Fixes #799.

Summary

• Make the frontmatter scanner skip dependency and generated-output directories before recursing.
• Covered dirs include node_modules, dist, build, out, coverage, ops, and dot-prefixed directories.
• Add a regression proving generated Markdown does not produce frontmatter_integrity warnings.

Validation

• bun test test/brain-writer.test.ts — 17 pass, 0 fail
• bun run typecheck
• git diff --check

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