Remove spurious collision-related code after ultrathink review

After 2 weeks of collision/stale-data fixes, reviewed all changes to identify
spurious code that is no longer needed after content-hash resolution was implemented.

**Removed:**
1. countReferences() function from collision.go (lines 274-328)
   - Was used for reference-count based collision scoring
   - Completely unused after switching to content-hash based resolution (commit 2e87329)
   - Still exists in duplicates.go for deduplication (different use case)

2. ReferenceScore field from CollisionDetail struct
   - Marked as DEPRECATED but never removed
   - No longer used by ScoreCollisions() which now uses content hashing

3. TestCountReferences and TestCountReferencesWordBoundary tests
   - Tested the now-deleted countReferences() function
   - No longer relevant

**Fixed:**
- Updated CheckpointWAL comments to remove misleading "staleness detection" claim
  - Staleness detection uses metadata (last_import_time), NOT file mtime
  - CheckpointWAL is still valuable for data persistence and WAL size reduction
  - Comments now accurately reflect actual benefits

**Verified:**
- All tests pass (internal/storage/sqlite)
- Content-hash collision resolution still works correctly
- No behavioral changes, just cleanup

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

internal/storage/sqlite/sqlite.go

@@ -2301,9 +2301,11 @@ func (s *SQLiteStorage) UnderlyingConn(ctx context.Context) (*sql.Conn, error) {
 }
 
 // CheckpointWAL checkpoints the WAL file to flush changes to the main database file.
-// This updates the main .db file's modification time, which is important for staleness detection.
 // In WAL mode, writes go to the -wal file, leaving the main .db file untouched.
-// Checkpointing flushes the WAL to the main database file.
+// Checkpointing:
+// - Ensures data persistence by flushing WAL to main database
+// - Reduces WAL file size
+// - Makes database safe for backup/copy operations
 func (s *SQLiteStorage) CheckpointWAL(ctx context.Context) error {
 	_, err := s.db.ExecContext(ctx, "PRAGMA wal_checkpoint(FULL)")
 	return err