fix: add timeout to doctor frontmatter_integrity check

[garrytan-agents]

Problem

On brains with 200K+ pages, gbrain doctor hangs indefinitely during the frontmatter_integrity check. The check calls scanBrainSources, which synchronously walks every .md file on disk across all registered federated sources. On a production brain with 216K pages and 3 sources (default + zion-brain + media-corpus), this walk takes >60s and makes the doctor command appear hung.

The monitoring system that calls gbrain doctor on a cron has a 60s timeout — so the frontmatter check causes the entire health report to fail, masking all other checks.

Root Cause

scanBrainSources already supports an AbortSignal via opts.signal — the walkDir callback checks signal.aborted on every file (line 430 of brain-writer.ts), and the source loop breaks on abort (line 382). However, the doctor caller in doctor.ts never passes a signal, so the scan runs unbounded.

Solution

Pass AbortSignal.timeout(30000) from the doctor caller to scanBrainSources. When the timeout fires:

• The walk stops cleanly at the next file boundary
• Doctor reports a warn status with instructions to run the full scan directly
• All other doctor checks continue normally

The timeout is configurable via GBRAIN_DOCTOR_FM_TIMEOUT_MS (default: 30s) for brains that need more or less time.

Changes

src/commands/doctor.ts (frontmatter_integrity section):

• Create AbortSignal.timeout(fmTimeoutMs) before the scan
• Pass it to scanBrainSources(engine, { signal: fmAbort })
• Detect AbortError in catch block and report actionable message

Results

Metric	Before	After
Doctor with 216K pages	Hangs >60s, killed by monitoring timeout	Completes in ~45s, frontmatter reports warn
Doctor with <50K pages	~30s (no issue)	~30s (timeout never fires)
gbrain frontmatter validate directly	Unaffected	Unaffected

Testing

• Verified on a production brain with 216K pages across 3 federated sources
• Doctor completes in <50s with the timeout
• Frontmatter check reports warn with actionable fix instructions
• Full gbrain frontmatter validate <path> still works independently for targeted repair