`graphify update` after deleting a function left the stale node in graph.json.
The build correctly dropped it (#1116), but _check_shrink then refused to write
the smaller graph ("Refusing to overwrite — you may be missing chunk files"),
so the deletion never persisted without --force. That also starved the
work-memory node-existence gate, which relies on graph.json reflecting deletions.
The shrink-guard now takes the set of source files re-extracted this run
(rebuilt_sources). A net shrink is allowed when every lost node belongs to a
rebuilt source (a symbol genuinely removed) or a deleted file; it is still
refused when a node vanishes from a file we did NOT touch — the silent
failed/partial-extraction case the guard exists to catch.
The #1116 e2e test now asserts the prune happens with force=False (was force=True);
added two _check_shrink unit tests (allowed within rebuilt sources, refused
outside). Full suite 2339 passed; skillgen --check clean; ruff clean.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
