fix(extract): don't classify deliberately-declined data JSON as failed (#2879)

[rajarshidattapy]

Fixes #2879.

The bug

extract()'s empty-result classifier could not tell "the extractor declined this file on purpose" from "extraction failed":

if (not _res.get("nodes")) and _get_extractor(_p) is not None:
    _failed_sources.append(_key)

Data-shaped JSON is deliberately not AST-walked (#1224 — it is left to the LLM semantic pass), but a .json extractor is registered, so a declined file satisfies both halves of that test. It landed in failed_sources, whose stated purpose is to keep those paths out of the processed set, so the incremental manifest never stamped it — and it was re-queued on every subsequent run, forever. On the reporter's 3,329-file repo that was 110 files with a blank ast_hash, all of them .json.

The fix

extract_json() already reports the decline explicitly:

return {"nodes": [], "edges": [], "skipped": "data json (not a config/manifest)"}

That marker just had no consumer. This honours it at the two call sites that needed it:

• failed_sources (Incremental manifest never retries files whose extractor failed on a missing extra #2543) skips results carrying skipped, so the CLI stamps them as processed;
• the Ruby: stable subset of files yields zero nodes in full-repo runs (0.9.6) — each extracts fine in isolation #1666 "produced zero nodes" warning skips them too, since a deliberate decline is not an anomaly worth warning about.

This is option (1) from the issue's Suggested direction, and needs no new marker — _get_extractor() stays pure dispatch-by-extension.

An empty result without the marker is still classified as failed, so the #1666/#2543 safety net is unchanged for genuine failures.

Tests

• test_extract_declined_data_json_is_not_failed — a data meta.json yields empty failed_sources and no zero-nodes warning, while a sibling package.json still extracts. Fails without the change.
• test_extract_genuinely_empty_json_still_failed — an extractor returning an empty result with no marker is still reported failed.

[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. No changes could be formally verified in this run.

---

Graphify review — findings

Treats extractor-declined files (those returning a skipped marker) as an intended outcome in extract() rather than a failure — they no longer get counted as empty sources, emit "zero nodes" warnings, or land in failed_sources (which previously re-queued them on every incremental run). Adds tests covering a declined data JSON and a guard that genuinely empty JSON is still reported as failed.

No blocking issues surfaced.

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 1730 functions depend on the 563 functions this change touches.

Health — this change adds coupling hotspots:

• new: extract() — 473 callers, 42 callees
• new: _rebuild_code() — 98 callers, 51 callees
• new: extract_xaml() — 19 callers, 17 callees
• new: extract_js() — 80 callers, 3 callees
• new: dispatch_command() — 2 callers, 117 callees
• new: _get_extractor() — 26 callers, 6 callees
• new: run_pipeline() — 8 callers, 13 callees
• new: collect_files() — 17 callers, 6 callees
• …and 22 more — each is listed as a finding

Verification — 1730 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: 1587 function(s) in the blast radius were not formally verified this run

Formal verification

Could not verify: Could not verify extract.

The verifier did not have enough to check extract, 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 `cache_root` is annotated `Path | None` — outside the synthesizable primitive/collection set

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

[safishamsi]

Shipped in v0.9.48 via authorship-preserving cherry-pick so you keep contributor-graph credit. Thanks @rajarshidattapy! Release: https://github.com/Graphify-Labs/graphify/releases/tag/v0.9.48