feat(core): implement incremental indexing

[prosdev]

Summary

Fixes the existing update() method to actually work. The infrastructure was already there, we just needed to wire it up.

Changes

1. Implement delete in vector store

• Added delete() using LanceDB SQL predicate (id IN (...))
• Properly escapes IDs to prevent SQL injection

2. Add new file detection

• detectChangedFiles() now returns { changed, added, deleted }
• Scans for files not in state to detect new files
• Handles deleted files (in state but not on disk)

3. Update method improvements

• Deletes documents for removed files
• Deletes old documents before re-indexing changed files
• Cleans up orphaned documents when symbols are removed from files
• Properly updates state after deletions

Test Results

Test Files  70 passed | 1 skipped (71)
Tests  1490 passed | 11 skipped (1501)

Usage

# First run: full index
dev index .

# Subsequent runs: incremental (only changed/new files)
dev update

# Force full re-index
dev index . --force

Closes #122