Fix Python submodule imports from external source roots

[hopstreax]

Summary

Fixes #3272 by correcting Python submodule resolution when imports originate outside the package's source root.

Previously, imports such as:

from towmo.core import helper

could fail to resolve helper.py when the importing file was outside a src/-style package tree, such as a test file under tests/.

Changes

• Added dynamic Python source-root discovery based on __init__.py package boundaries.

• Pass discovered source roots into Python module resolution as fallback candidates.

• Preserved the existing resolution order and relative-import behavior.

• Added fail-closed handling for ambiguous matches across multiple source roots.

• Discover source roots once per extraction batch to avoid repeated directory traversal.

• Added regression tests for:

  • Imports from both inside and outside src/.
  • Multiple source roots with distinct packages.
  • Ambiguous packages across multiple source roots.

Validation

• 12 passed — focused Python resolution tests.
• 19 passed, 442 deselected — Python-focused suite.
• 339 passed, 4 skipped, 1 failed — broader extraction/build suite.
• git diff --check passes cleanly.

The single broader-suite failure is the existing Windows MAX_PATH failure in test_c_include_out_of_root_target_id_is_deterministic_across_checkout_paths and is unrelated to this change.

[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

Resolves absolute Python imports made from outside the package tree (e.g. tests/ importing from src/) by discovering source-root directories across the corpus with _discover_python_source_roots and probing them in _resolve_python_module_path via a new source_roots argument. Resolution fails closed when multiple source roots yield conflicting candidates for the same module, binding only when there's a single unambiguous target.

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

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 1722 functions depend on the 144 functions this change touches.

Health — this change adds coupling hotspots:

• new: extract() — 522 callers, 43 callees
• new: _rebuild_code() — 113 callers, 50 callees
• new: _extract_generic() — 18 callers, 25 callees
• new: extract_js() — 85 callers, 4 callees
• new: extract_xaml() — 19 callers, 17 callees
• new: dispatch_command() — 2 callers, 123 callees
• new: extract_objc() — 27 callers, 9 callees
• new: _resolve_js_module_path() — 27 callers, 6 callees
• …and 32 more — each is listed as a finding

Verification — 1722 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: 735 function(s) in the blast radius were not formally verified this run

Formal verification

Could not verify: Could not verify \_collect\_python\_symbol\_resolution\_facts.

The verifier did not have enough to check \_collect\_python\_symbol\_resolution\_facts, 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: parameter `root` is annotated `Path` — outside the synthesizable primitive/collection set

Could not verify: Could not verify \_resolve\_python\_module\_path.

The verifier did not have enough to check \_resolve\_python\_module\_path, 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: parameter `current_path` is annotated `Path` — outside the synthesizable primitive/collection set

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