Add rename-prefix --repair flag and consolidate issue ID parsing

Enhances rename-prefix command with --repair flag to consolidate databases
with multiple prefixes. Creates shared issue ID utilities to eliminate code
duplication across import and rename operations.

Key changes:
- Add --repair flag to detect and consolidate multiple issue prefixes
- Create internal/utils/issue_id.go with ExtractIssuePrefix() and ExtractIssueNumber()
- Update all duplicate prefix extraction code to use shared utilities
- Add comprehensive tests for repair functionality

Generated with [Claude Code](https://claude.ai/code)
via [Happy](https://happy.engineering)

Co-Authored-By: Claude <noreply@anthropic.com>
Co-Authored-By: Happy <yesreply@happy.engineering>

cmd/bd/autoimport.go

@@ -13,6 +13,7 @@ import (
 
 	"github.com/steveyegge/beads/internal/storage"
 	"github.com/steveyegge/beads/internal/types"
+	"github.com/steveyegge/beads/internal/utils"
 )
 
 // checkAndAutoImport checks if the database is empty but git has issues.
@@ -174,7 +175,7 @@ func importFromGit(ctx context.Context, dbFilePath string, store storage.Storage
 		configuredPrefix, err := store.GetConfig(ctx, "issue_prefix")
 		if err == nil && strings.TrimSpace(configuredPrefix) == "" {
 			// Database has no prefix configured - derive from first issue
-			firstPrefix := extractPrefix(issues[0].ID)
+			firstPrefix := utils.ExtractIssuePrefix(issues[0].ID)
 			if firstPrefix != "" {
 				if err := store.SetConfig(ctx, "issue_prefix", firstPrefix); err != nil {
 					return fmt.Errorf("failed to set issue_prefix from imported issues: %w", err)

cmd/bd/helpers_test.go

@@ -2,6 +2,8 @@ package main
 
 import (
 	"testing"
+
+	"github.com/steveyegge/beads/internal/utils"
 )
 
 func TestIsBoundary(t *testing.T) {
@@ -82,9 +84,9 @@ func TestExtractPrefix(t *testing.T) {
 	}
 
 	for _, tt := range tests {
-		result := extractPrefix(tt.input)
+		result := utils.ExtractIssuePrefix(tt.input)
 		if result != tt.expected {
-			t.Errorf("extractPrefix(%q) = %q, want %q", tt.input, result, tt.expected)
+			t.Errorf("ExtractIssuePrefix(%q) = %q, want %q", tt.input, result, tt.expected)
 		}
 	}
 }

cmd/bd/import_phases.go

@@ -9,6 +9,7 @@ import (
 	"github.com/steveyegge/beads/internal/storage"
 	"github.com/steveyegge/beads/internal/storage/sqlite"
 	"github.com/steveyegge/beads/internal/types"
+	"github.com/steveyegge/beads/internal/utils"
 )
 
 // Phase 1: Get or create SQLite store for import
@@ -58,7 +59,7 @@ func handlePrefixMismatch(ctx context.Context, sqliteStore *sqlite.SQLiteStorage
 
 	// Analyze prefixes in imported issues
 	for _, issue := range issues {
-		prefix := extractPrefix(issue.ID)
+		prefix := utils.ExtractIssuePrefix(issue.ID)
 		if prefix != configuredPrefix {
 			result.PrefixMismatch = true
 			result.MismatchPrefixes[prefix]++
@@ -350,14 +351,6 @@ func importComments(ctx context.Context, sqliteStore *sqlite.SQLiteStorage, issu
 
 // Helper functions
 
-func extractPrefix(issueID string) string {
-	parts := strings.SplitN(issueID, "-", 2)
-	if len(parts) < 2 {
-		return "" // No prefix found
-	}
-	return parts[0]
-}
-
 func getPrefixList(prefixes map[string]int) []string {
 	var result []string
 	keys := make([]string, 0, len(prefixes))

cmd/bd/import_shared.go

@@ -9,6 +9,7 @@ import (
 
 	"github.com/steveyegge/beads/internal/storage"
 	"github.com/steveyegge/beads/internal/types"
+	"github.com/steveyegge/beads/internal/utils"
 )
 
 // fieldComparator handles comparison logic for a specific field type
@@ -261,7 +262,7 @@ func renameImportedIssuePrefixes(issues []*types.Issue, targetPrefix string) err
 	idMapping := make(map[string]string)
 
 	for _, issue := range issues {
-		oldPrefix := extractPrefix(issue.ID)
+		oldPrefix := utils.ExtractIssuePrefix(issue.ID)
 		if oldPrefix == "" {
 			return fmt.Errorf("cannot rename issue %s: malformed ID (no hyphen found)", issue.ID)
 		}

cmd/bd/rename_prefix.go

@@ -6,11 +6,14 @@ import (
 	"fmt"
 	"os"
 	"regexp"
+	"sort"
 	"strings"
 
 	"github.com/fatih/color"
 	"github.com/spf13/cobra"
+	"github.com/steveyegge/beads/internal/storage"
 	"github.com/steveyegge/beads/internal/types"
+	"github.com/steveyegge/beads/internal/utils"
 )
 
 var renamePrefixCmd = &cobra.Command{
@@ -26,12 +29,19 @@ Prefix validation rules:
 - Must end with a hyphen (e.g., 'kw-', 'work-')
 - Cannot be empty or just a hyphen
 
+Multiple prefix detection and repair:
+If issues have multiple prefixes (corrupted database), use --repair to consolidate them.
+The --repair flag will rename all issues with incorrect prefixes to the new prefix,
+preserving issues that already have the correct prefix.
+
 Example:
-  bd rename-prefix kw-         # Rename from 'knowledge-work-' to 'kw-'`,
+  bd rename-prefix kw-         # Rename from 'knowledge-work-' to 'kw-'
+  bd rename-prefix mtg- --repair  # Consolidate multiple prefixes into 'mtg-'`,
 	Args: cobra.ExactArgs(1),
 	Run: func(cmd *cobra.Command, args []string) {
 		newPrefix := args[0]
 		dryRun, _ := cmd.Flags().GetBool("dry-run")
+		repair, _ := cmd.Flags().GetBool("repair")
 
 		ctx := context.Background()
 
@@ -61,17 +71,47 @@ Example:
 
 		newPrefix = strings.TrimRight(newPrefix, "-")
 
-		if oldPrefix == newPrefix {
+		// Check for multiple prefixes first
-			fmt.Fprintf(os.Stderr, "Error: new prefix is the same as current prefix: %s\n", oldPrefix)
-			os.Exit(1)
-		}
-
 		issues, err := store.SearchIssues(ctx, "", types.IssueFilter{})
 		if err != nil {
 			fmt.Fprintf(os.Stderr, "Error: failed to list issues: %v\n", err)
 			os.Exit(1)
 		}
 
+		prefixes := detectPrefixes(issues)
+
+		if len(prefixes) > 1 {
+			// Multiple prefixes detected - requires repair mode
+			red := color.New(color.FgRed).SprintFunc()
+			yellow := color.New(color.FgYellow).SprintFunc()
+
+			fmt.Fprintf(os.Stderr, "%s Multiple prefixes detected in database:\n", red("✗"))
+			for prefix, count := range prefixes {
+				fmt.Fprintf(os.Stderr, "  - %s: %d issues\n", yellow(prefix), count)
+			}
+			fmt.Fprintf(os.Stderr, "\n")
+
+			if !repair {
+				fmt.Fprintf(os.Stderr, "Error: cannot rename with multiple prefixes. Use --repair to consolidate.\n")
+				fmt.Fprintf(os.Stderr, "Example: bd rename-prefix %s --repair\n", newPrefix)
+				os.Exit(1)
+			}
+
+			// Repair mode: consolidate all prefixes to newPrefix
+			if err := repairPrefixes(ctx, store, actor, newPrefix, issues, prefixes, dryRun); err != nil {
+				fmt.Fprintf(os.Stderr, "Error: failed to repair prefixes: %v\n", err)
+				os.Exit(1)
+			}
+			return
+		}
+
+		// Single prefix case - check if trying to rename to same prefix
+		if len(prefixes) == 1 && oldPrefix == newPrefix {
+			fmt.Fprintf(os.Stderr, "Error: new prefix is the same as current prefix: %s\n", oldPrefix)
+			os.Exit(1)
+		}
+
+		// issues already fetched above
 		if len(issues) == 0 {
 			fmt.Printf("No issues to rename. Updating prefix to %s\n", newPrefix)
 			if !dryRun {
@@ -150,6 +190,185 @@ func validatePrefix(prefix string) error {
 	return nil
 }
 
+// detectPrefixes analyzes all issues and returns a map of prefix -> count
+func detectPrefixes(issues []*types.Issue) map[string]int {
+	prefixes := make(map[string]int)
+	for _, issue := range issues {
+		prefix := utils.ExtractIssuePrefix(issue.ID)
+		if prefix != "" {
+			prefixes[prefix]++
+		}
+	}
+	return prefixes
+}
+
+// issueSort is used for sorting issues by prefix and number
+type issueSort struct {
+	issue  *types.Issue
+	prefix string
+	number int
+}
+
+// repairPrefixes consolidates multiple prefixes into a single target prefix
+// Issues with the correct prefix are left unchanged.
+// Issues with incorrect prefixes are sorted and renumbered sequentially.
+func repairPrefixes(ctx context.Context, st storage.Storage, actorName string, targetPrefix string, issues []*types.Issue, prefixes map[string]int, dryRun bool) error {
+	green := color.New(color.FgGreen).SprintFunc()
+	cyan := color.New(color.FgCyan).SprintFunc()
+	yellow := color.New(color.FgYellow).SprintFunc()
+
+	// Separate issues into correct and incorrect prefix groups
+	var correctIssues []*types.Issue
+	var incorrectIssues []issueSort
+
+	maxCorrectNumber := 0
+	for _, issue := range issues {
+		prefix := utils.ExtractIssuePrefix(issue.ID)
+		number := utils.ExtractIssueNumber(issue.ID)
+
+		if prefix == targetPrefix {
+			correctIssues = append(correctIssues, issue)
+			if number > maxCorrectNumber {
+				maxCorrectNumber = number
+			}
+		} else {
+			incorrectIssues = append(incorrectIssues, issueSort{
+				issue:  issue,
+				prefix: prefix,
+				number: number,
+			})
+		}
+	}
+
+	// Sort incorrect issues: first by prefix lexicographically, then by number
+	sort.Slice(incorrectIssues, func(i, j int) bool {
+		if incorrectIssues[i].prefix != incorrectIssues[j].prefix {
+			return incorrectIssues[i].prefix < incorrectIssues[j].prefix
+		}
+		return incorrectIssues[i].number < incorrectIssues[j].number
+	})
+
+	if dryRun {
+		fmt.Printf("DRY RUN: Would repair %d issues with incorrect prefixes\n\n", len(incorrectIssues))
+		fmt.Printf("Issues with correct prefix (%s): %d (highest number: %d)\n", cyan(targetPrefix), len(correctIssues), maxCorrectNumber)
+		fmt.Printf("Issues to repair: %d\n\n", len(incorrectIssues))
+
+		fmt.Printf("Planned renames (showing first 10):\n")
+		nextNumber := maxCorrectNumber + 1
+		for i, is := range incorrectIssues {
+			if i >= 10 {
+				fmt.Printf("... and %d more\n", len(incorrectIssues)-10)
+				break
+			}
+			oldID := is.issue.ID
+			newID := fmt.Sprintf("%s-%d", targetPrefix, nextNumber)
+			fmt.Printf("  %s -> %s\n", yellow(oldID), cyan(newID))
+			nextNumber++
+		}
+		return nil
+	}
+
+	// Perform the repairs
+	fmt.Printf("Repairing database with multiple prefixes...\n")
+	fmt.Printf("  Issues with correct prefix (%s): %d (highest: %s-%d)\n",
+		cyan(targetPrefix), len(correctIssues), targetPrefix, maxCorrectNumber)
+	fmt.Printf("  Issues to repair: %d\n\n", len(incorrectIssues))
+
+	oldPrefixPattern := regexp.MustCompile(`\b[a-z][a-z0-9-]*-(\d+)\b`)
+
+	// Build a map of all renames for text replacement
+	renameMap := make(map[string]string)
+	nextNumber := maxCorrectNumber + 1
+	for _, is := range incorrectIssues {
+		oldID := is.issue.ID
+		newID := fmt.Sprintf("%s-%d", targetPrefix, nextNumber)
+		renameMap[oldID] = newID
+		nextNumber++
+	}
+
+	// Rename each issue
+	for _, is := range incorrectIssues {
+		oldID := is.issue.ID
+		newID := renameMap[oldID]
+
+		// Apply text replacements in all issue fields
+		issue := is.issue
+		issue.ID = newID
+
+		// Replace all issue IDs in text fields using the rename map
+		replaceFunc := func(match string) string {
+			if newID, ok := renameMap[match]; ok {
+				return newID
+			}
+			return match
+		}
+
+		issue.Title = oldPrefixPattern.ReplaceAllStringFunc(issue.Title, replaceFunc)
+		issue.Description = oldPrefixPattern.ReplaceAllStringFunc(issue.Description, replaceFunc)
+		if issue.Design != "" {
+			issue.Design = oldPrefixPattern.ReplaceAllStringFunc(issue.Design, replaceFunc)
+		}
+		if issue.AcceptanceCriteria != "" {
+			issue.AcceptanceCriteria = oldPrefixPattern.ReplaceAllStringFunc(issue.AcceptanceCriteria, replaceFunc)
+		}
+		if issue.Notes != "" {
+			issue.Notes = oldPrefixPattern.ReplaceAllStringFunc(issue.Notes, replaceFunc)
+		}
+
+		// Update the issue in the database
+		if err := st.UpdateIssueID(ctx, oldID, newID, issue, actorName); err != nil {
+			return fmt.Errorf("failed to update issue %s -> %s: %w", oldID, newID, err)
+		}
+
+		fmt.Printf("  Renamed %s -> %s\n", yellow(oldID), cyan(newID))
+	}
+
+	// Update all dependencies to use new prefix
+	for oldPrefix := range prefixes {
+		if oldPrefix != targetPrefix {
+			if err := st.RenameDependencyPrefix(ctx, oldPrefix, targetPrefix); err != nil {
+				return fmt.Errorf("failed to update dependencies for prefix %s: %w", oldPrefix, err)
+			}
+		}
+	}
+
+	// Update counters for all old prefixes
+	for oldPrefix := range prefixes {
+		if oldPrefix != targetPrefix {
+			if err := st.RenameCounterPrefix(ctx, oldPrefix, targetPrefix); err != nil {
+				return fmt.Errorf("failed to update counter for prefix %s: %w", oldPrefix, err)
+			}
+		}
+	}
+
+	// Set the new prefix in config
+	if err := st.SetConfig(ctx, "issue_prefix", targetPrefix); err != nil {
+		return fmt.Errorf("failed to update config: %w", err)
+	}
+
+	// Schedule full export (IDs changed, incremental won't work)
+	markDirtyAndScheduleFullExport()
+
+	fmt.Printf("\n%s Successfully consolidated %d prefixes into %s\n",
+		green("✓"), len(prefixes), cyan(targetPrefix))
+	fmt.Printf("  %d issues repaired, %d issues unchanged\n", len(incorrectIssues), len(correctIssues))
+
+	if jsonOutput {
+		result := map[string]interface{}{
+			"target_prefix":     targetPrefix,
+			"prefixes_found":    len(prefixes),
+			"issues_repaired":   len(incorrectIssues),
+			"issues_unchanged":  len(correctIssues),
+			"highest_number":    nextNumber - 1,
+		}
+		enc := json.NewEncoder(os.Stdout)
+		enc.SetIndent("", "  ")
+		_ = enc.Encode(result)
+	}
+
+	return nil
+}
+
 func renamePrefixInDB(ctx context.Context, oldPrefix, newPrefix string, issues []*types.Issue) error {
 	// NOTE: Each issue is updated in its own transaction. A failure mid-way could leave
 	// the database in a mixed state with some issues renamed and others not.
@@ -203,5 +422,6 @@ func renamePrefixInDB(ctx context.Context, oldPrefix, newPrefix string, issues [
 
 func init() {
 	renamePrefixCmd.Flags().Bool("dry-run", false, "Preview changes without applying them")
+	renamePrefixCmd.Flags().Bool("repair", false, "Repair database with multiple prefixes by consolidating them")
 	rootCmd.AddCommand(renamePrefixCmd)
 }

cmd/bd/rename_prefix_repair_test.go

@@ -0,0 +1,100 @@
+package main
+
+import (
+	"context"
+	"testing"
+
+	"github.com/steveyegge/beads/internal/storage/sqlite"
+	"github.com/steveyegge/beads/internal/types"
+)
+
+func TestRepairMultiplePrefixes(t *testing.T) {
+	// Create a temporary database
+	dbPath := t.TempDir() + "/test.db"
+	store, err := sqlite.New(dbPath)
+	if err != nil {
+		t.Fatalf("failed to create store: %v", err)
+	}
+	defer store.Close()
+
+	ctx := context.Background()
+
+	// Set initial prefix
+	if err := store.SetConfig(ctx, "issue_prefix", "test"); err != nil {
+		t.Fatalf("failed to set prefix: %v", err)
+	}
+
+	// Create issues with multiple prefixes (simulating corruption)
+	// We'll manually create issues with different prefixes
+	issues := []*types.Issue{
+		{ID: "test-1", Title: "Test issue 1", Status: "open", Priority: 2, IssueType: "task"},
+		{ID: "test-2", Title: "Test issue 2", Status: "open", Priority: 2, IssueType: "task"},
+		{ID: "old-1", Title: "Old issue 1", Status: "open", Priority: 2, IssueType: "task"},
+		{ID: "old-2", Title: "Old issue 2", Status: "open", Priority: 2, IssueType: "task"},
+		{ID: "another-1", Title: "Another issue 1", Status: "open", Priority: 2, IssueType: "task"},
+	}
+
+	for _, issue := range issues {
+		if err := store.CreateIssue(ctx, issue, "test"); err != nil {
+			t.Fatalf("failed to create issue %s: %v", issue.ID, err)
+		}
+	}
+
+	// Verify we have multiple prefixes
+	allIssues, err := store.SearchIssues(ctx, "", types.IssueFilter{})
+	if err != nil {
+		t.Fatalf("failed to search issues: %v", err)
+	}
+
+	prefixes := detectPrefixes(allIssues)
+	if len(prefixes) != 3 {
+		t.Fatalf("expected 3 prefixes, got %d: %v", len(prefixes), prefixes)
+	}
+
+	// Test repair
+	if err := repairPrefixes(ctx, store, "test", "test", allIssues, prefixes, false); err != nil {
+		t.Fatalf("repair failed: %v", err)
+	}
+
+	// Verify all issues now have correct prefix
+	allIssues, err = store.SearchIssues(ctx, "", types.IssueFilter{})
+	if err != nil {
+		t.Fatalf("failed to search issues after repair: %v", err)
+	}
+
+	prefixes = detectPrefixes(allIssues)
+	if len(prefixes) != 1 {
+		t.Fatalf("expected 1 prefix after repair, got %d: %v", len(prefixes), prefixes)
+	}
+
+	if _, ok := prefixes["test"]; !ok {
+		t.Fatalf("expected prefix 'test', got %v", prefixes)
+	}
+
+	// Verify the original test-1 and test-2 are unchanged
+	for _, id := range []string{"test-1", "test-2"} {
+		issue, err := store.GetIssue(ctx, id)
+		if err != nil {
+			t.Fatalf("expected issue %s to exist unchanged: %v", id, err)
+		}
+		if issue == nil {
+			t.Fatalf("expected issue %s to exist", id)
+		}
+	}
+
+	// Verify the others were renumbered
+	issue, err := store.GetIssue(ctx, "test-3")
+	if err != nil || issue == nil {
+		t.Fatalf("expected test-3 to exist (renamed from another-1)")
+	}
+
+	issue, err = store.GetIssue(ctx, "test-4")
+	if err != nil || issue == nil {
+		t.Fatalf("expected test-4 to exist (renamed from old-1)")
+	}
+
+	issue, err = store.GetIssue(ctx, "test-5")
+	if err != nil || issue == nil {
+		t.Fatalf("expected test-5 to exist (renamed from old-2)")
+	}
+}

internal/utils/issue_id.go

@@ -0,0 +1,26 @@
+package utils
+
+import (
+	"fmt"
+	"strings"
+)
+
+// ExtractIssuePrefix extracts the prefix from an issue ID like "bd-123" -> "bd"
+func ExtractIssuePrefix(issueID string) string {
+	parts := strings.SplitN(issueID, "-", 2)
+	if len(parts) < 2 {
+		return ""
+	}
+	return parts[0]
+}
+
+// ExtractIssueNumber extracts the number from an issue ID like "bd-123" -> 123
+func ExtractIssueNumber(issueID string) int {
+	parts := strings.SplitN(issueID, "-", 2)
+	if len(parts) < 2 {
+		return 0
+	}
+	var num int
+	fmt.Sscanf(parts[1], "%d", &num)
+	return num
+}