/codebase-index-coverage.test.ts	Tests cover missing root directories, documented roots, module-name collisions, and allowlisted root gaps.
Index and script documentation alignment CLAUDE.md, docs/codebase-index.md, docs/scripts-index.md, docs/branch-review-ledger.md	Repository layout, top-level directory guidance, script counts, and the coverage review record were updated.

Outstanding issue record correction

Layer / File(s)	Summary
Issue 143 ledger correction docs/outstanding-issues.md	The issue record now reflects the committed fail-open change, its undistributed branch state, and corrected path-mangling details.

Estimated code review effort: 3 (Moderate) | ~20 minutes

Sequence Diagram(s)

sequenceDiagram
  participant Git
  participant CoverageChecker
  participant CodebaseIndex
  participant Allowlist
  Git->>CoverageChecker: provide tracked repository paths
  CoverageChecker->>CoverageChecker: discover root, module, and route groups
  CoverageChecker->>CodebaseIndex: extract documented coverage spans
  CodebaseIndex-->>CoverageChecker: documented entries
  CoverageChecker->>Allowlist: check suppressed gaps
  CoverageChecker-->>CodebaseIndex: report remaining missing entries

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Possibly related PRs

• BigSimmo/Database#1109: Both PRs update docs/outstanding-issues.md ledger content.
• BigSimmo/Database#1193: Both PRs append records to docs/branch-review-ledger.md.

Suggested reviewers: cursoragent

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 50.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Title check	✅ Passed	The title matches the docs-only cleanup theme and mentions real parts of the change, though it omits the root-coverage update.
Description check	✅ Passed	The description covers Summary, Verification, Not run, and Risk; only non-critical template sections are missing for this docs-only PR.

✨ Finishing Touches 💡 1

📝 Generate docstrings 💡

• Create stacked PR
• Commit on current branch

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[BigSimmo]

@cursoragent resolve merge conflict

[cursor]

Merge conflict on PR #1458 is resolved and pushed.

Commit: b1006572 — merged origin/main into claude/root-dir-coverage-gate-v2

Conflicts resolved:

• docs/codebase-index.md — kept the new .cursor/ / .design-sync/ / .vscode/ rows, and kept main’s rag-coverage-gate entry
• docs/scripts-index.md — kept the corrected 191/206 counts
• docs/outstanding-issues.md — took main’s #144 renumber and #135–#137 status updates; kept this PR’s MSYS-corrected #143 text

Verified: docs:check-index (49 covered), check:outstanding-issues, docs:check-scripts, ledger guard, and the 10 coverage unit tests all pass. git merge-tree against origin/main is clean (16 ahead, 0 behind).

PR: #1458

  

[coderabbitai]

Actionable comments posted: 1

Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (1)

scripts/check-codebase-index-coverage.mjs (1)

135-145: 📐 Maintainability & Code Quality | 🟡 Minor | ⚡ Quick win

Update the success message for root coverage.

discoverGroups() now adds kind: "root" groups, but the success path at Line 163 still describes the total as “top-level modules/routes.” Use “top-level directories/modules/routes” or “coverage groups” so successful output accurately reflects the new scope.

Proposed fix

-    `${INDEX_PATH} coverage OK: all ${groups.length} top-level modules/routes and ${tables.missing.length + tables.stale.length === 0 ? "all" : "checked"} schema tables are indexed.`,
+    `${INDEX_PATH} coverage OK: all ${groups.length} top-level directories/modules/routes and ${tables.missing.length + tables.stale.length === 0 ? "all" : "checked"} schema tables are indexed.`,

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@scripts/check-codebase-index-coverage.mjs` around lines 135 - 145, Update the
success message in the coverage reporting path that consumes discoverGroups() so
it no longer describes the total only as “top-level modules/routes”; refer to
“top-level directories/modules/routes” or “coverage groups,” while preserving
the existing success behavior and formatting.

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@docs/outstanding-issues.md`:
- Line 163: The issue description redundantly repeats the primary-checkout state
and does not identify the affected artifact. Update issue `#143`’s “Why this is
not a fix” text to state clearly that the fail-open hook copy used by the shared
core.hooksPath is untracked in the primary checkout, so the mitigation is not
version-controlled or distributed. Remove the duplicated sentence while
preserving the surrounding distribution and merge-status details.

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Outside diff comments:
In `@scripts/check-codebase-index-coverage.mjs`:
- Around line 135-145: Update the success message in the coverage reporting path
that consumes discoverGroups() so it no longer describes the total only as
“top-level modules/routes”; refer to “top-level directories/modules/routes” or
“coverage groups,” while preserving the existing success behavior and
formatting.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: CHILL

Plan: Pro

Run ID: 32c5d0ac-2329-48a3-adc6-19dfa883d0f5

📥 Commits

Reviewing files that changed from the base of the PR and between 9e1d9cf and b100657.

📒 Files selected for processing (7)

• CLAUDE.md
• docs/branch-review-ledger.md
• docs/codebase-index.md
• docs/outstanding-issues.md
• docs/scripts-index.md
• scripts/check-codebase-index-coverage.mjs
• tests/codebase-index-coverage.test.ts