fix(build): preserve calls edges over references on undirected collap…

[abhiramArise]

Fixes #2391.

The sort by (source, target, relation) before G.add_edge was added for deterministic collapse order, but that also meant alphabetical order picked the survivor whenever two different relations landed on the same (src, tgt) pair — references always beat calls since "calls" < "references". G.add_edge just overwrites, no merge.

Added a small _RELATION_PRIORITY table so the higher-information relation wins the collapse instead of whichever sorts last. Unlisted relations default to priority 0, so anything not in the table keeps the old behavior — no regression there.

Left out the multigraph route and the also_relations merge idea from the issue to keep this focused on the actual data-loss bug; can follow up separately if maintainers want either.

Added a test covering both input orderings (since the bug is order-dependent) confirming calls survives a collapse with references either way.

Ran the full test_build.py suite before/after on a clean checkout — the 14 pre-existing failures (missing rapidfuzz/tree-sitter-javascript deps, one unrelated _semantic_id_remap bug) are identical with and without this change.

[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 modifies the edge collapse logic in build_from_json (graphify/build.py) for undirected graphs, where multiple edges landing on the same node pair get merged into one. It introduces a _RELATION_PRIORITY table and, when two edges on the same pair carry different relations, keeps the higher-priority relation instead of relying solely on the deterministic sort order. A new test with a helper (_same_pair_calls_references_extraction) verifies that a calls edge survives collapse against a references edge regardless of input order. The remaining changed symbols appear to be test-file rationale/comment blocks and unchanged surrounding tests included in the diff scope.

Worth a look

• Priority tie between different relations lets last-write clobber unexpectedly — graphify/build.py:1074 · 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 — 798 functions depend on the 196 functions this change touches.

Health — this change adds coupling hotspots:

• worse: build_from_json() — 143 callers, 14 callees

Verification — 798 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: 597 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).