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/importer/importer.go

@@ -111,8 +111,7 @@ func ImportIssues(ctx context.Context, dbPath string, store storage.Storage, iss
 		return nil, err
 	}
 
-	// Checkpoint WAL to update main .db file timestamp
-	// This ensures staleness detection sees the database as fresh
+	// Checkpoint WAL to ensure data persistence and reduce WAL file size
 	if err := sqliteStore.CheckpointWAL(ctx); err != nil {
 		// Non-fatal - just log warning
 		fmt.Fprintf(os.Stderr, "Warning: failed to checkpoint WAL: %v\n", err)