Orphaned merkle files not cleaned up on index clear

[Retengart]

Problem

When index is cleared via Zilliz Cloud console (not via clear_index tool), local merkle files remain.

Current Behavior

clearIndex() in context.ts calls FileSynchronizer.deleteSnapshot(), but if user deletes collection directly in cloud:

1. Cloud collection gone
2. Local ~/.context/merkle/<hash>.json remains
3. Local ~/.context/mcp-codebase-snapshot.json still lists codebase (until cloud sync removes it)

Impact

Disk space waste from orphaned merkle files over time.

Expected Behavior

Background sync should detect missing cloud collections and clean up corresponding merkle files.

Location

• packages/mcp/src/handlers.ts:118-124 - removes from snapshot but not merkle
• packages/core/src/sync/synchronizer.ts:329-347 - deleteSnapshot()