Merge remote-tracking branch 'origin/main' into improve-sync-jsonl-msg

README.md

@@ -193,7 +193,6 @@ bd init --stealth
 ```
 
 **Stealth mode configures:**
-- **Global gitattributes** (`~/.config/git/attributes`) - Enables beads merge for `**/.beads/issues.jsonl` files across all repos
 - **Global gitignore** (`~/.config/git/ignore`) - Ignores `**/.beads/` and `**/.claude/settings.local.json` globally
 - **Claude Code settings** (`.claude/settings.local.json`) - Adds `bd onboard` instruction for AI agents
 

cmd/bd/init.go

@@ -31,7 +31,6 @@ and database file. Optionally specify a custom issue prefix.
 With --no-db: creates .beads/ directory and issues.jsonl file instead of SQLite database.
 
 With --stealth: configures global git settings for invisible beads usage:
-  • Global gitattributes for beads merge support across all repos
   • Global gitignore to prevent beads files from being committed
   • Claude Code settings with bd onboard instruction
   Perfect for personal use without affecting repo collaborators.`,
@@ -1166,11 +1165,6 @@ func setupStealthMode(verbose bool) error {
 		return fmt.Errorf("failed to get user home directory: %w", err)
 	}
 
-	// Setup global gitattributes
-	if err := setupGlobalGitAttributes(homeDir, verbose); err != nil {
-		return fmt.Errorf("failed to setup global gitattributes: %w", err)
-	}
-
 	// Setup global gitignore
 	if err := setupGlobalGitIgnore(homeDir, verbose); err != nil {
 		return fmt.Errorf("failed to setup global gitignore: %w", err)
@@ -1185,7 +1179,6 @@ func setupStealthMode(verbose bool) error {
 		green := color.New(color.FgGreen).SprintFunc()
 		cyan := color.New(color.FgCyan).SprintFunc()
 		fmt.Printf("\n%s Stealth mode configured successfully!\n\n", green("✓"))
-		fmt.Printf("  Global gitattributes: %s\n", cyan("configured for beads merge"))
 		fmt.Printf("  Global gitignore: %s\n", cyan(".beads/ and .claude/settings.local.json ignored"))
 		fmt.Printf("  Claude settings: %s\n\n", cyan("configured with bd onboard instruction"))
 		fmt.Printf("Your beads setup is now %s - other repo collaborators won't see any beads-related files.\n\n", cyan("invisible"))
@@ -1194,99 +1187,6 @@ func setupStealthMode(verbose bool) error {
 	return nil
 }
 
-// setupGlobalGitAttributes configures global gitattributes for beads merge
-func setupGlobalGitAttributes(homeDir string, verbose bool) error {
-	// Check if user already has a global gitattributes file configured
-	cmd := exec.Command("git", "config", "--global", "core.attributesfile")
-	output, err := cmd.Output()
-
-	var attributesPath string
-
-	if err == nil && len(output) > 0 {
-		// User has already configured a global gitattributes file, use it
-		attributesPath = strings.TrimSpace(string(output))
-		if verbose {
-			fmt.Printf("Using existing configured global gitattributes file: %s\n", attributesPath)
-		}
-	} else {
-		// No global gitattributes file configured, check if standard location exists
-		configDir := filepath.Join(homeDir, ".config", "git")
-		standardAttributesPath := filepath.Join(configDir, "attributes")
-
-		if _, err := os.Stat(standardAttributesPath); err == nil {
-			// Standard global gitattributes file exists, use it
-			// No need to set git config - git automatically uses this standard location
-			attributesPath = standardAttributesPath
-			if verbose {
-				fmt.Printf("Using existing global gitattributes file: %s\n", attributesPath)
-			}
-		} else {
-			// No global gitattributes file exists, create one in standard location
-			// No need to set git config - git automatically uses this standard location
-			attributesPath = standardAttributesPath
-
-			// Ensure config directory exists
-			if err := os.MkdirAll(configDir, 0755); err != nil {
-				return fmt.Errorf("failed to create git config directory: %w", err)
-			}
-
-			if verbose {
-				fmt.Printf("Creating new global gitattributes file: %s\n", attributesPath)
-			}
-		}
-	}
-
-	// Read existing attributes file if it exists
-	var existingContent string
-	// #nosec G304 - user config path
-	if content, err := os.ReadFile(attributesPath); err == nil {
-		existingContent = string(content)
-	}
-
-	// Check if beads merge attribute already exists
-	beadsPattern := "**/.beads/issues.jsonl merge=beads"
-	if strings.Contains(existingContent, beadsPattern) {
-		if verbose {
-			fmt.Printf("Global gitattributes already configured for beads\n")
-		}
-		return nil
-	}
-
-	// Append beads configuration
-	newContent := existingContent
-	if !strings.HasSuffix(newContent, "\n") && len(newContent) > 0 {
-		newContent += "\n"
-	}
-	newContent += "\n# Beads merge configuration (added by bd init --stealth)\n"
-	newContent += beadsPattern + "\n"
-
-	// Write the updated attributes file
-	// #nosec G306 - config file needs 0644
-	if err := os.WriteFile(attributesPath, []byte(newContent), 0644); err != nil {
-		return fmt.Errorf("failed to write global gitattributes: %w", err)
-	}
-
-	// Configure the beads merge driver
-	cmd = exec.Command("git", "config", "--global", "merge.beads.driver", "bd merge %A %O %A %B")
-	if output, err := cmd.CombinedOutput(); err != nil {
-		return fmt.Errorf("failed to configure beads merge driver: %w\n%s", err, output)
-	}
-
-	cmd = exec.Command("git", "config", "--global", "merge.beads.name", "bd JSONL merge driver")
-	if output, err := cmd.CombinedOutput(); err != nil {
-		// Non-fatal, the name is just descriptive
-		if verbose {
-			fmt.Fprintf(os.Stderr, "Warning: failed to set merge driver name: %v\n%s", err, output)
-		}
-	}
-
-	if verbose {
-		fmt.Printf("Configured global gitattributes for beads merge\n")
-	}
-
-	return nil
-}
-
 // setupGlobalGitIgnore configures global gitignore to ignore beads and claude files
 func setupGlobalGitIgnore(homeDir string, verbose bool) error {
 	// Check if user already has a global gitignore file configured

internal/storage/memory/memory.go

@@ -30,6 +30,9 @@ type MemoryStorage struct {
 	metadata     map[string]string             // Metadata key-value pairs
 	counters     map[string]int                // Prefix -> Last ID
 
+	// Indexes for O(1) lookups
+	externalRefToID map[string]string // ExternalRef -> IssueID
+
 	// For tracking
 	dirty map[string]bool // IssueIDs that have been modified
 
@@ -40,16 +43,17 @@ type MemoryStorage struct {
 // New creates a new in-memory storage backend
 func New(jsonlPath string) *MemoryStorage {
 	return &MemoryStorage{
-		issues:       make(map[string]*types.Issue),
+		issues:          make(map[string]*types.Issue),
-		dependencies: make(map[string][]*types.Dependency),
+		dependencies:    make(map[string][]*types.Dependency),
-		labels:       make(map[string][]string),
+		labels:          make(map[string][]string),
-		events:       make(map[string][]*types.Event),
+		events:          make(map[string][]*types.Event),
-		comments:     make(map[string][]*types.Comment),
+		comments:        make(map[string][]*types.Comment),
-		config:       make(map[string]string),
+		config:          make(map[string]string),
-		metadata:     make(map[string]string),
+		metadata:        make(map[string]string),
-		counters:     make(map[string]int),
+		counters:        make(map[string]int),
-		dirty:        make(map[string]bool),
+		externalRefToID: make(map[string]string),
-		jsonlPath:    jsonlPath,
+		dirty:           make(map[string]bool),
+		jsonlPath:       jsonlPath,
 	}
 }
 
@@ -67,6 +71,11 @@ func (m *MemoryStorage) LoadFromIssues(issues []*types.Issue) error {
 		// Store the issue
 		m.issues[issue.ID] = issue
 
+		// Index external ref for O(1) lookup
+		if issue.ExternalRef != nil && *issue.ExternalRef != "" {
+			m.externalRefToID[*issue.ExternalRef] = issue.ID
+		}
+
 		// Store dependencies
 		if len(issue.Dependencies) > 0 {
 			m.dependencies[issue.ID] = issue.Dependencies
@@ -184,6 +193,11 @@ func (m *MemoryStorage) CreateIssue(ctx context.Context, issue *types.Issue, act
 	m.issues[issue.ID] = issue
 	m.dirty[issue.ID] = true
 
+	// Index external ref for O(1) lookup
+	if issue.ExternalRef != nil && *issue.ExternalRef != "" {
+		m.externalRefToID[*issue.ExternalRef] = issue.ID
+	}
+
 	// Record event
 	event := &types.Event{
 		IssueID:   issue.ID,
@@ -244,6 +258,11 @@ func (m *MemoryStorage) CreateIssues(ctx context.Context, issues []*types.Issue,
 		m.issues[issue.ID] = issue
 		m.dirty[issue.ID] = true
 
+		// Index external ref for O(1) lookup
+		if issue.ExternalRef != nil && *issue.ExternalRef != "" {
+			m.externalRefToID[*issue.ExternalRef] = issue.ID
+		}
+
 		// Record event
 		event := &types.Event{
 			IssueID:   issue.ID,
@@ -288,28 +307,31 @@ func (m *MemoryStorage) GetIssueByExternalRef(ctx context.Context, externalRef s
 	m.mu.RLock()
 	defer m.mu.RUnlock()
 
-	// Linear search through all issues to find match by external_ref
+	// O(1) lookup using index
-	for _, issue := range m.issues {
+	issueID, exists := m.externalRefToID[externalRef]
-		if issue.ExternalRef != nil && *issue.ExternalRef == externalRef {
+	if !exists {
-			// Return a copy to avoid mutations
+		return nil, nil
-			issueCopy := *issue
-
-			// Attach dependencies
-			if deps, ok := m.dependencies[issue.ID]; ok {
-				issueCopy.Dependencies = deps
-			}
-
-			// Attach labels
-			if labels, ok := m.labels[issue.ID]; ok {
-				issueCopy.Labels = labels
-			}
-
-			return &issueCopy, nil
-		}
 	}
 
-	// Not found
+	issue, exists := m.issues[issueID]
-	return nil, nil
+	if !exists {
+		return nil, nil
+	}
+
+	// Return a copy to avoid mutations
+	issueCopy := *issue
+
+	// Attach dependencies
+	if deps, ok := m.dependencies[issue.ID]; ok {
+		issueCopy.Dependencies = deps
+	}
+
+	// Attach labels
+	if labels, ok := m.labels[issue.ID]; ok {
+		issueCopy.Labels = labels
+	}
+
+	return &issueCopy, nil
 }
 
 // UpdateIssue updates fields on an issue
@@ -375,9 +397,23 @@ func (m *MemoryStorage) UpdateIssue(ctx context.Context, id string, updates map[
 				issue.Assignee = ""
 			}
 		case "external_ref":
+			// Update external ref index
+			oldRef := issue.ExternalRef
 			if v, ok := value.(string); ok {
+				// Remove old index entry if exists
+				if oldRef != nil && *oldRef != "" {
+					delete(m.externalRefToID, *oldRef)
+				}
+				// Add new index entry
+				if v != "" {
+					m.externalRefToID[v] = id
+				}
 				issue.ExternalRef = &v
 			} else if value == nil {
+				// Remove old index entry if exists
+				if oldRef != nil && *oldRef != "" {
+					delete(m.externalRefToID, *oldRef)
+				}
 				issue.ExternalRef = nil
 			}
 		}
@@ -417,10 +453,16 @@ func (m *MemoryStorage) DeleteIssue(ctx context.Context, id string) error {
 	defer m.mu.Unlock()
 
 	// Check if issue exists
-	if _, ok := m.issues[id]; !ok {
+	issue, ok := m.issues[id]
+	if !ok {
 		return fmt.Errorf("issue not found: %s", id)
 	}
 
+	// Remove external ref index entry
+	if issue.ExternalRef != nil && *issue.ExternalRef != "" {
+		delete(m.externalRefToID, *issue.ExternalRef)
+	}
+
 	// Delete the issue
 	delete(m.issues, id)
 

internal/storage/memory/memory_test.go

@@ -879,3 +879,145 @@ func TestClose(t *testing.T) {
 		t.Error("Store should be closed")
 	}
 }
+
+func TestGetIssueByExternalRef(t *testing.T) {
+	store := setupTestMemory(t)
+	defer store.Close()
+
+	ctx := context.Background()
+
+	// Create an issue with external ref
+	extRef := "github#123"
+	issue := &types.Issue{
+		Title:       "Test issue with external ref",
+		Status:      types.StatusOpen,
+		Priority:    1,
+		IssueType:   types.TypeTask,
+		ExternalRef: &extRef,
+	}
+
+	if err := store.CreateIssue(ctx, issue, "test-user"); err != nil {
+		t.Fatalf("CreateIssue failed: %v", err)
+	}
+
+	// Lookup by external ref should find it
+	found, err := store.GetIssueByExternalRef(ctx, "github#123")
+	if err != nil {
+		t.Fatalf("GetIssueByExternalRef failed: %v", err)
+	}
+	if found == nil {
+		t.Fatal("Expected to find issue by external ref")
+	}
+	if found.ID != issue.ID {
+		t.Errorf("Expected issue ID %s, got %s", issue.ID, found.ID)
+	}
+
+	// Lookup by non-existent ref should return nil
+	notFound, err := store.GetIssueByExternalRef(ctx, "nonexistent")
+	if err != nil {
+		t.Fatalf("GetIssueByExternalRef failed: %v", err)
+	}
+	if notFound != nil {
+		t.Error("Expected nil for non-existent external ref")
+	}
+
+	// Update external ref and verify index is updated
+	newRef := "github#456"
+	if err := store.UpdateIssue(ctx, issue.ID, map[string]interface{}{
+		"external_ref": newRef,
+	}, "test-user"); err != nil {
+		t.Fatalf("UpdateIssue failed: %v", err)
+	}
+
+	// Old ref should not find anything
+	oldRefResult, err := store.GetIssueByExternalRef(ctx, "github#123")
+	if err != nil {
+		t.Fatalf("GetIssueByExternalRef failed: %v", err)
+	}
+	if oldRefResult != nil {
+		t.Error("Old external ref should not find issue after update")
+	}
+
+	// New ref should find the issue
+	newRefResult, err := store.GetIssueByExternalRef(ctx, "github#456")
+	if err != nil {
+		t.Fatalf("GetIssueByExternalRef failed: %v", err)
+	}
+	if newRefResult == nil {
+		t.Fatal("New external ref should find issue")
+	}
+	if newRefResult.ID != issue.ID {
+		t.Errorf("Expected issue ID %s, got %s", issue.ID, newRefResult.ID)
+	}
+
+	// Delete issue and verify index is cleaned up
+	if err := store.DeleteIssue(ctx, issue.ID); err != nil {
+		t.Fatalf("DeleteIssue failed: %v", err)
+	}
+
+	// External ref should not find anything after delete
+	deletedResult, err := store.GetIssueByExternalRef(ctx, "github#456")
+	if err != nil {
+		t.Fatalf("GetIssueByExternalRef failed: %v", err)
+	}
+	if deletedResult != nil {
+		t.Error("External ref should not find issue after delete")
+	}
+}
+
+func TestGetIssueByExternalRefLoadFromIssues(t *testing.T) {
+	store := New("")
+	defer store.Close()
+
+	ctx := context.Background()
+
+	// Load issues with external refs
+	extRef1 := "jira#100"
+	extRef2 := "jira#200"
+	issues := []*types.Issue{
+		{
+			ID:          "bd-1",
+			Title:       "Issue 1",
+			Status:      types.StatusOpen,
+			Priority:    1,
+			IssueType:   types.TypeTask,
+			ExternalRef: &extRef1,
+		},
+		{
+			ID:          "bd-2",
+			Title:       "Issue 2",
+			Status:      types.StatusOpen,
+			Priority:    2,
+			IssueType:   types.TypeBug,
+			ExternalRef: &extRef2,
+		},
+		{
+			ID:        "bd-3",
+			Title:     "Issue 3 (no external ref)",
+			Status:    types.StatusOpen,
+			Priority:  3,
+			IssueType: types.TypeFeature,
+		},
+	}
+
+	if err := store.LoadFromIssues(issues); err != nil {
+		t.Fatalf("LoadFromIssues failed: %v", err)
+	}
+
+	// Both external refs should be indexed
+	found1, err := store.GetIssueByExternalRef(ctx, "jira#100")
+	if err != nil {
+		t.Fatalf("GetIssueByExternalRef failed: %v", err)
+	}
+	if found1 == nil || found1.ID != "bd-1" {
+		t.Errorf("Expected to find bd-1 by external ref jira#100")
+	}
+
+	found2, err := store.GetIssueByExternalRef(ctx, "jira#200")
+	if err != nil {
+		t.Fatalf("GetIssueByExternalRef failed: %v", err)
+	}
+	if found2 == nil || found2.ID != "bd-2" {
+		t.Errorf("Expected to find bd-2 by external ref jira#200")
+	}
+}