bug: newly-excluded files are never evicted from the graph — the walk skips them, reconcile only evicts deleted files; stale nodes persist until untrack+track

[tiendungdev]

Env: gortex daemon vv0.61.0+58dc39b, Windows 11 Pro (10.0.26200), one tracked repo (~2.6k files, 124,734 nodes), MCP facade v1.

Repro

1. A directory of generated markdown (4 files) and a legacy TS helper tree (~250 files) are indexed.
2. Add both to exclude: in the repo's .gortex.yaml; restart the daemon so the config is actually loaded (see the companion reload issue).
3. Full workspace_admin {operation:"reindex"} → the walk honors the exclusion: file_count drops 2613 → 2305 (= exactly the newly-excluded files).
4. But node_count/edge_count are unchanged, and search {operation:"files"} still returns the excluded files. A scoped reindex over just the excluded dirs doesn't evict them either.
5. Full workspace_admin {operation:"index"} (cold path): same — nodes persist.

Analysis

Reindex "evicts nodes for deleted files". An excluded-but-still-present file is simply never visited by the walk, so it is neither re-parsed nor treated as deleted — its nodes and edges become permanent orphans. The only purge path today is untrack + track (full retrack), which is expensive and risks daemon-side session/notes state.

This is also a steady source of the "graph holds purgeable rows" problem reported in #311: every exclude-list refinement strands another batch of nodes.

Expected

After a config change, files that fall outside the admission set should be evicted on the next walk (present-but-excluded ⇒ same as deleted), or a prune/reindex --evict-excluded escape hatch should exist.