fix(extract): stop a built-in base class from inheriting across languages (#2812)

[ousamabenyounes]

Fixes #2812.

The bug

class FooApiException extends \Exception in PHP mints a sourceless Exception
stub, because the base class is not defined in the corpus. _rewire_unique_stub_nodes
then binds that stub to the one same-labelled real definition found anywhere in
the corpus — and in a PHP + TypeScript monorepo that definition is an unrelated
TypeScript class Exception. The reporter's ~6k-file repo got 12 phantom
inherits edges from first-party PHP exception classes onto one TS class, which
pushed it into the top-10 god nodes and produced a false cross-community bridge
question.

The fix

The rewire now refuses a supertype edge when the referring file's language names
its own built-in throwable and the resolved target lives in a different language
family. Three deliberate choices:

• Per edge, not per stub. One sourceless Exception stub collects referrers
  from every language that names it. Deciding on the stub's referrer families as a
  set would let a single TypeScript referrer re-open the cross-language bind for
  the PHP ones. The check reads edge["source_file"], and sits next to the
  existing C#-scoped carve-out in the same loop.
• Built-in throwables only, not a blanket family gate on the type path. A corpus
  really can declare BookStore in one language and subclass it from another —
  test_extract_rewires_unique_inheritance_stub_to_real_definition pins exactly
  that, and this PR leaves it passing untouched. But Exception named from a PHP
  file is always PHP's own, so a same-named class in another language cannot be
  what it refers to.
• Case-folded for case-insensitive languages. PHP resolves class names
  case-insensitively, so extends \exception names the same built-in
  (mirrors the existing real_by_label / real_by_label_ci pair, Case-folded cross-file resolution collides distinct identifiers (Path/PATH) → false super-hubs in case-sensitive languages #1581).

_LANGUAGE_BUILTIN_GLOBALS was not reused: it is a flat set consulted at call
sites and has no per-language scoping, which is what this path needs.

Relationship to #2365

#2365 proposes hoisting the interop family gate to every unique match, which
would also close this issue but changes existing behaviour — it has to rewrite
test_extract_rewires_unique_inheritance_stub_to_real_definition, whose
Python↔C# rewire is currently intended. This PR is additive and takes the
narrower position that only a language's own built-ins can never be foreign.
If you prefer the blanket gate, #2365 supersedes this and I'll close it.

Test verification (RED → GREEN)

RED — new tests against unmodified v8 (b2cd362), production file reverted:

$ git checkout origin/v8 -- graphify/extract.py
$ uv run --frozen pytest tests/test_extract.py -q -k rewire --tb=line
FAILED tests/test_extract.py::test_rewire_does_not_bind_supertype_stub_across_language
FAILED tests/test_extract.py::test_rewire_builtin_supertype_guard_folds_case_insensitive_languages
FAILED tests/test_extract.py::test_rewire_builtin_supertype_guard_is_per_edge_not_per_stub
3 failed, 8 passed, 191 deselected, 1 warning in 0.54s

$ uv run --frozen pytest tests/test_multilang.py::test_php_builtin_base_class_never_inherits_from_cross_language_class -q --tb=line
FAILED tests/test_multilang.py::test_php_builtin_base_class_never_inherits_from_cross_language_class
1 failed, 1 warning in 0.31s

The failure is the reported leak verbatim:

E   AssertionError: PHP supertype leaked cross-language:
    {'source': 'packages_fooapiexception_fooapiexception',
     'target': 'app_exception_exception', 'relation': 'inherits', ...}

GREEN — same tests with the fix:

$ uv run --frozen pytest tests/test_extract.py -q -k rewire
11 passed, 191 deselected, 1 warning in 0.56s

$ uv run --frozen pytest tests/test_multilang.py::test_php_builtin_base_class_never_inherits_from_cross_language_class -q
1 passed, 1 warning in 0.26s

Full suite, unchanged against the v8 baseline (the 4 failures are pre-existing
in my local environment — 3 test_ollama backend-detection tests read env vars I
have set, and test_collect_files_skips_hidden — all 4 fail identically on clean
v8):

$ uv run --frozen pytest tests/ -q
4 failed, 4882 passed, 11 skipped, 4 warnings in 131.39s

ruff check clean on the touched files, and the five tools.skillgen
validators (--check, --audit-coverage, --schema-singleton,
--monolith-roundtrip, --always-on-roundtrip) all pass.

[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

Blocks cross-language stub rewiring for built-in exception types in _rewire_unique_stub_nodes: a PHP class FooApiException extends \Exception no longer fuses onto a same-named TypeScript Exception class. Adds per-family built-in throwable tables (_LANGUAGE_BUILTIN_BASE_CLASSES plus a case-folded companion) and a per-edge _names_own_builtin_base guard that keeps the stub as the external base only when the referring and target families differ, leaving same-language rewires intact.

No blocking issues surfaced. 1 lower-confidence candidate did not survive cross-model review.

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 2038 functions depend on the 860 functions this change touches.

Health — this change adds coupling hotspots:

• new: extract() — 475 callers, 42 callees
• new: _rebuild_code() — 98 callers, 50 callees
• new: extract_xaml() — 19 callers, 17 callees
• new: extract_js() — 80 callers, 3 callees
• new: dispatch_command() — 2 callers, 119 callees
• new: _get_extractor() — 26 callers, 6 callees
• new: run_pipeline() — 8 callers, 13 callees
• new: collect_files() — 17 callers, 6 callees
• …and 23 more — each is listed as a finding

Verification — 2038 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: 1890 function(s) in the blast radius were not formally verified this run

Formal verification

Could not verify: Could not verify \_rewire\_unique\_stub\_nodes.

The verifier did not have enough to check \_rewire\_unique\_stub\_nodes, 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: the input domain has 81 values but only 9 distinct were tested — a small finite domain must be EXHAUSTED, not sampled (an untested input could invert the result)

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