chore: add stderr.write lint rule and document repo standards gaps

[BYK]

Summary

Adds automated enforcement and documentation for patterns that fell through existing checks during PR #904 review.

Changes

Automated Enforcement

• New GritQL rule (no-stderr-write-in-commands.grit): Bans stderr.write() in src/commands/**. Complements the existing no-stdout-write-in-commands.grit rule. Commands should use logger.withTag() for warnings and log.debug() for diagnostics.
• Fix existing violation in issue/merge.ts: The --into preference warning now uses log.warn() instead of this.stderr.write().

Documentation (AGENTS.md)

Four new sections addressing gaps identified during PR #904 review:

1. Catch Block Logging — Prohibits silent catch blocks in production code. Every catch must re-throw, log with log.debug()/log.warn(), or include a fallback with logging.

2. Command File Structure — Commands should focus on arg parsing, API orchestration, and output dispatch. Extract formatting into src/lib/formatters/<domain>.ts when files exceed ~400 lines.

3. Adding New Utility Files — Lookup table of existing shared modules to check before creating new utility files (duration formatting, hex ID validation, pagination, etc.). Prevents accidental duplication.

4. Project Filtering in API Calls — Documents that different API endpoints use different project filtering mechanisms (buildProjectQuery vs projectSlugs vs project parameter). Prevents double-filtering bugs.

[github-actions]

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[github-actions]

Codecov Results 📊

✅ 6660 passed | Total: 6660 | Pass Rate: 100% | Execution Time: 0ms

📊 Comparison with Base Branch

Metric	Change
Total Tests	—
Passed Tests	—
Failed Tests	—
Skipped Tests	—

✨ No test changes detected

All tests are passing successfully.

✅ Patch coverage is 100.00%. Project has 13517 uncovered lines.
✅ Project coverage is 76.61%. Comparing base (base) to head (head).

Coverage diff

@@            Coverage Diff             @@
##          main       #PR       +/-##
==========================================
+ Coverage    76.61%    76.61%        —%
==========================================
  Files          303       303         —
  Lines        57796     57794        -2
  Branches         0         0         —
==========================================
+ Hits         44276     44277        +1
- Misses       13520     13517        -3
- Partials         0         0         —

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