`graphify update` preserved old edges keyed only on endpoint-node membership, so a
removed import's edge survived forever whenever both endpoint nodes still existed
(e.g. a.py no longer imports b, but both a and b are still present). The stale edge
drove phantom circular-dependency findings; `--force` didn't help (it only gates
the node-count shrink guard), only a clean rebuild did.
_rebuild_code (watch.py) now also drops preserved edges whose source_file was
re-extracted this run — an edge is owned by the file it was extracted from, and the
fresh extraction re-emits whichever ones still exist. Scoped to source_file
ownership (and the full-rebuild case, where evict_sources lists only deleted
files), so edges with no source_file or owned by a non-re-extracted file are kept —
cross-file edges that merely point at a re-extracted file (#1402 sourceless
stubs/rewire) are not over-pruned.
Reported by @UltronOfSpace (#1521). Regression test: a removed import's edge is
gone after update; verified no over-prune (still-present imports survive) and no
regression to deleted-file pruning.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
safishamsi
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