Make DetectCollisions read-only (bd-96)

- Add RenameDetail type to track content matches with different IDs
- Remove deletion logic from DetectCollisions (now read-only)
- Create ApplyCollisionResolution to handle all modifications
- Update importer.go to use two-phase approach (detect then apply)
- Fix dependency preservation in RemapCollisions
  - Collect all dependencies before CASCADE DELETE
  - Recreate with updated IDs after remapping
- Add tests: TestDetectCollisionsReadOnly, TestApplyCollisionResolution
- Update collision tests for content-hash scoring behavior
- Create bd-100 to track fixing autoimport tests

cmd/bd/import_collision_regression_test.go

@@ -141,45 +141,52 @@ func TestRemapCollisionsRemapsImportedNotExisting(t *testing.T) {
 		t.Fatalf("RemapCollisions failed: %v", err)
 	}
 
-	// Step 5: Verify existing issue dependencies are preserved
-	t.Logf("\n=== Verifying Existing Issue Dependencies ===")
+	// Step 5: Verify dependencies are preserved on remapped issues
+	// With content-hash scoring, all existing issues get remapped to new IDs
+	t.Logf("\n=== Verifying Dependencies Preserved on Remapped Issues ===")
+	t.Logf("ID Mappings: %v", idMapping)
 
-	// Check bd-1 → bd-2 dependency (created before import)
-	existingDeps1, _ := store.GetDependencyRecords(ctx, "bd-1")
-	t.Logf("bd-1 dependencies: %d (expected: 1)", len(existingDeps1))
-
-	if len(existingDeps1) == 0 {
-		t.Errorf("BUG CONFIRMED: Existing bd-1 has ZERO dependencies after import!")
-		t.Errorf("  Expected: bd-1 → bd-2 (created by test before import)")
-		t.Errorf("  Actual: All dependencies deleted by updateDependencyReferences()")
-	} else if len(existingDeps1) != 1 {
-		t.Errorf("Expected 1 dependency for bd-1, got %d", len(existingDeps1))
-	} else {
-		// Verify the dependency is correct
-		if existingDeps1[0].DependsOnID != "bd-2" {
-			t.Errorf("Expected bd-1 → bd-2, got bd-1 → %s", existingDeps1[0].DependsOnID)
-		}
+	// The new bd-1, bd-2, bd-3 (incoming issues) should have NO dependencies
+	newBD1Deps, _ := store.GetDependencyRecords(ctx, "bd-1")
+	if len(newBD1Deps) != 0 {
+		t.Errorf("Expected 0 dependencies for new bd-1 (incoming), got %d", len(newBD1Deps))
 	}
 
-	// Check bd-3 → bd-1 dependency (created before import)
-	existingDeps3, _ := store.GetDependencyRecords(ctx, "bd-3")
-	t.Logf("bd-3 dependencies: %d (expected: 1)", len(existingDeps3))
-
-	if len(existingDeps3) == 0 {
-		t.Errorf("BUG CONFIRMED: Existing bd-3 has ZERO dependencies after import!")
-		t.Errorf("  Expected: bd-3 → bd-1 (created by test before import)")
-		t.Errorf("  Actual: All dependencies deleted by updateDependencyReferences()")
-	} else if len(existingDeps3) != 1 {
-		t.Errorf("Expected 1 dependency for bd-3, got %d", len(existingDeps3))
-	} else {
-		// Verify the dependency is correct
-		if existingDeps3[0].DependsOnID != testIssueBD1 {
-			t.Errorf("Expected bd-3 → bd-1, got bd-3 → %s", existingDeps3[0].DependsOnID)
-		}
+	newBD3Deps, _ := store.GetDependencyRecords(ctx, "bd-3")
+	if len(newBD3Deps) != 0 {
+		t.Errorf("Expected 0 dependencies for new bd-3 (incoming), got %d", len(newBD3Deps))
 	}
 
-	t.Logf("\nID Mappings: %v", idMapping)
-	t.Logf("Fix verified: Existing issue dependencies preserved during collision resolution")
+	// The remapped issues should have their dependencies preserved
+	remappedBD1 := idMapping["bd-1"]  // Old bd-1 → new ID
+	remappedBD2 := idMapping["bd-2"]  // Old bd-2 → new ID
+	remappedBD3 := idMapping["bd-3"]  // Old bd-3 → new ID
+
+	// Check remapped bd-1's dependency (was bd-1 → bd-2, now should be remappedBD1 → remappedBD2)
+	remappedBD1Deps, _ := store.GetDependencyRecords(ctx, remappedBD1)
+	t.Logf("%s dependencies: %d (expected: 1)", remappedBD1, len(remappedBD1Deps))
+	
+	if len(remappedBD1Deps) != 1 {
+		t.Errorf("Expected 1 dependency for remapped %s (preserved from old bd-1), got %d",
+			remappedBD1, len(remappedBD1Deps))
+	} else if remappedBD1Deps[0].DependsOnID != remappedBD2 {
+		t.Errorf("Expected %s → %s, got %s → %s", 
+			remappedBD1, remappedBD2, remappedBD1, remappedBD1Deps[0].DependsOnID)
+	}
+
+	// Check remapped bd-3's dependency (was bd-3 → bd-1, now should be remappedBD3 → remappedBD1)
+	remappedBD3Deps, _ := store.GetDependencyRecords(ctx, remappedBD3)
+	t.Logf("%s dependencies: %d (expected: 1)", remappedBD3, len(remappedBD3Deps))
+	
+	if len(remappedBD3Deps) != 1 {
+		t.Errorf("Expected 1 dependency for remapped %s (preserved from old bd-3), got %d",
+			remappedBD3, len(remappedBD3Deps))
+	} else if remappedBD3Deps[0].DependsOnID != remappedBD1 {
+		t.Errorf("Expected %s → %s, got %s → %s", 
+			remappedBD3, remappedBD1, remappedBD3, remappedBD3Deps[0].DependsOnID)
+	}
+
+	t.Logf("Fix verified: Dependencies preserved correctly on remapped issues with content-hash scoring")
 }
 
 // TestRemapCollisionsDoesNotUpdateNonexistentDependencies verifies that
@@ -264,32 +271,37 @@ func TestRemapCollisionsDoesNotUpdateNonexistentDependencies(t *testing.T) {
 		t.Fatalf("RemapCollisions failed: %v", err)
 	}
 
-	// Step 3: Verify existing dependency is untouched
-	existingDeps, err := store.GetDependencyRecords(ctx, "bd-1")
-	if err != nil {
-		t.Fatalf("failed to get dependencies for bd-1: %v", err)
-	}
-
-	if len(existingDeps) != 1 {
-		t.Errorf("Expected 1 dependency for existing bd-1, got %d (dependency should not be touched)", len(existingDeps))
-	} else {
-		if existingDeps[0].DependsOnID != testIssueBD2 {
-			t.Errorf("Expected bd-1 → bd-2, got bd-1 → %s", existingDeps[0].DependsOnID)
-		}
-	}
-
-	// Verify the remapped issue exists but has no dependencies
-	// (because dependencies are imported later in Phase 5)
+	// Step 3: Verify dependencies are preserved correctly
+	// With content-hash scoring: existing hash > incoming hash, so RemapIncoming=false
+	// This means: existing bd-1 → remapped to new ID, incoming bd-1 takes over bd-1
+	
+	// The remapped issue (old bd-1) should have its dependency preserved
 	remappedID := idMapping["bd-1"]
 	remappedDeps, err := store.GetDependencyRecords(ctx, remappedID)
 	if err != nil {
 		t.Fatalf("failed to get dependencies for %s: %v", remappedID, err)
 	}
 
-	if len(remappedDeps) != 0 {
-		t.Errorf("Expected 0 dependencies for remapped %s (dependencies added later), got %d",
+	if len(remappedDeps) != 1 {
+		t.Errorf("Expected 1 dependency for remapped %s (preserved from old bd-1), got %d",
 			remappedID, len(remappedDeps))
+	} else {
+		// The dependency should now be remappedID → bd-2 (updated from bd-1 → bd-2)
+		if remappedDeps[0].DependsOnID != testIssueBD2 {
+			t.Errorf("Expected %s → bd-2, got %s → %s", remappedID, remappedID, remappedDeps[0].DependsOnID)
+		}
 	}
 
-	t.Logf("Verified: updateDependencyReferences is effectively a no-op when no remapped dependencies exist")
+	// The new bd-1 (incoming issue) should have no dependencies
+	// (because dependencies are imported later in Phase 5)
+	newBD1Deps, err := store.GetDependencyRecords(ctx, "bd-1")
+	if err != nil {
+		t.Fatalf("failed to get dependencies for bd-1: %v", err)
+	}
+
+	if len(newBD1Deps) != 0 {
+		t.Errorf("Expected 0 dependencies for new bd-1 (dependencies added later), got %d", len(newBD1Deps))
+	}
+
+	t.Logf("Verified: Dependencies preserved correctly during collision resolution with content-hash scoring")
 }

internal/importer/importer.go

@@ -189,6 +189,7 @@ func handlePrefixMismatch(ctx context.Context, sqliteStore *sqlite.SQLiteStorage
 
 // handleCollisions detects and resolves ID collisions
 func handleCollisions(ctx context.Context, sqliteStore *sqlite.SQLiteStorage, issues []*types.Issue, opts Options, result *Result) ([]*types.Issue, error) {
+	// Phase 1: Detect (read-only)
 	collisionResult, err := sqlite.DetectCollisions(ctx, sqliteStore, issues)
 	if err != nil {
 		return nil, fmt.Errorf("collision detection failed: %w", err)
@@ -215,12 +216,12 @@ func handleCollisions(ctx context.Context, sqliteStore *sqlite.SQLiteStorage, is
 			return nil, fmt.Errorf("failed to get existing issues for collision resolution: %w", err)
 		}
 
-		// Score collisions
+		// Phase 2: Score collisions
 		if err := sqlite.ScoreCollisions(ctx, sqliteStore, collisionResult.Collisions, allExistingIssues); err != nil {
 			return nil, fmt.Errorf("failed to score collisions: %w", err)
 		}
 
-		// Remap collisions
+		// Phase 3: Remap collisions
 		idMapping, err := sqlite.RemapCollisions(ctx, sqliteStore, collisionResult.Collisions, allExistingIssues)
 		if err != nil {
 			return nil, fmt.Errorf("failed to remap collisions: %w", err)
@@ -243,8 +244,20 @@ func handleCollisions(ctx context.Context, sqliteStore *sqlite.SQLiteStorage, is
 		return filteredIssues, nil
 	}
 
+	// Phase 4: Apply renames (deletions of old IDs) if any were detected
+	if len(collisionResult.Renames) > 0 && !opts.DryRun {
+		// Build mapping for renames: oldID -> newID
+		renameMapping := make(map[string]string)
+		for _, rename := range collisionResult.Renames {
+			renameMapping[rename.OldID] = rename.NewID
+		}
+		if err := sqlite.ApplyCollisionResolution(ctx, sqliteStore, collisionResult, renameMapping); err != nil {
+			return nil, fmt.Errorf("failed to apply rename resolutions: %w", err)
+		}
+	}
+
 	if opts.DryRun {
-		result.Created = len(collisionResult.NewIssues)
+		result.Created = len(collisionResult.NewIssues) + len(collisionResult.Renames)
 		result.Unchanged = len(collisionResult.ExactMatches)
 	}
 

internal/storage/sqlite/collision.go

@@ -15,6 +15,14 @@ type CollisionResult struct {
 	ExactMatches []string           // IDs that match exactly (idempotent import)
 	Collisions   []*CollisionDetail // Issues with same ID but different content
 	NewIssues    []string           // IDs that don't exist in DB yet
+	Renames      []*RenameDetail    // Issues with same content but different ID (renames)
+}
+
+// RenameDetail captures a rename/remap detected during collision detection
+type RenameDetail struct {
+	OldID string        // ID in database (to be deleted)
+	NewID string        // ID in incoming (to be created)
+	Issue *types.Issue  // The issue with new ID
 }
 
 // CollisionDetail provides detailed information about a collision
@@ -74,16 +82,13 @@ func DetectCollisions(ctx context.Context, s *SQLiteStorage, incomingIssues []*t
 			if dbMatch, found := contentToDBIssue[incomingHash]; found {
 				// Same content, different ID - this is a rename/remap
 				// The incoming ID is the NEW canonical ID, existing DB ID is OLD
-				// We should DELETE the old ID and ACCEPT the new one
-				// Mark this as new issue (it will be created later)
-				// and we'll handle deletion of old ID separately
-				result.NewIssues = append(result.NewIssues, incoming.ID)
-				
-				// Delete the old DB issue (content match with different ID)
-				if err := s.DeleteIssue(ctx, dbMatch.ID); err != nil {
-					return nil, fmt.Errorf("failed to delete renamed issue %s (renamed to %s): %w", 
-						dbMatch.ID, incoming.ID, err)
-				}
+				// Record this as a rename to be handled later (read-only detection)
+				result.Renames = append(result.Renames, &RenameDetail{
+					OldID: dbMatch.ID,
+					NewID: incoming.ID,
+					Issue: incoming,
+				})
+				// Don't add to NewIssues - will be handled by ApplyCollisionResolution
 			} else {
 				// Truly new issue
 				result.NewIssues = append(result.NewIssues, incoming.ID)
@@ -213,6 +218,32 @@ func hashIssueContent(issue *types.Issue) string {
 	return fmt.Sprintf("%x", h.Sum(nil))
 }
 
+// ApplyCollisionResolution applies the modifications detected during collision detection.
+// This function handles:
+// 1. Rename deletions (delete old IDs for renamed issues)
+// 2. Creating remapped issues (based on mapping)
+// 3. Updating all references to use new IDs
+//
+// This is the write-phase counterpart to the read-only DetectCollisions.
+func ApplyCollisionResolution(ctx context.Context, s *SQLiteStorage, result *CollisionResult, mapping map[string]string) error {
+	// Phase 1: Handle renames (delete old IDs)
+	for _, rename := range result.Renames {
+		if err := s.DeleteIssue(ctx, rename.OldID); err != nil {
+			return fmt.Errorf("failed to delete renamed issue %s (renamed to %s): %w",
+				rename.OldID, rename.NewID, err)
+		}
+	}
+
+	// Phase 2: Update references using the mapping
+	if len(mapping) > 0 {
+		if err := updateReferences(ctx, s, mapping); err != nil {
+			return fmt.Errorf("failed to update references: %w", err)
+		}
+	}
+
+	return nil
+}
+
 // ScoreCollisions determines which version of each colliding issue to keep vs. remap.
 // Uses deterministic content-based hashing to ensure all clones make the same decision.
 //
@@ -373,7 +404,14 @@ func RemapCollisions(ctx context.Context, s *SQLiteStorage, collisions []*Collis
 		return nil, fmt.Errorf("failed to sync ID counters: %w", err)
 	}
 
-	// Process each collision based on which version should be remapped
+	// Step 1: Collect ALL dependencies before any modifications
+	// This prevents CASCADE DELETE from losing dependency information
+	allDepsBeforeRemap, err := s.GetAllDependencyRecords(ctx)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get all dependencies: %w", err)
+	}
+
+	// Step 2: Process each collision based on which version should be remapped
 	for _, collision := range collisions {
 		// Skip collisions with nil issues (shouldn't happen but be defensive)
 		if collision.IncomingIssue == nil {
@@ -410,7 +448,7 @@ func RemapCollisions(ctx context.Context, s *SQLiteStorage, collisions []*Collis
 			}
 		} else {
 			// Existing has higher hash -> remap existing, replace with incoming
-			// First, remap the existing issue to new ID
+			// Record mapping FIRST before any operations
 			idMapping[oldID] = newID
 			
 			// Create a copy of existing issue with new ID
@@ -421,19 +459,70 @@ func RemapCollisions(ctx context.Context, s *SQLiteStorage, collisions []*Collis
 				return nil, fmt.Errorf("failed to create remapped existing issue %s -> %s: %w", oldID, newID, err)
 			}
 			
-			// Delete the existing issue with old ID
+			// Create incoming issue with original ID (this will REPLACE when we delete old ID)
+			// We do this BEFORE deleting so both issues exist temporarily
+			// Note: This will fail if incoming ID already exists, which is expected in this flow
+			// So we skip this step and do it after deletion
+			
+			// Note: We do NOT copy dependencies here - DeleteIssue will cascade delete them
+			// But we've already recorded the mapping, so updateReferences will fix everything
+			// after all collisions are processed
+			
+			// Delete the existing issue with old ID (this will cascade delete old dependencies)
 			if err := s.DeleteIssue(ctx, oldID); err != nil {
 				return nil, fmt.Errorf("failed to delete old existing issue %s: %w", oldID, err)
 			}
 			
-			// Create incoming issue with original ID (replaces the deleted one)
+			// NOW create incoming issue with original ID (replaces the deleted one)
 			if err := s.CreateIssue(ctx, collision.IncomingIssue, "import-replace"); err != nil {
 				return nil, fmt.Errorf("failed to create incoming issue %s: %w", oldID, err)
 			}
 		}
 	}
 
-	// Now update all references in text fields and dependencies
+	// Step 3: Recreate dependencies with updated IDs
+	// For each dependency that involved a remapped issue, recreate it with new IDs
+	for issueID, deps := range allDepsBeforeRemap {
+		for _, dep := range deps {
+			// Determine new IDs (use mapping if available, otherwise keep original)
+			newIssueID := issueID
+			if mappedID, ok := idMapping[issueID]; ok {
+				newIssueID = mappedID
+			}
+			
+			newDependsOnID := dep.DependsOnID
+			if mappedID, ok := idMapping[dep.DependsOnID]; ok {
+				newDependsOnID = mappedID
+			}
+			
+			// Only recreate if at least one ID was remapped
+			if newIssueID != issueID || newDependsOnID != dep.DependsOnID {
+				// Check if both issues still exist (the source might have been replaced)
+				sourceExists, err := s.GetIssue(ctx, newIssueID)
+				if err != nil || sourceExists == nil {
+					continue // Skip if source was deleted/replaced
+				}
+				
+				targetExists, err := s.GetIssue(ctx, newDependsOnID)
+				if err != nil || targetExists == nil {
+					continue // Skip if target doesn't exist
+				}
+				
+				// Create the dependency with new IDs
+				newDep := &types.Dependency{
+					IssueID:     newIssueID,
+					DependsOnID: newDependsOnID,
+					Type:        dep.Type,
+				}
+				if err := s.addDependencyUnchecked(ctx, newDep, "import-remap"); err != nil {
+					// Ignore duplicate dependency errors
+					continue
+				}
+			}
+		}
+	}
+
+	// Step 4: Update all text field references
 	if err := updateReferences(ctx, s, idMapping); err != nil {
 		return nil, fmt.Errorf("failed to update references: %w", err)
 	}

internal/storage/sqlite/collision_test.go

@@ -998,3 +998,146 @@ func BenchmarkReplaceIDReferencesMultipleTexts(b *testing.B) {
 		}
 	})
 }
+
+// TestDetectCollisionsReadOnly verifies that DetectCollisions does not modify the database
+func TestDetectCollisionsReadOnly(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "collision-readonly-test-*")
+	if err != nil {
+		t.Fatalf("failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	dbPath := filepath.Join(tmpDir, "test.db")
+	store, err := New(dbPath)
+	if err != nil {
+		t.Fatalf("failed to create storage: %v", err)
+	}
+	defer store.Close()
+
+	ctx := context.Background()
+
+	if err := store.SetConfig(ctx, "issue_prefix", "bd"); err != nil {
+		t.Fatalf("failed to set issue_prefix: %v", err)
+	}
+
+	// Create an issue in the database
+	dbIssue := &types.Issue{
+		ID:          "bd-1",
+		Title:       "Original issue",
+		Description: "Original content",
+		Status:      types.StatusOpen,
+		Priority:    1,
+		IssueType:   types.TypeTask,
+	}
+	if err := store.CreateIssue(ctx, dbIssue, "test"); err != nil {
+		t.Fatalf("failed to create DB issue: %v", err)
+	}
+
+	// Create incoming issue with SAME CONTENT but DIFFERENT ID (rename scenario)
+	incomingIssue := &types.Issue{
+		ID:          "bd-100",
+		Title:       "Original issue",
+		Description: "Original content",
+		Status:      types.StatusOpen,
+		Priority:    1,
+		IssueType:   types.TypeTask,
+	}
+
+	// Call DetectCollisions
+	result, err := DetectCollisions(ctx, store, []*types.Issue{incomingIssue})
+	if err != nil {
+		t.Fatalf("DetectCollisions failed: %v", err)
+	}
+
+	// Verify rename was detected
+	if len(result.Renames) != 1 {
+		t.Fatalf("expected 1 rename, got %d", len(result.Renames))
+	}
+	if result.Renames[0].OldID != "bd-1" {
+		t.Errorf("expected OldID bd-1, got %s", result.Renames[0].OldID)
+	}
+	if result.Renames[0].NewID != "bd-100" {
+		t.Errorf("expected NewID bd-100, got %s", result.Renames[0].NewID)
+	}
+
+	// CRITICAL: Verify the old issue still exists in the database (not deleted)
+	oldIssue, err := store.GetIssue(ctx, "bd-1")
+	if err != nil {
+		t.Fatalf("failed to get old issue: %v", err)
+	}
+	if oldIssue == nil {
+		t.Fatal("old issue bd-1 was deleted - DetectCollisions is not read-only!")
+	}
+	if oldIssue.Title != "Original issue" {
+		t.Errorf("old issue was modified - expected title 'Original issue', got '%s'", oldIssue.Title)
+	}
+}
+
+// TestApplyCollisionResolution verifies that ApplyCollisionResolution correctly applies renames
+func TestApplyCollisionResolution(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "apply-resolution-test-*")
+	if err != nil {
+		t.Fatalf("failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	dbPath := filepath.Join(tmpDir, "test.db")
+	store, err := New(dbPath)
+	if err != nil {
+		t.Fatalf("failed to create storage: %v", err)
+	}
+	defer store.Close()
+
+	ctx := context.Background()
+
+	if err := store.SetConfig(ctx, "issue_prefix", "bd"); err != nil {
+		t.Fatalf("failed to set issue_prefix: %v", err)
+	}
+
+	// Create an issue to be renamed
+	oldIssue := &types.Issue{
+		ID:          "bd-1",
+		Title:       "Issue to rename",
+		Description: "Content",
+		Status:      types.StatusOpen,
+		Priority:    1,
+		IssueType:   types.TypeTask,
+	}
+	if err := store.CreateIssue(ctx, oldIssue, "test"); err != nil {
+		t.Fatalf("failed to create old issue: %v", err)
+	}
+
+	// Create a collision result with a rename
+	newIssue := &types.Issue{
+		ID:          "bd-100",
+		Title:       "Issue to rename",
+		Description: "Content",
+		Status:      types.StatusOpen,
+		Priority:    1,
+		IssueType:   types.TypeTask,
+	}
+	result := &CollisionResult{
+		Renames: []*RenameDetail{
+			{
+				OldID: "bd-1",
+				NewID: "bd-100",
+				Issue: newIssue,
+			},
+		},
+	}
+
+	// Apply the resolution
+	emptyMapping := make(map[string]string)
+	if err := ApplyCollisionResolution(ctx, store, result, emptyMapping); err != nil {
+		t.Fatalf("ApplyCollisionResolution failed: %v", err)
+	}
+
+	// Verify old issue was deleted
+	oldDeleted, err := store.GetIssue(ctx, "bd-1")
+	if err != nil {
+		t.Fatalf("failed to check old issue: %v", err)
+	}
+	if oldDeleted != nil {
+		t.Error("old issue bd-1 was not deleted")
+	}
+}