Skip non-scaffold files in tool config sync

[olddognewflex]

Problem

checkToolConfigSync treats any co-existing CLAUDE.md / AGENTS.md / .cursorrules / .windsurfrules / .github/copilot-instructions.md as byte-identical copies installed from .tool-configs/, and raises TOOL_CONFIG_DRIFT whenever two differ.

That assumption fails in repos where those files have independent owners. Real case: a repo with a hand-written CLAUDE.md (project context) and an AGENTS.md generated by tkt sync-pack (managed skill pack, "do not edit by hand"). Neither file ever came from .tool-configs/, and the warning is unfixable — making them match would either clobber the managed block or duplicate machine-regenerated content that re-drifts on the next sync.

Fix

Every .tool-configs/ template carries a ROUTER.md scaffold pointer. A file now participates in the mirror comparison only when its content includes that marker:

• Non-copies (no marker) are skipped entirely — no comparison, no warning.
• Genuine drift between real scaffold copies is still flagged, including when non-copies sit alongside them.

Trade-off: a copy edited so heavily that the ROUTER.md pointer is removed drops out of the check — at that point it is no longer a scaffold anchor, so silence is the correct behaviour.

Testing

• Existing drift fixtures updated to carry the marker.
• Two new tests: hand-written + generated coexistence produces no issue; comparison still runs among the remaining real copies when non-copies are present.
• npx vitest run test/checkers.test.ts — 54/54 pass.
• Verified against the originating repo: TOOL_CONFIG_DRIFT false positive gone, drift score 88 → 91, real checks unaffected.

[theDakshJaitly]

The scaffold-copy detection remains too broad. ROUTER.md is not unique to mex-generated tool configs: independently owned CLAUDE.md and AGENTS.md files can legitimately tell agents to read ROUTER.md, causing this code to compare them and still report TOOL_CONFIG_DRIFT. I reproduced this with two unrelated files containing ordinary See ROUTER.md guidance. Please add a dedicated scaffold sentinel, such as an HTML mex-tool-config comment, to the generated templates and match that instead, with a regression test where non-scaffold files mention ROUTER.md. The focused tests, full suite (371 tests), and typecheck otherwise pass.

[olddognewflex]

Addressed in 5f37ac4 (landing on this branch via the fork's main).

• Generated .tool-configs/ templates now carry a dedicated sentinel comment (<!-- mex-tool-config: managed copy from .tool-configs/ ... -->), added to all four markdown templates and the repo's own .mex/.tool-configs/ copies.
• checkToolConfigSync matches only that sentinel instead of the ROUTER.md substring, so independently owned CLAUDE.md/AGENTS.md files that merely mention ROUTER.md are no longer compared.
• Regression test added: two non-scaffold files each containing ordinary "See ROUTER.md" guidance produce no TOOL_CONFIG_DRIFT.

372 tests pass, typecheck clean.

One trade-off to note: copies installed from pre-sentinel templates won't carry the marker, so the checker skips them until they're re-copied — a false negative rather than a false positive, which seems the right direction, but happy to add migration handling if you'd prefer.