Fix needs_update flag dot/no-dot mismatch in skill runbooks

[ayushcodes10]

skill.md's cleanup step targeted graphify-out/.needs_update (with a
leading dot), but every actual writer/reader of the flag uses the name
WITHOUT a dot: watch.py's needs_update path, and cli.py's
out_path("needs_update") check. The cleanup command never matched the
real file, and any staleness check written against the documented
(dotted) name would silently never fire.

This fixes the one purely mechanical bug in #2671 -- the dot/no-dot
naming mismatch. The issue's larger proposal (adding a staleness-check
paragraph to the fast-path text, propagated across skill*.md variants)
is a separate maintainer call about wording/scope and isn't included
here.

Fix the three source fragments (core.md, and the two monolith bodies
aider.md/devin.md) and regenerate all 16 skill*.md variants plus their
expected/ snapshots via skillgen. Add a sanctioned-diff predicate in
gen.py's monolith-roundtrip guard so the deliberate one-line change to
the two monolith bodies passes review instead of reading as
unreviewed drift.

Verified end-to-end: with the old (dotted) command, rm -f graphify-out/.needs_update does not remove a real
graphify-out/needs_update file (the form watch.py actually writes);
with the fix it does. All four skillgen validators (--check,
--audit-coverage, --schema-singleton, --monolith-roundtrip,
--always-on-roundtrip) pass, and the full test suite (4314 tests)
passes.

Fixes #2671.

[ayushcodes10]

@safishamsi this PR's CI run is waiting on approval (first-time contributor gate) — could you approve the workflow run when you get a chance? Happy to address any review feedback in the meantime.

[graphify-labs]

Graphify reviewed this change.

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

Formal verification. 1 change(s) tested, no difference found (not proven).

---

Graphify review — findings

This PR appears to revert a set of previously unreleased 0.9.44 changes back into a 0.9.43 (unreleased) state. In the CHANGELOG it removes the 0.9.44 section (covering hook .graphifyrc node-limit baking, CLAUDE.md config-dir handling, JS/TS shadowing fixes, gitignore-tracked-file handling, doctest/Catch2 recovery, the affected absolute-seed root resolution, lazy require edges, and OCaml external-call fixes) and marks 0.9.43 as unreleased. It also removes YouTube badges from the README and reverts the affected/resolve_seed/format_affected code that derived a repo root from the graph location back to using Path.cwd(), dropping the root parameter. The touched symbols span a large number of tests (languages, extract, detect, hooks, install) and skill/tooling files, indicating the revert extends across test fixtures and skill manifests as well as the core detect/extract/affected/CLI modules.

No blocking issues surfaced. 4 lower-confidence candidates did not survive cross-model review.

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 4563 functions depend on the 3398 functions this change touches.

Health — this change adds coupling hotspots:

• new: extract() — 454 callers, 41 callees
• new: _rebuild_code() — 95 callers, 51 callees
• new: detect() — 93 callers, 14 callees
• new: _extract_generic() — 18 callers, 23 callees
• new: save_manifest() — 34 callers, 11 callees
• new: extract_files_direct() — 17 callers, 20 callees
• new: extract_xaml() — 19 callers, 17 callees
• new: extract_corpus_parallel() — 26 callers, 10 callees
• …and 76 more

Verification — 4563 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: 4480 function(s) in the blast radius were not formally verified this run

Formal verification

Could not verify: Could not verify \_as\_repo\_relative.

The verifier did not have enough to check \_as\_repo\_relative, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `root` is annotated `Path | None` — outside the synthesizable primitive/collection set

No difference found (not proven): No behavior difference found in format\_affected (not a proof).

The verifier ran both versions of format\_affected on many inputs and saw identical behavior every time. Strong evidence the change is safe, but evidence, not a proof.

Guarantee: Empirical: differential testing (both versions run on many generated inputs). A divergence on an untested input remains possible, so this is 'no counterexample found', not 'proven equivalent'.

Note: An input the sampler did not try could still differ.

Could not verify: Could not verify resolve\_seed.

The verifier did not have enough to check resolve\_seed, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `root` is annotated `Path | None` — outside the synthesizable primitive/collection set

Could not verify: Could not verify dispatch\_command.

The verifier did not have enough to check dispatch\_command, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: not verifiable: all 23 sampled inputs raised on both versions — the function never executed, so 'no divergence' would be vacuous (mostly SystemExit — names the real obstacle, not a sampling gap)

Could not verify: Could not verify detect.

The verifier did not have enough to check detect, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `root` is annotated `Path` — outside the synthesizable primitive/collection set

Could not verify: Could not verify ignored\_predicate.

The verifier did not have enough to check ignored\_predicate, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `root` is annotated `Path` — outside the synthesizable primitive/collection set

Could not verify: Could not verify extract\_cpp.

The verifier did not have enough to check extract\_cpp, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `path` is annotated `Path` — outside the synthesizable primitive/collection set

Could not verify: Could not verify \_extract\_generic.

The verifier did not have enough to check \_extract\_generic, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `path` is annotated `Path` — outside the synthesizable primitive/collection set

Could not verify: Could not verify \_require\_imports\_js.

The verifier did not have enough to check \_require\_imports\_js, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: not verifiable: all 200 sampled inputs raised on both versions — the function never executed, so 'no divergence' would be vacuous (mostly AttributeError — names the real obstacle, not a sampling gap)

Could not verify: Could not verify extract\_ocaml.

The verifier did not have enough to check extract\_ocaml, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `path` is annotated `Path` — outside the synthesizable primitive/collection set

Could not verify: Could not verify install.

The verifier did not have enough to check install, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `path` is annotated `Path` — outside the synthesizable primitive/collection set

Could not verify: Could not verify \_install\_hook.

The verifier did not have enough to check \_install\_hook, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `hooks_dir` is annotated `Path` — outside the synthesizable primitive/collection set

Could not verify: Could not verify status.

The verifier did not have enough to check status, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `path` is annotated `Path` — outside the synthesizable primitive/collection set

Could not verify: Could not verify install.

The verifier did not have enough to check install, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: not verifiable: all 23 sampled inputs raised on both versions — the function never executed, so 'no divergence' would be vacuous (mostly SystemExit — names the real obstacle, not a sampling gap)

· 84 more finding(s) on lines outside this diff (see the check run).