fix(extract): regenerate cross-file edges via one-hop context files (#2230) - #2382

Graphify reviewed this change.

Looks safe to merge — no coupling regressions and no blocking issues, checked against the code graph (not a self-assessment).

Graphify review — findings

This PR addresses an incremental-extraction issue (#2230) where running extract() on only the changed files caused cross-file edges (e.g. A imports/calls B.helper) to be dropped when the neighbor file B was unchanged. The change adds a step in extract() that discovers one hop of in-root neighbor files via target_file, loads them to provide symbol-resolution facts, then strips those neighbor-owned nodes/edges (by source_file) before returning so ownership stays with the unchanged file for the merge to preserve. It also adds tests in tests/test_incremental.py covering both the direct extract() API (asserting incremental A-edges match a full extract and that B's nodes/edges aren't returned) and the CLI flow across clustered and --no-cluster modes. Surface area is concentrated in graphify/extract.py (the new context-file collection/loading and post-processing filter) and the two new incremental tests.

No blocking issues surfaced. 7 lower-confidence candidates did not survive cross-model review.