Module-aware dependency resolution

Status: implemented and verified on fix/module-aware-resolver. Base: origin/main at d33ccc0.

Contract

• Resolve dependencies through module identity, imports and lexical bindings, without matching unrelated symbols by their unqualified name.
• Detect from . import models followed by models.Project.objects.all() by resolving the known Project prefix; no Django runtime or type inference.
• Preserve v1 YAML, collector matching, CodeElement, Dependency, reports, layer membership pairs, suppression and CLI exit-code contracts.
• Preserve file-wide module-import propagation and nearest-definition local import ownership, including uncollected nested definitions.
• Index included files without collected elements for package re-exports.
• Do not execute imports. Ambiguous and dynamic targets must not create guessed links. Do not implement general control-flow or instance-type analysis.

Steps

1. Add integration regressions for module targets, aliases, relative imports, package re-exports, duplicate names, known attribute prefixes and shadowing.
2. Build one internal module/symbol resolver from the included ASTs. Infer regular-package and scan-directory roots, including conventional src roots; keep duplicate module candidates ambiguous.
3. Route all visitor target lookups through the resolver. Keep explicit target maps supported for callers that supply a context-free visitor directly.
4. Pass included files and analysis paths from the runner; preserve all existing rule, ownership and reporting behavior. Correct invalid import test fixtures while retaining their original ownership and violation assertions.
5. Document resolution and static boundaries; run focused tests, make check, review the complete scoped diff independently and fix in-scope findings.

Verification

• Baseline: 181 tests passed before changes.
• Added 31 integration regressions covering the issue, import identity, lexical scopes, package boundaries, re-exports, ambiguity, and existing v1 YAML.
• Corrected invalid import paths in legacy fixtures while preserving their original dependency ownership and violation assertions.
• make check passed: Ruff, mypy, dependency audit, and all 212 tests on Python 3.14.
• All 212 tests passed on Python 3.8; one Python 3.12+ generic-syntax test skipped.
• CI coverage gates passed: 96.18% line coverage and 90.70% branch coverage.
• Targeted mutation verification covered 1,115 mutants in the resolver and analyzer: 848 killed, 267 survived, no execution errors or untested mutants. Scores remain report-only; CI runs core and resolver scopes separately.
• Independent review approved the scoped diff after regression fixes; git diff --check passed.