fix(extract): preserve stub edges that would become self-loops

[zrh805]

Summary

• keep a unique stub unresolved when rewiring it onto an existing edge neighbor would produce a false self-loop
• cover the generic rewire guard plus Python qualified decorators and Kotlin anonymous-object supertypes

Fixes #2374

Validation

• uv run --frozen pytest tests/test_extract.py tests/test_python_decorators.py tests/test_kotlin_object_literal.py (180 passed, 1 skipped)
• uv run --frozen ruff check graphify tests
• uv run --frozen graphify update .

The full suite completed with 3,898 passed / 36 skipped; its 12 unrelated failures are caused by an optional openai dependency missing from this environment, example.com resolving to a blocked internal test address, and an existing batch-order assertion.

[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 _rewire_unique_stub_nodes function in graphify/extract.py to prevent a stub node from being resolved onto a node it already shares an edge with, which would create a self-loop. To do this, it builds a stub_neighbors map tracking each stub's edge endpoints and adds that as an exclusion condition before remapping. The change is referenced as fixing issue #2374 (false self-loops). Three new tests are added covering the scenario directly at the function level, plus end-to-end cases for Kotlin anonymous object literals inheriting an external base and Python qualified decorators (@app.list_tools()).

No blocking issues surfaced.

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 1421 functions depend on the 501 functions this change touches.

Health — this change adds coupling hotspots:

• worse: extract() — 360 callers, 29 callees
• worse: _rewire_unique_stub_nodes() — 7 callers, 6 callees

Verification — 1421 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: 1293 function(s) in the blast radius were not formally verified this run

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

[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 _rewire_unique_stub_nodes in graphify/extract.py to prevent a stub node from being resolved onto a node it's already directly connected to via an edge. It builds a stub_neighbors mapping tracking each stub's edge endpoints and adds a guard so remapping is skipped when the unique candidate is a neighbor, with the stated intent of avoiding false self-loops (#2374). The rest of the diff adds test coverage across three test files, exercising this behavior for a Python qualified decorator case, a Kotlin anonymous object supertype case, and a direct unit test of the rewiring function.

No blocking issues surfaced.

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 1421 functions depend on the 501 functions this change touches.

Health — this change adds coupling hotspots:

• worse: extract() — 360 callers, 29 callees
• worse: _rewire_unique_stub_nodes() — 7 callers, 6 callees

Verification — 1421 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: 1293 function(s) in the blast radius were not formally verified this run

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