Canonical Filament extraction engine + malformed-document parse failure (#127)

[kreneskyp]

Summary

This branch adds the canonical one-document Filament extraction engine (FR-040/FR-041, US-015, NFR-020) and the shared graph fixture corpus, and fixes issue #127: the engine treated a malformed document as a clean extraction, so per-document parse failures never reached Filament's index_errors.

#127 fix — malformed frontmatter now surfaces a parse failure

The engine previously returned only a no_frontmatter informational diagnostic (empty errors) whenever parse_document yielded no frontmatter — including when a complete but unparsable ---…--- fence block was present. The MarkStale → apply_stale path only records documents with a non-empty errors list, so those failures vanished.

Fix — parser reports the fact, boundary owns the policy:

• extract_frontmatter (FR-006) now returns a typed FrontmatterStatus { Absent, Present, Malformed } — the single authority for the classification. Parity-preserving: frontmatter/body outputs are byte-identical, so the TS/Py sweep is unaffected. Empty / whitespace / comment-only blocks (YAML null) classify as Absent (a clean skip — e.g. a ---\n\n--- thematic-break pair), not Malformed.
• extract_filament_core reads that status on the no-frontmatter branch (cold path only) and, for Malformed, emits a parse_failed error plus a frontmatter_unparsable error-severity diagnostic so the failure reaches index_errors.

Spec & tests

• Split the FR-040 behavior bullet; added FR-040-AC-6 and FR-006-AC-7 with a CR-010 note.
• Matrix rows TC-657 (filament boundary) and TC-658 (parser status), coverage 339 → 341.
• Gap-analysis SpecReview under reviews/ (Verdict CONDITIONAL; FND-002 resolved, FND-001 accepted).

Verification

• make ci locally: 344 lib + all integration tests pass, clippy -D warnings clean, fmt-check / audit-unsafe / deny green, spec dogfood green, SpecReview quire-validated.
• Incidental: fixed two pre-existing clippy errors (extract_tier2 complex return type → Tier2Extraction alias; stable_id needless borrow) that a newer stable clippy flags and that block the gate.

Closes #127

🤖 Generated with Claude Code

[kreneskyp]

Superseded by the rebased-onto-main PR (canonical Filament extraction under FR-045/FR-046). This branch was built on a stale base (12 commits behind main, colliding FR-040/FR-041/CR-010/TC numbering) and can't merge as-is.