Implement bd merge command with dependency migration and text references

- Add performMerge() with dependency migration in both directions
- Implement updateMergeTextReferences() for text reference updates
- Close source issues with 'Merged into bd-X' reason
- Fix store initialization panic by checking daemon mode earlier
- Add TODO for transaction support (deferred, see bd-215 for idempotency approach)

Closes bd-202, bd-193, bd-194, bd-195, bd-196
Related: bd-190 (merge epic), bd-215 (idempotency enhancement)

Amp-Thread-ID: https://ampcode.com/threads/T-30fe297d-4713-4f84-abc9-3bd264caa4c6
Co-authored-by: Amp <amp@ampcode.com>

cmd/bd/merge.go

@@ -4,10 +4,13 @@ import (
 	"context"
 	"fmt"
 	"os"
+	"regexp"
 	"strings"
+	"time"
 
 	"github.com/fatih/color"
 	"github.com/spf13/cobra"
+	"github.com/steveyegge/beads/internal/types"
 )
 
 var mergeCmd = &cobra.Command{
@@ -26,6 +29,12 @@ Example:
   bd merge bd-10 bd-11 bd-12 --into bd-10 --dry-run`,
 	Args: cobra.MinimumNArgs(1),
 	Run: func(cmd *cobra.Command, args []string) {
+		// Check daemon mode first before accessing store
+		if daemonClient != nil {
+			fmt.Fprintf(os.Stderr, "Error: merge command not yet supported in daemon mode (see bd-190)\n")
+			os.Exit(1)
+		}
+
 		targetID, _ := cmd.Flags().GetString("into")
 		if targetID == "" {
 			fmt.Fprintf(os.Stderr, "Error: --into flag is required\n")
@@ -41,12 +50,6 @@ Example:
 			os.Exit(1)
 		}
 
-		// TODO: Add RPC support when daemon implements MergeIssues
-		if daemonClient != nil {
-			fmt.Fprintf(os.Stderr, "Error: merge command not yet supported in daemon mode (see bd-190)\n")
-			os.Exit(1)
-		}
-
 		// Direct mode
 		ctx := context.Background()
 
@@ -119,8 +122,173 @@ func validateMerge(targetID string, sourceIDs []string) error {
 }
 
 // performMerge executes the merge operation
+// TODO(bd-202): Add transaction support for atomicity
 func performMerge(ctx context.Context, targetID string, sourceIDs []string) error {
-	// TODO: Implement actual merge logic in bd-190
+	// Step 1: Migrate dependencies from source issues to target
-	// This is a placeholder for validation purposes
+	for _, sourceID := range sourceIDs {
-	return fmt.Errorf("merge operation not yet implemented (see bd-190)")
+		// Get all dependencies where source is the dependent (source depends on X)
+		deps, err := store.GetDependencyRecords(ctx, sourceID)
+		if err != nil {
+			return fmt.Errorf("failed to get dependencies for %s: %w", sourceID, err)
+		}
+
+		// Migrate each dependency to target
+		for _, dep := range deps {
+			// Skip if target already has this dependency
+			existingDeps, err := store.GetDependencyRecords(ctx, targetID)
+			if err != nil {
+				return fmt.Errorf("failed to check target dependencies: %w", err)
+			}
+
+			alreadyExists := false
+			for _, existing := range existingDeps {
+				if existing.DependsOnID == dep.DependsOnID && existing.Type == dep.Type {
+					alreadyExists = true
+					break
+				}
+			}
+
+			if !alreadyExists && dep.DependsOnID != targetID {
+				// Add dependency to target
+				newDep := &types.Dependency{
+					IssueID:     targetID,
+					DependsOnID: dep.DependsOnID,
+					Type:        dep.Type,
+					CreatedAt:   time.Now(),
+					CreatedBy:   actor,
+				}
+				if err := store.AddDependency(ctx, newDep, actor); err != nil {
+					return fmt.Errorf("failed to migrate dependency %s -> %s: %w", targetID, dep.DependsOnID, err)
+				}
+			}
+		}
+
+		// Get all dependencies where source is the dependency (X depends on source)
+		allDeps, err := store.GetAllDependencyRecords(ctx)
+		if err != nil {
+			return fmt.Errorf("failed to get all dependencies: %w", err)
+		}
+
+		for issueID, depList := range allDeps {
+			for _, dep := range depList {
+				if dep.DependsOnID == sourceID {
+					// Remove old dependency
+					if err := store.RemoveDependency(ctx, issueID, sourceID, actor); err != nil {
+						// Ignore "not found" errors as they may have been cleaned up
+						if !strings.Contains(err.Error(), "not found") {
+							return fmt.Errorf("failed to remove dependency %s -> %s: %w", issueID, sourceID, err)
+						}
+					}
+
+					// Add new dependency to target (if not self-reference)
+					if issueID != targetID {
+						newDep := &types.Dependency{
+							IssueID:     issueID,
+							DependsOnID: targetID,
+							Type:        dep.Type,
+							CreatedAt:   time.Now(),
+							CreatedBy:   actor,
+						}
+						if err := store.AddDependency(ctx, newDep, actor); err != nil {
+							// Ignore if dependency already exists
+							if !strings.Contains(err.Error(), "UNIQUE constraint failed") {
+								return fmt.Errorf("failed to add dependency %s -> %s: %w", issueID, targetID, err)
+							}
+						}
+					}
+				}
+			}
+		}
+	}
+
+	// Step 2: Update text references in all issues
+	if err := updateMergeTextReferences(ctx, sourceIDs, targetID); err != nil {
+		return fmt.Errorf("failed to update text references: %w", err)
+	}
+
+	// Step 3: Close source issues
+	for _, sourceID := range sourceIDs {
+		reason := fmt.Sprintf("Merged into %s", targetID)
+		if err := store.CloseIssue(ctx, sourceID, reason, actor); err != nil {
+			return fmt.Errorf("failed to close source issue %s: %w", sourceID, err)
+		}
+	}
+
+	return nil
+}
+
+// updateMergeTextReferences updates text references from source IDs to target ID
+func updateMergeTextReferences(ctx context.Context, sourceIDs []string, targetID string) error {
+	// Get all issues to scan for references
+	allIssues, err := store.SearchIssues(ctx, "", types.IssueFilter{})
+	if err != nil {
+		return fmt.Errorf("failed to get all issues: %w", err)
+	}
+
+	updatedCount := 0
+	for _, issue := range allIssues {
+		// Skip source issues (they're being closed anyway)
+		isSource := false
+		for _, srcID := range sourceIDs {
+			if issue.ID == srcID {
+				isSource = true
+				break
+			}
+		}
+		if isSource {
+			continue
+		}
+
+		updates := make(map[string]interface{})
+
+		// Check each source ID for references
+		for _, sourceID := range sourceIDs {
+			// Build regex pattern to match issue IDs with word boundaries
+			idPattern := `(^|[^A-Za-z0-9_-])(` + regexp.QuoteMeta(sourceID) + `)($|[^A-Za-z0-9_-])`
+			re := regexp.MustCompile(idPattern)
+			replacementText := `$1` + targetID + `$3`
+
+			// Update description
+			if issue.Description != "" && re.MatchString(issue.Description) {
+				if _, exists := updates["description"]; !exists {
+					updates["description"] = issue.Description
+				}
+				updates["description"] = re.ReplaceAllString(updates["description"].(string), replacementText)
+			}
+
+			// Update notes
+			if issue.Notes != "" && re.MatchString(issue.Notes) {
+				if _, exists := updates["notes"]; !exists {
+					updates["notes"] = issue.Notes
+				}
+				updates["notes"] = re.ReplaceAllString(updates["notes"].(string), replacementText)
+			}
+
+			// Update design
+			if issue.Design != "" && re.MatchString(issue.Design) {
+				if _, exists := updates["design"]; !exists {
+					updates["design"] = issue.Design
+				}
+				updates["design"] = re.ReplaceAllString(updates["design"].(string), replacementText)
+			}
+
+			// Update acceptance criteria
+			if issue.AcceptanceCriteria != "" && re.MatchString(issue.AcceptanceCriteria) {
+				if _, exists := updates["acceptance_criteria"]; !exists {
+					updates["acceptance_criteria"] = issue.AcceptanceCriteria
+				}
+				updates["acceptance_criteria"] = re.ReplaceAllString(updates["acceptance_criteria"].(string), replacementText)
+			}
+		}
+
+		// Apply updates if any
+		if len(updates) > 0 {
+			if err := store.UpdateIssue(ctx, issue.ID, updates, actor); err != nil {
+				return fmt.Errorf("failed to update issue %s: %w", issue.ID, err)
+			}
+			updatedCount++
+		}
+	}
+
+	return nil
 }