Update leaves stale graph sources after renames or final-file deletion

[oleksii-tumanov]

Problem

graphify update can leave stale graph entries when the last supported file is deleted or a rename reports only its destination. The removed source remains in graph.json.

Expected

Reconcile extractor-backed sources with files still present, while preserving semantic and out-of-scope records.

Reproduction

1. Build from only.py, delete it, and run graphify update ..
2. Or rename old.py to renamed.py with only the destination in changed_paths.
3. The deleted or old source remains in graph.json.

[safishamsi]

Fixed via #1623, merged to v8 as 8d8d2b8. The rebuild now reconciles extractor-backed sources against files still present, so a deleted last-file or a destination-only rename no longer leaves stale nodes in graph.json. Ships next release.