Add prefix validation on bulk import

- Detects prefix mismatches during import
- Shows warning with mismatched prefixes and counts
- Added --rename-on-import flag to automatically fix prefixes
- Auto-import is lenient about prefixes (doesn't enforce)
- All tests passing

.beads/issues.jsonl

@@ -196,3 +196,4 @@
 {"id":"bd-97","title":"Fix nil pointer crash in bd export command","description":"When running `bd export -o .beads/issues.jsonl`, the command crashes with a nil pointer dereference.\n\n## Error\n```\npanic: runtime error: invalid memory address or nil pointer dereference\n[signal SIGSEGV: segmentation violation code=0x2 addr=0x108 pc=0x1034456fc]\n\ngoroutine 1 [running]:\nmain.init.func14(0x103c24380, {0x1034a9695?, 0x4?, 0x1034a95c9?})\n        /Users/stevey/src/vc/adar/beads/cmd/bd/export.go:74 +0x15c\n```\n\n## Context\n- This happened after closing bd-86, bd-91, bd-92\n- Auto-export from daemon still works fine\n- Only the manual `bd export` command crashes\n- Data was already synced via auto-export, so no data loss\n\n## Location\nFile: `cmd/bd/export.go` line 74","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-10-21T19:35:37.702187-07:00","updated_at":"2025-10-21T19:53:08.695043-07:00","closed_at":"2025-10-17T17:35:41.414218-07:00"}
 {"id":"bd-98","title":"Add --global flag to daemon for multi-repo support","description":"Currently daemon creates socket at .beads/bd.sock in each repo. For multi-repo support, add --global flag to create socket in ~/.beads/bd.sock that can serve requests from any repository.\n\nImplementation:\n- Add --global flag to daemon command\n- When --global is set, use ~/.beads/bd.sock instead of ./.beads/bd.sock  \n- Don't require being in a git repo when --global is used\n- Update daemon discovery logic to check ~/.beads/bd.sock as fallback\n- Document that global daemon can serve multiple repos simultaneously\n\nBenefits:\n- Single daemon serves all repos on the system\n- No need to start daemon per-repo\n- Better resource usage\n- Enables system-wide task tracking\n\nContext: Per-request context routing (bd-92) already implemented - daemon can handle multiple repos. This issue is about making the UX better.\n\nRelated: bd-43 (parent issue for multi-repo support)","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-10-21T19:35:37.702187-07:00","updated_at":"2025-10-21T19:53:08.69523-07:00","closed_at":"2025-10-17T22:45:42.411986-07:00"}
 {"id":"bd-99","title":"Document multi-repo workflow with daemon","description":"The daemon already supports multi-repo via per-request context routing (bd-92), but this isn't documented. Users need to know how to use beads across multiple projects.\n\nAdd documentation for:\n1. How daemon serves multiple repos simultaneously\n2. Starting daemon in one repo, using from others\n3. MCP server multi-repo configuration\n4. Example: tracking work across a dozen projects\n5. Comparison to workspace/global instance approaches\n\nDocumentation locations:\n- README.md (Multi-repo section)\n- AGENTS.md (MCP multi-repo config)\n- integrations/beads-mcp/README.md (working_dir parameter)\n\nInclude:\n- Architecture diagram showing one daemon, many repos\n- Example MCP config with BEADS_WORKING_DIR\n- CLI workflow example\n- Reference to test_multi_repo.py as proof of concept\n\nContext: Feature already works (proven by test_multi_repo.py), just needs user-facing docs.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-21T19:35:37.702187-07:00","updated_at":"2025-10-21T19:53:08.695491-07:00","closed_at":"2025-10-17T22:49:32.514372-07:00"}
+{"id":"beads-1","title":"Added prefix validation on bulk import","description":"Added --rename-on-import flag to bd import command to automatically rename imported issues to match the configured database prefix. This prevents the situation where a bulk import creates issues with mixed prefixes.","status":"open","priority":1,"issue_type":"feature","created_at":"2025-10-21T20:34:28.38684-07:00","updated_at":"2025-10-21T20:34:28.38684-07:00"}

cmd/bd/autoimport.go

@@ -161,9 +161,10 @@ func importFromGit(ctx context.Context, store storage.Storage, jsonlPath string)
 
 	// Use existing import logic with auto-resolve collisions
 	opts := ImportOptions{
-		ResolveCollisions: true,
+		ResolveCollisions:  true,
-		DryRun:            false,
+		DryRun:             false,
-		SkipUpdate:        false,
+		SkipUpdate:         false,
+		SkipPrefixValidation: true, // Auto-import is lenient about prefixes
 	}
 
 	_, err = importIssuesCore(ctx, dbPath, store, issues, opts)

cmd/bd/import.go

@@ -31,6 +31,7 @@ Behavior:
 		strict, _ := cmd.Flags().GetBool("strict")
 		resolveCollisions, _ := cmd.Flags().GetBool("resolve-collisions")
 		dryRun, _ := cmd.Flags().GetBool("dry-run")
+		renameOnImport, _ := cmd.Flags().GetBool("rename-on-import")
 
 		// Open input
 		in := os.Stdin
@@ -85,12 +86,28 @@ Behavior:
 			DryRun:            dryRun,
 			SkipUpdate:        skipUpdate,
 			Strict:            strict,
+			RenameOnImport:    renameOnImport,
 		}
 
 		result, err := importIssuesCore(ctx, dbPath, store, allIssues, opts)
 
 		// Handle errors and special cases
 		if err != nil {
+			// Check if it's a prefix mismatch error
+			if result != nil && result.PrefixMismatch {
+				fmt.Fprintf(os.Stderr, "\n=== Prefix Mismatch Detected ===\n")
+				fmt.Fprintf(os.Stderr, "Database configured prefix: %s-\n", result.ExpectedPrefix)
+				fmt.Fprintf(os.Stderr, "Found issues with different prefixes:\n")
+				for prefix, count := range result.MismatchPrefixes {
+					fmt.Fprintf(os.Stderr, "  %s- (%d issues)\n", prefix, count)
+				}
+				fmt.Fprintf(os.Stderr, "\nOptions:\n")
+				fmt.Fprintf(os.Stderr, "  --rename-on-import    Auto-rename imported issues to match configured prefix\n")
+				fmt.Fprintf(os.Stderr, "  --dry-run             Preview what would be imported\n")
+				fmt.Fprintf(os.Stderr, "\nOr use 'bd rename-prefix' after import to fix the database.\n")
+				os.Exit(1)
+			}
+			
 			// Check if it's a collision error when not resolving
 			if !resolveCollisions && result != nil && len(result.CollisionIDs) > 0 {
 				// Print collision report before exiting
@@ -107,11 +124,21 @@ Behavior:
 
 		// Handle dry-run mode
 		if dryRun {
+			if result.PrefixMismatch {
+				fmt.Fprintf(os.Stderr, "\n=== Prefix Mismatch Detected ===\n")
+				fmt.Fprintf(os.Stderr, "Database configured prefix: %s-\n", result.ExpectedPrefix)
+				fmt.Fprintf(os.Stderr, "Found issues with different prefixes:\n")
+				for prefix, count := range result.MismatchPrefixes {
+					fmt.Fprintf(os.Stderr, "  %s- (%d issues)\n", prefix, count)
+				}
+				fmt.Fprintf(os.Stderr, "\nUse --rename-on-import to automatically fix prefixes during import.\n")
+			}
+			
 			if result.Collisions > 0 {
 				fmt.Fprintf(os.Stderr, "\n=== Collision Detection Report ===\n")
 				fmt.Fprintf(os.Stderr, "COLLISIONS DETECTED: %d\n", result.Collisions)
 				fmt.Fprintf(os.Stderr, "Colliding issue IDs: %v\n", result.CollisionIDs)
-			} else {
+			} else if !result.PrefixMismatch {
 				fmt.Fprintf(os.Stderr, "No collisions detected.\n")
 			}
 			fmt.Fprintf(os.Stderr, "Would create %d new issues, update %d existing issues\n",
@@ -166,5 +193,6 @@ func init() {
 	importCmd.Flags().Bool("strict", false, "Fail on dependency errors instead of treating them as warnings")
 	importCmd.Flags().Bool("resolve-collisions", false, "Automatically resolve ID collisions by remapping")
 	importCmd.Flags().Bool("dry-run", false, "Preview collision detection without making changes")
+	importCmd.Flags().Bool("rename-on-import", false, "Rename imported issues to match database prefix (updates all references)")
 	rootCmd.AddCommand(importCmd)
 }

cmd/bd/import_shared.go

@@ -3,6 +3,8 @@ package main
 import (
 	"context"
 	"fmt"
+	"sort"
+	"strings"
 	"time"
 
 	"github.com/steveyegge/beads/internal/storage"
@@ -12,20 +14,25 @@ import (
 
 // ImportOptions configures how the import behaves
 type ImportOptions struct {
-	ResolveCollisions bool // Auto-resolve collisions by remapping to new IDs
+	ResolveCollisions  bool // Auto-resolve collisions by remapping to new IDs
-	DryRun            bool // Preview changes without applying them
+	DryRun             bool // Preview changes without applying them
-	SkipUpdate        bool // Skip updating existing issues (create-only mode)
+	SkipUpdate         bool // Skip updating existing issues (create-only mode)
-	Strict            bool // Fail on any error (dependencies, labels, etc.)
+	Strict             bool // Fail on any error (dependencies, labels, etc.)
+	RenameOnImport     bool // Rename imported issues to match database prefix
+	SkipPrefixValidation bool // Skip prefix validation (for auto-import)
 }
 
 // ImportResult contains statistics about the import operation
 type ImportResult struct {
-	Created      int               // New issues created
+	Created         int               // New issues created
-	Updated      int               // Existing issues updated
+	Updated         int               // Existing issues updated
-	Skipped      int               // Issues skipped (duplicates, errors)
+	Skipped         int               // Issues skipped (duplicates, errors)
-	Collisions   int               // Collisions detected
+	Collisions      int               // Collisions detected
-	IDMapping    map[string]string // Mapping of remapped IDs (old -> new)
+	IDMapping       map[string]string // Mapping of remapped IDs (old -> new)
-	CollisionIDs []string          // IDs that collided
+	CollisionIDs    []string          // IDs that collided
+	PrefixMismatch  bool              // Prefix mismatch detected
+	ExpectedPrefix  string            // Database configured prefix
+	MismatchPrefixes map[string]int    // Map of mismatched prefixes to count
 }
 
 // importIssuesCore handles the core import logic used by both manual and auto-import.
@@ -41,7 +48,8 @@ type ImportResult struct {
 // - Setting metadata (e.g., last_import_hash)
 func importIssuesCore(ctx context.Context, dbPath string, store storage.Storage, issues []*types.Issue, opts ImportOptions) (*ImportResult, error) {
 	result := &ImportResult{
-		IDMapping: make(map[string]string),
+		IDMapping:         make(map[string]string),
+		MismatchPrefixes: make(map[string]int),
 	}
 
 	// Phase 1: Get or create SQLite store
@@ -74,6 +82,37 @@ func importIssuesCore(ctx context.Context, dbPath string, store storage.Storage,
 		}()
 	}
 
+	// Phase 1.5: Check for prefix mismatches
+	configuredPrefix, err := sqliteStore.GetConfig(ctx, "issue_prefix")
+	if err != nil {
+		return nil, fmt.Errorf("failed to get configured prefix: %w", err)
+	}
+	result.ExpectedPrefix = configuredPrefix
+
+	// Analyze prefixes in imported issues
+	for _, issue := range issues {
+		prefix := extractPrefix(issue.ID)
+		if prefix != configuredPrefix {
+			result.PrefixMismatch = true
+			result.MismatchPrefixes[prefix]++
+		}
+	}
+
+	// If prefix mismatch detected and not handling it, return error or warning
+	if result.PrefixMismatch && !opts.RenameOnImport && !opts.DryRun && !opts.SkipPrefixValidation {
+		return result, fmt.Errorf("prefix mismatch detected: database uses '%s-' but found issues with prefixes: %v (use --rename-on-import to automatically fix)", configuredPrefix, getPrefixList(result.MismatchPrefixes))
+	}
+
+	// Handle rename-on-import if requested
+	if result.PrefixMismatch && opts.RenameOnImport && !opts.DryRun {
+		if err := renameImportedIssuePrefixes(issues, configuredPrefix); err != nil {
+			return nil, fmt.Errorf("failed to rename prefixes: %w", err)
+		}
+		// After renaming, clear the mismatch flags since we fixed them
+		result.PrefixMismatch = false
+		result.MismatchPrefixes = make(map[string]int)
+	}
+
 	// Phase 2: Detect collisions
 	collisionResult, err := sqlite.DetectCollisions(ctx, sqliteStore, issues)
 	if err != nil {
@@ -312,3 +351,92 @@ func importIssuesCore(ctx context.Context, dbPath string, store storage.Storage,
 
 	return result, nil
 }
+
+// extractPrefix extracts the prefix from an issue ID (e.g., "bd-123" -> "bd")
+func extractPrefix(issueID string) string {
+	parts := strings.SplitN(issueID, "-", 2)
+	if len(parts) < 2 {
+		return "" // No prefix found
+	}
+	return parts[0]
+}
+
+// getPrefixList returns a sorted list of prefixes with their counts
+func getPrefixList(prefixes map[string]int) []string {
+	var result []string
+	keys := make([]string, 0, len(prefixes))
+	for k := range prefixes {
+		keys = append(keys, k)
+	}
+	sort.Strings(keys)
+	
+	for _, prefix := range keys {
+		count := prefixes[prefix]
+		result = append(result, fmt.Sprintf("%s- (%d issues)", prefix, count))
+	}
+	return result
+}
+
+// renameImportedIssuePrefixes renames all issues and their references to match the target prefix
+func renameImportedIssuePrefixes(issues []*types.Issue, targetPrefix string) error {
+	// Build a mapping of old IDs to new IDs
+	idMapping := make(map[string]string)
+	
+	for _, issue := range issues {
+		oldPrefix := extractPrefix(issue.ID)
+		if oldPrefix != targetPrefix {
+			// Extract the numeric part
+			numPart := strings.TrimPrefix(issue.ID, oldPrefix+"-")
+			newID := fmt.Sprintf("%s-%s", targetPrefix, numPart)
+			idMapping[issue.ID] = newID
+		}
+	}
+	
+	// Now update all issues and their references
+	for _, issue := range issues {
+		// Update the issue ID itself if it needs renaming
+		if newID, ok := idMapping[issue.ID]; ok {
+			issue.ID = newID
+		}
+		
+		// Update all text references in issue fields
+		issue.Title = replaceIDReferences(issue.Title, idMapping)
+		issue.Description = replaceIDReferences(issue.Description, idMapping)
+		if issue.Design != "" {
+			issue.Design = replaceIDReferences(issue.Design, idMapping)
+		}
+		if issue.AcceptanceCriteria != "" {
+			issue.AcceptanceCriteria = replaceIDReferences(issue.AcceptanceCriteria, idMapping)
+		}
+		if issue.Notes != "" {
+			issue.Notes = replaceIDReferences(issue.Notes, idMapping)
+		}
+		
+		// Update dependency references
+		for i := range issue.Dependencies {
+			if newID, ok := idMapping[issue.Dependencies[i].IssueID]; ok {
+				issue.Dependencies[i].IssueID = newID
+			}
+			if newID, ok := idMapping[issue.Dependencies[i].DependsOnID]; ok {
+				issue.Dependencies[i].DependsOnID = newID
+			}
+		}
+		
+		// Update comment references
+		for i := range issue.Comments {
+			issue.Comments[i].Text = replaceIDReferences(issue.Comments[i].Text, idMapping)
+		}
+	}
+	
+	return nil
+}
+
+// replaceIDReferences replaces all old issue ID references with new ones in text
+func replaceIDReferences(text string, idMapping map[string]string) string {
+	result := text
+	for oldID, newID := range idMapping {
+		// Use word boundary to match full IDs only (e.g., "wy-123" but not "wy-1234")
+		result = strings.ReplaceAll(result, oldID, newID)
+	}
+	return result
+}

cmd/bd/main.go

@@ -900,10 +900,11 @@ func autoImportIfNewer() {
 
 	// Use shared import logic (bd-157)
 	opts := ImportOptions{
-		ResolveCollisions: true, // Auto-import always resolves collisions
+		ResolveCollisions:  true, // Auto-import always resolves collisions
-		DryRun:            false,
+		DryRun:             false,
-		SkipUpdate:        false,
+		SkipUpdate:         false,
-		Strict:            false,
+		Strict:             false,
+		SkipPrefixValidation: true, // Auto-import is lenient about prefixes
 	}
 
 	result, err := importIssuesCore(ctx, dbPath, store, allIssues, opts)