fix(hooks): auto-stage .gemini, .claude, .codex directories on commit

[konard]

Summary

Fixes #170

The pre-commit hook and setup infrastructure had three issues preventing automatic backup of AI agent config directories (.gemini, .claude, .codex):

1. .claude was listed in .gitignore — making it impossible to track in git
2. Pre-commit hook only staged .knowledge directories — .gemini, .claude, .codex were never auto-staged
3. setup-pre-commit-hook.js required a manual git config core.hooksPath .githooks step — easy to forget, causing all hooks (including pre-push session backup) to never activate

Changes

• .gitignore: Remove .claude entry so the directory can be tracked
• .githooks/pre-commit: Add auto-staging loop for .gemini, .claude, .codex directories (same pattern as existing .knowledge staging)
• scripts/setup-pre-commit-hook.js:
  • Include AI directory staging in the generated pre-commit hook template
  • Auto-configure core.hooksPath = .githooks instead of printing a manual instruction

How it works

On every git commit, the pre-commit hook now:

1. Splits/stages .knowledge directories (existing behavior)
2. Auto-stages any existing .gemini, .claude, .codex directories (new)
3. Checks file size limits (existing behavior)
4. Runs secret guard (existing behavior)

On git push, the existing pre-push hook (which was already in .githooks/pre-push) runs session backup via session-backup-gist.js. This hook was already correct — the problem was that core.hooksPath was never set, so it was never invoked.

Root cause

The setup-pre-commit-hook.js script (run via npm run setup:pre-commit-hook) only printed a message telling the user to run git config core.hooksPath .githooks manually. If that step was skipped, no hooks ran at all — neither pre-commit nor pre-push.

Tests

Added packages/app/tests/hooks/pre-commit-ai-dirs.test.ts with 10 tests covering:

AI directory auto-staging logic (isolated temp git repos):

• ∀ dir ∈ {.gemini, .claude, .codex}: exists(dir) → staged(dir/*)
• Skips non-existent directories without error
• Stages nested files recursively
• Handles empty directories gracefully

setup-pre-commit-hook.js:

• Creates .githooks/pre-commit with executable permissions
• Generated hook contains AI directory staging snippet
• Configures git core.hooksPath to .githooks
• Idempotent — running setup twice produces identical result

Committed files verification:

• .gitignore does not block .claude, .gemini, .codex
• Hook file has correct shebang, strict mode, and staging logic

Test plan

• All 10 new tests pass locally (vitest)
• Full test suite passes (166 tests across app + lib)
• Lint passes with zero errors (ESLint, Biome, TypeScript)
• No code duplicates detected
• CI checks passing

🤖 Generated with Claude Code

[konard]

🤖 Solution Draft Log

This log file contains the complete execution trace of the AI solution draft process.

💰 Cost estimation:

• Public pricing estimate: $4.237149
• Calculated by Anthropic: $2.325822 USD
• Difference: $-1.911327 (-45.11%)

🤖 Models used:

• Tool: Claude
• Requested: opus
• Model: Claude Opus 4.6 (claude-opus-4-6)

📎 Log file uploaded as Gist (953KB)

• View complete solution draft log

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Now working session is ended, feel free to review and add any feedback on the solution draft.

[skulidropek]

Напиши тесты
Надо иметь гарантии того что логика работает

[konard]

🔄 Auto-restart triggered (iteration 1)

Reason: New comment(s) from non-bot user(s): skulidropek

Starting new session to address the issues.

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[konard]

@skulidropek Added tests as requested! 🧪

packages/app/tests/hooks/pre-commit-ai-dirs.test.ts — 10 tests covering:

1. AI directory auto-staging logic (4 tests in isolated temp git repos):

   • Stages all three directories when they exist
   • Skips non-existent directories without error
   • Stages nested files recursively
   • Handles empty directories gracefully

2. setup-pre-commit-hook.js (4 tests):

   • Creates hook file with executable permissions
   • Generated hook contains the AI staging snippet
   • Configures core.hooksPath automatically
   • Idempotent — running twice gives identical result

3. Committed files verification (2 tests):

   • .gitignore doesn't block .claude, .gemini, .codex
   • Hook file has correct shebang, strict mode, and staging logic

All 166 tests pass (app + lib), zero lint errors, zero duplicates.

[konard]

🔄 Auto-restart-until-mergeable Log (iteration 1)

This log file contains the complete execution trace of the AI solution draft process.

💰 Cost estimation:

• Public pricing estimate: $6.714196
• Calculated by Anthropic: $4.182234 USD
• Difference: $-2.531963 (-37.71%)

🤖 Models used:

• Tool: Claude
• Requested: opus
• Model: Claude Opus 4.6 (claude-opus-4-6)

📎 Log file uploaded as Gist (2635KB)

• View complete solution draft log

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Now working session is ended, feel free to review and add any feedback on the solution draft.

[konard]

✅ Ready to merge

This pull request is now ready to be merged:

• All CI checks have passed
• No merge conflicts
• No pending changes

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