fix(cache): skip caching edges-but-no-nodes semantic results so model…

[SinghAman21]

…-omitted files re-dispatch instead of freezing out of the graph (#2927)

On large batches the model sometimes omits a file from its response but still emits edges attributed to it. We cached that {"nodes": [], "edges": [...]} result keyed by content hash, so every later run was a cache hit and the file never got extracted again — its edges dangled and were pruned, and the "a re-run will retry them" warning wasn't actually true.
What changed

• save_semantic_cache skips writing per-file entries that have edges but zero nodes (with a warning), so the file genuinely re-dispatches next run
• load_cached treats already-poisoned entries (from older versions) as a miss, so existing caches self-heal on the next complete extraction
• _stamped_manifest_files no longer stamps an edges-only file as up-to-date — otherwise warm incremental runs would skip it even with the cache fixed
  Hyperedge-only results are untouched and still cache normally (hyperedge-only doc output never stamped in manifest — perpetual re-extraction #1920). Multi-chunk merges are unaffected since the check runs on the merged result.

[graphify-labs]

Graphify reviewed this change.

Worth a look — the grounded gate found no coupling regressions or blocking issues, but 2 advisory finding(s) below merit a look before merge.

Formal verification. No changes could be formally verified in this run.

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Graphify review — findings

Treats a semantic result with edges but zero nodes as a model-omission artifact (#2927): save_semantic_cache skips writing such entries (with a RuntimeWarning), load_cached reads existing poisoned entries as a miss for self-healing re-dispatch, and _stamped_manifest_files drops edges from stamping so those files re-queue. Preserves multi-chunk accumulation onto node-bearing entries and keeps hyperedge-only results (#1920) valid. Adds cache and CLI tests covering the skip, merge, self-heal, and hyperedge/AST exemptions.

Worth a look

• save_semantic_cache drops edge-only results — graphify/cache.py:1552 · Escalate · medium
  • agreed by 2 of 2 members but NOT verified (no proof, no reproducing execution) — consensus is not a verdict; needs human review
• Semantic save skips valid hyperedge-bearing results when edges are also present — graphify/cache.py:1561 · Escalate · medium
  • agreed by 2 of 2 members but NOT verified (no proof, no reproducing execution) — consensus is not a verdict; needs human review

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 1460 functions depend on the 373 functions this change touches.

Health — this change adds coupling hotspots:

• new: extract() — 474 callers, 42 callees
• new: _rebuild_code() — 98 callers, 50 callees
• new: detect() — 108 callers, 15 callees
• new: save_semantic_cache() — 59 callers, 11 callees
• new: load_cached() — 45 callers, 7 callees
• new: extract_corpus_parallel() — 26 callers, 11 callees
• new: file_hash() — 45 callers, 6 callees
• new: dispatch_command() — 2 callers, 119 callees
• …and 19 more — each is listed as a finding

Verification — 1460 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: 1144 function(s) in the blast radius were not formally verified this run

Formal verification

Could not verify: Could not verify load\_cached.

The verifier did not have enough to check load\_cached, 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 save\_semantic\_cache.

The verifier did not have enough to check save\_semantic\_cache, 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 \_stamped\_manifest\_files.

The verifier did not have enough to check \_stamped\_manifest\_files, 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

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