chore: full maintenance pass (2026-06)

[llbbl]

Closes #3

Full maintenance pass on chore/maintenance-2026-06. Tests: 279 → 306 pass · Lint: clean · 0 security vulnerabilities.

Bug fixes

• bun lockfile detection (src/lib/detect.ts) — now recognizes both bun.lock (Bun 1.2+ text format) and bun.lockb. Modern Bun projects were misdetected as npm.
• .gitignore coverage-entry matcher (src/lib/detect.ts) — strict matching of the 6 patterns that actually ignore root coverage/ (coverage, coverage/, /coverage, /coverage/, **/coverage, **/coverage/). Was matching coverage-final.json and similar.
• hasCoverageConfig false positives (src/lib/vitest-config.ts) — strips comments and string-literal contents before applying the coverage: regex so // coverage: mentions or URLs don't fool the check command.
• Zero-line files in filterBelowThreshold (src/lib/coverage.ts) — skip files with lines.total === 0 (type-only .d.ts, empty barrels) instead of reporting them as misleading "0% / 0 of 0".

Polish

• Warn on malformed config (src/lib/config.ts) — readPackageJsonConfig / config-file loader no longer swallow parse errors silently. Writes a one-line [uncov] warning: ... to stderr (ENOENT still silent via err.code).
• --help documentation (src/cli.ts) — adds --coverage-path, -c <p> and --force to the OPTIONS section.

Dep bumps (low-risk minor/patch)

• @biomejs/biome 2.4.6 → 2.4.16
• @types/bun 1.3.10 → 1.3.14

Cleanup

• Removed unused barrel files: src/{commands,lib,utils}/index.ts (knip flagged, no consumers).
• Un-exported internal-only types FileCoverage, CoverageMetric in src/lib/coverage.ts.
• Stopped tracking .beads/ (issue-tracker state moved to local-only), removed dead .gitattributes (only held the bd merge rule), removed bd-installed git hooks (.git/hooks/post-merge, pre-commit).
• Reorganized .gitignore: single "Agent / IDE context" section grouping .claude/, .gemini/, .cursor/, .agent/, .amp/, .codex/, .antigravity/, and the per-tool *.md context files.

Test plan

• bun test — 306 pass
• bun run lint — clean
• bun audit — 0 vulnerabilities
• bunx knip — targeted findings cleared

[socket-security]

Review the following changes in direct dependencies. Learn more about Socket for GitHub.

Diff	Package	Supply Chain Security	Vulnerability	Quality	Maintenance	License
	@​types/​bun@​1.3.10 ⏵ 1.3.14
	@​biomejs/​biome@​2.4.6 ⏵ 2.4.16	+1			+1

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[codecov]

Codecov Report

❌ Patch coverage is 91.17647% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 95.74%. Comparing base (8e5ae02) to head (985b24a).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/lib/vitest-config.ts	84.61%	2 Missing ⚠️
src/lib/config.ts	90.90%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main       #4      +/-   ##
==========================================
- Coverage   95.88%   95.74%   -0.14%     
==========================================
  Files          13       13              
  Lines         680      705      +25     
==========================================
+ Hits          652      675      +23     
- Misses         28       30       +2     

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