fix(update): reconcile removed and renamed sources#1623
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Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Summary
Fix #1622
Reconcile stored extractor-backed sources with the current corpus during full and incremental rebuilds. Source-path compatibility and reconciliation are isolated from
_rebuild_code; semantic and out-of-scope records remain preserved.Result
graph.jsonno longer retainsonly.pyafter deletion orold.pyafter a destination-only rename. Coverage includes code and document sources, subdirectory roots, legacy markers, symlinks, and hyperedges.Testing
python -m pytest tests/test_watch.py -q(52 passed, 2 skipped; optionalwatchdogunavailable)ruff check graphify/watch.py tests/test_watch.py(passed)python -m tools.skillgen --check(134 artifacts matched)