* feat(cli): add --skip-skills and --index-only flags to analyze command
The `installSkills()` call in `generateAIContextFiles()` runs
unconditionally, injecting 6 skill files into `.claude/skills/gitnexus/`
even when `--skip-agents-md` is passed. This is problematic for bulk
indexing operations on read-only mirrors or third-party repos.
Add two new flags:
- `--skip-skills`: suppress standard GitNexus skill file injection
- `--index-only`: pure index mode that suppresses all file injection
(AGENTS.md, CLAUDE.md, and skills), writing only to `.gitnexus/`
This gives users three levels of control:
- `--skip-agents-md` — suppress only root context files
- `--skip-skills` — suppress only skill injection
- `--index-only` — suppress everything (pure indexing)
Discovery context: while bulk-indexing 176 repos with
`--skip-agents-md`, all 144 indexed repos were contaminated with
`.claude/skills/gitnexus/` files requiring manual cleanup.
* fix(cli): address PR #742 review — gate community skills, drop dangling refs, add tests
Bot review (#742) flagged three issues with the original commit:
1. `--index-only --skills` still wrote community-derived skill files
to `.claude/skills/generated/`. The `--skills` branch in analyze.ts
was not gated by `skipAll`, so the "skip all file injection" contract
was violated. Gate `generateSkillFiles()` with `!skipAll` so
`--index-only` truly wins over `--skills`.
2. `--skip-skills` without `--skip-agents-md` produced AGENTS.md /
CLAUDE.md that still referenced `.claude/skills/gitnexus/*/SKILL.md`
files that were never installed — every agent load incurred 6
failed reads. Pass `skipSkills` through to `generateGitNexusContent()`
and omit the standard-skill rows (and the entire `## CLI` heading
when the table is empty). Community skills, when present via
`--skills`, are unaffected.
3. No filesystem tests for `skipSkills` / `indexOnly`. Add three
regression guards to `test/unit/ai-context.test.ts`:
- `.claude/skills/gitnexus/` is NOT created when skipSkills=true
- Nothing is written when both skipAgentsMd and skipSkills are true
(the resolved-flag state from --index-only)
- AGENTS.md/CLAUDE.md routing table omits standard skill references
when skipSkills=true, but preserves the load-bearing imperative
sections (Always Do / Never Do / Resources)
* test(cli): PR 1485 review follow-ups (help text, gate test, --skip-skills docs)
- Assert --skip-skills and --index-only in analyze --help (skip-git-cli.test.ts).
- Export shouldGenerateCommunitySkillFiles; unit-test index-only+skills gate.
- Clarify --skip-skills does not suppress --skills community files; --index-only for full skip.
Co-authored-by: Cursor <cursoragent@cursor.com>
* fix(cli): warn when --index-only silently overrides --skills
Address review findings on PR 1485 follow-ups:
- analyze.ts emits a one-line note when both --index-only and --skills
are set, so users see why a pipeline re-index ran with no skill files
written.
- index.ts --skills help text now flags the --index-only override.
- shouldGenerateCommunitySkillFiles JSDoc documents the dual role of
the gate (community skills + AGENTS.md/CLAUDE.md re-generation).
- skip-git-cli.test.ts pins the override-warning surface end-to-end.
---------
Co-authored-by: Gergő Magyar <gergomagyar@icloud.com>
Co-authored-by: Cursor <cursoragent@cursor.com>
`upsertGitNexusSection` in ai-context.ts uses `indexOf` to locate the
bounds of the GitNexus section in CLAUDE.md / AGENTS.md before
replacement. `indexOf` matches the first occurrence of the marker
anywhere in the file, including inline prose references in backtick-
quoted fragments mid-sentence.
The shipped CLAUDE.md contains exactly such a reference ("See the
`<!-- gitnexus:start --> … <!-- gitnexus:end -->` block in AGENTS.md
for the canonical MCP tools..."). Running `gitnexus analyze` on a
fresh install matches those inline markers as section delimiters and
replaces the prose between them with the full ~100-line injected
block, breaking the backtick and corrupting markdown for every user.
Fix: new private `findSectionMarkerIndex` helper that only matches
markers occupying their own line — preceded by `\n` or start-of-file,
followed by `\n` / `\r` (CRLF files) / end-of-file. `\r` is explicit
so CRLF-terminated sections on Windows (core.autocrlf = true) still
match. The generator always emits markers alone on their line, so
every legitimate section continues to update in place; only inline
prose references now fall through to the append branch, which leaves
existing content untouched.
Two new unit tests:
- #1041 regression — seed CLAUDE.md with the shipped inline prose
line, run analyze twice, assert inline prose preserved verbatim
and marker counts stay at 2/2 (1 inline + 1 section-position)
- CRLF handling — seed a CRLF file with inline prose + legitimate
section, run analyze, assert section replaced in place, inline
prose preserved, stale stub content removed
No destructive ops, no bypass flags, no new deps. Behaviour change
is strictly narrowing — files that previously updated correctly
still do; files that previously got corrupted now fall through to
the safer append branch.
Closes#1041.
* feat: configure prettier with pre-commit hook integration
Add prettier, lint-staged, and prettier-plugin-tailwindcss at the repo
root with husky pre-commit hook integration. Moves husky from
gitnexus/ to root package.json for reliable hook installation.
- Root package.json with prepare/format/format:check scripts
- .prettierrc with endOfLine:lf and tailwindStylesheet for TW v4
- .prettierignore excluding fixtures, vendor, generated, *.d.ts, *.md
- .gitattributes enforcing LF line endings for Windows consistency
- Pre-commit hook uses direct node_modules/.bin/ paths (no npx)
* style: apply prettier formatting to entire codebase
One-time bulk format. No logic changes.
Use .git-blame-ignore-revs to skip this commit in git blame.
* chore: add .git-blame-ignore-revs for prettier format commit
* perf: pre-commit hook runs only tests related to staged files
Use vitest --related to scope test execution to tests that import
the changed files, instead of running the full suite on every commit.
* perf: remove vitest from pre-commit hook, keep in CI only
Pre-commit now runs lint-staged + tsc only. Tests run in CI
(ci-tests.yml) where they belong — keeps commits fast.
* ci: add prettier format check to quality workflow
PRs will now fail if code isn't formatted with prettier.
- 59 test files covering unit and integration tests
- vitest config with coverage thresholds and fork pooling
- Test fixtures (mini-repo + multi-language sample code)
- Add vitest + coverage-v8 to devDependencies
- Add test scripts (test, test:integration, test:all, test:watch, test:coverage)
- Move typescript to devDependencies where it belongs
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
