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fix(skill): structurally extract docs, fix whole-file node ID drift - #2548

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dolakzdenek:fix/skill-doc-structural-extraction
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fix(skill): structurally extract docs, fix whole-file node ID drift#2548
dolakzdenek wants to merge 1 commit into
Graphify-Labs:v8from
dolakzdenek:fix/skill-doc-structural-extraction

fix(skill): structurally extract docs with a registered extractor, fi…

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Graphify Labs / Graphify succeeded Aug 8, 2026 in 0s

Graphify — looks good

Looks safe to merge — no coupling regressions and no blocking issues, checked against the code graph (not a self-assessment).

Details

Graphify reviewed this change.

Looks safe to merge — no coupling regressions and no blocking issues, checked against the code graph (not a self-assessment).


Graphify review — findings

This PR extends the skill pipeline's "Part A" structural extraction so it runs over documentation/paper files whose extensions have a registered structural extractor (e.g. .md, .mdx, .qmd, .skill), not just code files. To support this, it adds a new structural_extensions() helper in graphify/extract.py (exposed via graphify/__init__.py) that returns the set of extensions backed by a structural extractor, and rewrites the Part A snippets across the many per-agent skill markdown files and their generated/expected test fixtures to use it. The changes span the skill generator tooling, expected-output fixtures, and associated tests.

No blocking issues surfaced. 2 lower-confidence candidates did not survive cross-model review.

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 2562 functions depend on the 1464 functions this change touches.

Health — grade A; 10 existing hotspot(s) in the area this change touches (pre-existing, not introduced here):

  • extract() — 375 callers, 39 callees (high)
  • _rebuild_code() — 93 callers, 52 callees (high)
  • extract_xaml() — 19 callers, 17 callees (high)
  • dispatch_command() — 2 callers, 118 callees (high)
  • _get_extractor() — 24 callers, 6 callees (high)
  • run_pipeline() — 8 callers, 13 callees (high)
  • collect_files() — 17 callers, 6 callees (high)
  • render() — 13 callers, 5 callees (high)
  • …and 2 more

Verification — 2562 functions in the blast radius were not formally verified this run (proofs are advisory here).

Gate & verification

graphify gate

PASS — objectively clean (no health regressions, tests not run — proofs not run this pass (advisory)). Grounded, not self-assessed.

Advisory (not blocking):

  • verification_scope: 2432 function(s) in the blast radius were not formally verified this run