Fix AST uses edge confidence (#3539)

[hopstreax]

Summary

Fixes #3539

AST cross-file uses edges were incorrectly emitted as INFERRED / 0.95 / 0.8 even though they are deterministically extracted from explicit Python AST syntax.

This PR updates these edges to use the EXTRACTED confidence tier.

Changes

• Emit Python AST cross-file uses edges as EXTRACTED with confidence_score: 1.0.
• Set their graph weight to 1.0, consistent with other structurally extracted relationships.
• Update existing uses tests to reflect the corrected confidence tier.
• Add regression coverage for uses edge metadata.
• Add regression coverage for references + uses collapse preserving the extracted metadata.
• Leave build.py, Apex, and other language extractors unchanged.

Validation

• Focused uses tests: 10 passed
• test_extract.py: 223 passed, 8 skipped
• Confidence, relation-collapse, build/dedup, symbol-resolution, and language tests all pass.
• git diff --check: clean.

The one unrelated failure encountered in the broader extraction suite is a pre-existing Windows MAX_PATH fixture-path issue.

[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.

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Graphify review — findings

Reclassifies cross-file Python import uses edges from INFERRED/0.95 (weight 0.8) to EXTRACTED/1.0 (weight 1.0), on the grounds that these edges come from explicit source syntax rather than inference. Renames the test helper _inferred_uses to _uses_edges and updates the existing suite to match, and adds test_3539_ast_uses_edge_metadata_is_extracted plus test_3539_references_and_uses_collapse_retains_extracted_metadata covering the new metadata and the references/uses collapse in build_from_json.

No blocking issues surfaced. 3 lower-confidence candidates did not survive cross-model review.

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 2169 functions depend on the 570 functions this change touches.

Health — this change adds coupling hotspots:

• new: extract() — 591 callers, 44 callees
• new: _rebuild_code() — 116 callers, 51 callees
• new: _extract_generic() — 18 callers, 26 callees
• new: extract_js() — 85 callers, 4 callees
• new: extract_xaml() — 19 callers, 17 callees
• new: _resolve_js_module_path() — 34 callers, 9 callees
• new: dispatch_command() — 2 callers, 124 callees
• new: extract_objc() — 27 callers, 9 callees
• …and 35 more — each is listed as a finding

Verification — 2169 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: 1227 function(s) in the blast radius were not formally verified this run

Test selection

Test selection

34 of 275 test file(s) selected (12%) via static blast radius.

• tests/test_astro_extraction.py — impact
• tests/test_build.py — impact
• tests/test_cjs_module_extension.py — impact
• tests/test_cpp_nested_and_cli.py — impact
• tests/test_dotnet.py — impact
• tests/test_extract.py — impact, changed-test
• tests/test_forwarding_review_findings.py — impact
• tests/test_import_extension_resolution.py — impact
• tests/test_indirect_dispatch.py — impact
• tests/test_indirect_dispatch_assign_return.py — impact
• tests/test_indirect_dispatch_getattr.py — impact
• tests/test_js_exported_scalar_bindings.py — impact
• tests/test_languages.py — impact
• tests/test_multilang.py — impact
• tests/test_package_json_subpath_imports.py — impact
• tests/test_pascal.py — impact
• tests/test_pascal_resolution.py — impact
• tests/test_phantom_external_import.py — impact
• tests/test_python_import_resolution.py — impact
• tests/test_python_parse_memoization.py — impact
• tests/test_python_underscore_resolution.py — impact
• tests/test_rationale.py — impact
• tests/test_resolve_memoization.py — impact
• tests/test_ruby_resolution.py — impact
• tests/test_scala_self_type.py — impact
• tests/test_source_key_memoization.py — impact
• tests/test_src_layout_import_resolution.py — impact
• tests/test_swift_computed_properties.py — impact
• tests/test_trailing_newline_not_a_syntax_error.py — impact
• tests/test_ts_new_expression_calls.py — impact
• tests/test_typescript_module_extensions.py — impact
• tests/test_unmapped_at_alias_resolution.py — impact
• tests/test_vue_extraction.py — impact
• tests/test_walk_python_tree_iterative.py — impact

Selection is safe under the controlled-regression assumption; always-run tests + a periodic full run are the backstops. Advisory — it never changes the check verdict.

Formal verification

Could not verify: Could not verify \_resolve\_cross\_file\_imports.

The verifier did not have enough to check \_resolve\_cross\_file\_imports, 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: non-vacuity: domain too small (only 2 distinct inputs exercised, need 3) — 'no divergence' would be near-vacuous

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