fix: reject POM entity declarations

[dsfaccini]

This pull request was posted by codex-tui using gpt-5.6-sol on behalf of David.

Summary

• reject Maven POMs containing DTD or entity declarations before ElementTree parsing
• preserve ordinary default-namespaced POM ingestion
• add an internal-entity regression test

Fixes #3224.

Validation

• uv run --frozen pytest tests/test_manifest_ingest.py — pass
• changed-file pre-commit hooks — pass
• GRAPHIFY_MAX_WORKERS=2 uv run --frozen graphify update . — pass

[graphify-labs]

Graphify reviewed this change.

Worth a look — the grounded gate found no coupling regressions or blocking issues, but 1 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

Hardens _parse_pom against XML entity-expansion attacks by rejecting any POM containing a <!DOCTYPE or <!ENTITY> declaration before handing it to ElementTree, raising a ValueError that surfaces as a parse error with empty nodes/edges rather than parsing untrusted expansion. Adds a test covering the internal-entity rejection path and renames the existing namespaced-POM test for clarity.

Worth a look

• POM parser rejects valid XML comments containing doctype/entity text — graphify/manifest_ingest.py:273 · 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 — 1342 functions depend on the 37 functions this change touches.

Health — this change adds coupling hotspots:

• new: extract() — 520 callers, 43 callees
• new: _rebuild_code() — 113 callers, 50 callees
• new: detect() — 108 callers, 15 callees
• new: dispatch_command() — 2 callers, 123 callees
• new: detect_incremental() — 23 callers, 7 callees
• new: _get_extractor() — 26 callers, 6 callees
• new: _is_sensitive() — 36 callers, 4 callees
• new: classify_file() — 43 callers, 3 callees
• …and 13 more — each is listed as a finding

Verification — 1342 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: 545 function(s) in the blast radius were not formally verified this run

Formal verification

Could not verify: Could not verify \_parse\_pom.

The verifier did not have enough to check \_parse\_pom, 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 ParseError — names the real obstacle, not a sampling gap)

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