_reconcile_existing_graph treated "source identity absent from the collected
corpus" as deletion and evicted its nodes/edges/hyperedges. But corpus absence
is ambiguous: it's also what you see when a file still exists and merely stopped
being collected (ignore rules or filters changed). Upgrading into the merged-
.gitignore scan semantics (#1363) mass-evicted 655 nodes from a deliberately-
built, .gitignore'd docs dir whose files were present the whole time — reported
as a successful rebuild.
Fail-closed: before evicting a corpus-absent identity, require Path(identity)
.exists() is False (identity is an absolute path). Alive-but-excluded sources
are preserved (nodes, edges, hyperedges) and a loud line reports how many were
kept and why. True deletions and renames still evict (old path gone from disk);
a full extract --force still purges deliberate exclusions via the AST ownership
rule. Existence is memoized (one stat per file that left the corpus).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
