Summary

Two walkers used by the frontmatter surface — collectFiles (used by gbrain frontmatter validate) and walkDir (used by scanBrainSources → doctor's frontmatter_integrity check) — were recursing into every subdirectory without filtering. Two other walkers in the same codebase already skip the same three directories — these two were the outliers:

• walkDir() at src/commands/frontmatter.ts:421 (used by gbrain frontmatter generate): if (entry === '.git' || entry === 'node_modules' || entry === '.obsidian') continue;
• src/core/disk-walk.ts:56 (canonical brain walker): if (entry.name.startsWith('.') || entry.name === 'node_modules') continue;

Result: gbrain frontmatter validate AND gbrain doctor on any project with installed dependencies flood the report with MISSING_OPEN false-positives on third-party HISTORY.md, CHANGELOG.md, and readme.md files inside node_modules/.

Closes #799 (filed by @metaWuming, 2026-05-10) — reporter saw 869 doctor warnings on three federated code sources, all entirely from node_modules/.

Diff scope

src/commands/frontmatter.ts | 5 +++++
src/core/brain-writer.ts    | 8 ++++++++
2 files changed, 13 insertions(+)

Two commits, both apply the same skip-list pattern at the existing per-entry filter point. No API change. Match the exact pattern at frontmatter.ts:421 and disk-walk.ts:56 for consistency.

Real-behavior proof

Environment: macOS 14, bun 1.3.8, gbrain on master (post-rebase) → branched as fix/frontmatter-validate-skip-node-modules. Test source: ~/projects/veefriends-kb (Next.js project, real node_modules/ with 71 third-party MD files).

Before (origin/master)

gbrain frontmatter validate (collectFiles walker):

$ gbrain frontmatter validate /Users/watson/projects/veefriends-kb
Found 71 issue(s) across 71 file(s) (scanned 126)

/Users/watson/projects/veefriends-kb/node_modules/router/HISTORY.md
  [MISSING_OPEN]:1 Frontmatter must start with --- on the first non-empty line
/Users/watson/projects/veefriends-kb/node_modules/es-object-atoms/CHANGELOG.md
  [MISSING_OPEN]:1 Frontmatter must start with --- on the first non-empty line
... (all 71 are node_modules artifacts)

gbrain doctor (scanBrainSources walkDir):

2170 frontmatter issue(s) across 11 source(s)

(Per #799 reporter on a different project: 869 doctor warnings, all node_modules MISSING_OPEN.)

After (this PR)

gbrain frontmatter validate:

$ gbrain frontmatter validate /Users/watson/projects/veefriends-kb
OK — 55 file(s) scanned, no frontmatter issues

55 files scanned instead of 126 — node_modules/ correctly skipped.

gbrain doctor:

2099 frontmatter issue(s) across 10 source(s)

Drop of 71 (= the vfkb node_modules false-positives now correctly excluded). The remaining 2099 are real MISSING_OPEN cases in registered diary paths, not node_modules.

Regression check — non-node_modules source still reports real issues

$ gbrain frontmatter validate ~/atlas/agents/terminal/memory
Found 7 issue(s) across 7 file(s) (scanned 135)

Same count before and after on a source without node_modules/.

Verification

$ bun run typecheck
$ tsc --noEmit
(exit 0)

$ bun run verify
OK: no JSON.stringify(x)::jsonb interpolation pattern in src/
OK: max_stalled defaults are 5 in all schema sources
OK: all rowToPage feeder projections include source_id
check-progress-to-stdout: OK (no banned stdout \r patterns)
check-test-isolation: OK (367 non-serial unit files scanned)
[check-wasm-embedded] OK — compiled binary produced real semantic chunks.
[check-admin-scope-drift] ok: 5 scopes match
OK: src/cli.ts is git-tracked as executable (100755)
OK: no direct derived-table writes outside the reconcile layer in src/ + scripts/
(all 11 checks pass)

What was NOT tested

• .obsidian exclusion wasn't exercised against a real Obsidian vault in this session. Followed the existing pattern from walkDir():421 which includes .obsidian — behavior is identical to that walker.
• No unit test added — the existing test/frontmatter-*.test.ts files don't have a fixture for "walker recurses into excluded directories." Adding one would require a fixture project with a node_modules/ shim. Happy to add one if you'd prefer.

Test plan

• CI green
• Reviewer runs gbrain frontmatter validate <any-node-project> pre and post fix; node_modules entries should disappear post-fix
• Reviewer runs gbrain doctor on the same project; frontmatter_integrity count should drop by the number of node_modules .md files
• gbrain frontmatter validate <non-node-project> reports the same count before and after (regression check)

Commits

1. 75151d9 fix(frontmatter validate): skip .git, node_modules, .obsidian in collectFiles
2. 5cd7c12 fix(doctor): scanBrainSources walkDir also skips .git / node_modules / .obsidian

Closes #799.