Do not warn for intentionally skipped sources

[EmanuelFaria]

Summary: Exclude extractor results that explicitly report skipped from the zero-node failure warning. Data-shaped JSON is deliberately skipped to keep datasets and response dumps from flooding the code graph, so warning that those files failed and will retry is false noise. Regression coverage: new data-JSON skip test; zero-node and extractor registry suites passed with 6 tests; all 87 real PersonalOS intentional JSON skips emitted no false warnings; ruff passed.

[graphify-labs]

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

Graphify reviewed this change.

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

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Graphify review — findings

This PR updates the "empty sources" detection in extract() so that per-file results marked with a skipped flag are no longer treated as failed extractions (previously only nodes or error short-circuited the check). It adds a test asserting that data-shaped JSON, which is intentionally skipped, produces no nodes and does not emit a "zero nodes" warning. The change touches one condition in graphify/extract.py and adds one new test in tests/test_zero_node_no_cache.py.

No blocking issues surfaced.

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 1199 functions depend on the 193 functions this change touches.

Health — this change adds coupling hotspots:

• worse: extract() — 352 callers, 28 callees

Verification — 1199 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: 1072 function(s) in the blast radius were not formally verified this run

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