fix(drift): stop DEAD_COMMAND and INDEX_MISSING_ENTRY false positives

[dyk1454683243-sudo]

What

Two small, independent drift-checker false positives from #203:

1. DEAD_COMMAND — bare yarn / pnpm no longer look up builtins (install, add, dlx, ci, …) as package.json scripts. yarn run / pnpm run still resolve the following token as a script, so a real missing script stays flagged.
2. INDEX_MISSING_ENTRY — checkIndexSync now counts patterns/INDEX.md frontmatter edges[].target as INDEX references, using the same extractFrontmatter / edges[].target shape as stale-pattern.ts. Sibling targets (syntax-extractor-review.md) and patterns/*.md targets both count.

Why

Fixes #203

mex check reported pnpm install as a missing script and reported a pattern reached only through an INDEX frontmatter edge as unreferenced. The sibling stale-pattern checker already treats those edges as canonical navigation.

Type of change

• Bug fix
• New feature
• Refactor
• Docs
• CI/Tooling

How to test

1. npx vitest run test/checkers.test.ts
2. Confirm pnpm install / yarn add are not DEAD_COMMAND, and pnpm lint / yarn run missing still are.
3. Confirm an INDEX edge-only pattern is not INDEX_MISSING_ENTRY, and a file with no link or edge still is.
4. npm run typecheck

Checklist

• Focused checker tests pass (npx vitest run test/checkers.test.ts — 111/111)
• Typecheck passes (npm run typecheck)
• Tests pass (npm test) — full suite hits this environment's Node SQLite-without-FTS5 limitation; failures are graph/wiki/hub, not these checkers
• No breaking changes (or documented below)
• Tested locally with a real project

Code-graph changes

• This PR targets main
• A linked issue agrees on the bounded extractor/resolver scope
• The change follows the frozen LanguageExtractor or FrameworkResolver interface
• A focused fixture and assertions for the expected node/edge shape are included
• Any new grammar WASM, extension mapping, extractor, or resolver is registered
• No graph identity, reconciliation, schema, or drift-semantics changes are included, or a core / discuss-first issue is linked above