fix(init): ensure sync branch persistence on init

Problem:
- Sync branch setup occurred before the config file was initialized
- Persistence only targeted the database, leading to loss on re-init

Solution:
- Reorder initialization to create the config file before sync setup
- Synchronize sync branch state to both config file and database

Impact:
- Settings are preserved across re-initialization and DB clears
- Better consistency between file and database state

Fixes: #927 (Bug 3)

cmd/bd/init.go

@@ -287,24 +287,6 @@ With --stealth: configures per-repository git settings for invisible beads usage
 			os.Exit(1)
 		}
 
-		// Set sync.branch only if explicitly specified via --branch flag
-		// GH#807: Do NOT auto-detect current branch - if sync.branch is set to main/master,
-		// the worktree created by bd sync will check out main, preventing the user from
-		// checking out main in their working directory (git error: "'main' is already checked out")
-		//
-		// When --branch is not specified, bd sync will commit directly to the current branch
-		// (the original behavior before sync branch feature)
-		if branch != "" {
-			if err := syncbranch.Set(ctx, store, branch); err != nil {
-				fmt.Fprintf(os.Stderr, "Error: failed to set sync branch: %v\n", err)
-				_ = store.Close()
-				os.Exit(1)
-			}
-			if !quiet {
-				fmt.Printf("  Sync branch: %s\n", branch)
-			}
-		}
-
 		// === TRACKING METADATA (Pattern B: Warn and Continue) ===
 		// Tracking metadata enhances functionality (diagnostics, version checks, collision detection)
 		// but the system works without it. Failures here degrade gracefully - we warn but continue.
@@ -386,6 +368,27 @@ With --stealth: configures per-repository git settings for invisible beads usage
 			}
 		}
 
+		// Set sync.branch only if explicitly specified via --branch flag
+		// GH#807: Do NOT auto-detect current branch - if sync.branch is set to main/master,
+		// the worktree created by bd sync will check out main, preventing the user from
+		// checking out main in their working directory (git error: "'main' is already checked out")
+		//
+		// When --branch is not specified, bd sync will commit directly to the current branch
+		// (the original behavior before sync branch feature)
+		//
+		// GH#927: This must run AFTER createConfigYaml() so that config.yaml exists
+		// and syncbranch.Set() can update it via config.SetYamlConfig() (PR#910 mechanism)
+		if branch != "" {
+			if err := syncbranch.Set(ctx, store, branch); err != nil {
+				fmt.Fprintf(os.Stderr, "Error: failed to set sync branch: %v\n", err)
+				_ = store.Close()
+				os.Exit(1)
+			}
+			if !quiet {
+				fmt.Printf("  Sync branch: %s\n", branch)
+			}
+		}
+
 		// Check if git has existing issues to import (fresh clone scenario)
 		// With --from-jsonl: import from local file instead of git history
 		if fromJSONL {

cmd/bd/init_test.go

@@ -1188,6 +1188,64 @@ func TestInitBranchPersistsToConfigYaml(t *testing.T) {
 	}
 }
 
+// TestInitReinitWithBranch verifies that --branch flag works on reinit
+// GH#927: When reinitializing with --branch, config.yaml should be updated even if it exists
+func TestInitReinitWithBranch(t *testing.T) {
+	// Reset global state
+	origDBPath := dbPath
+	defer func() { dbPath = origDBPath }()
+	dbPath = ""
+
+	// Reset Cobra flags
+	initCmd.Flags().Set("branch", "")
+	initCmd.Flags().Set("force", "false")
+
+	tmpDir := t.TempDir()
+	t.Chdir(tmpDir)
+
+	// Initialize git repo first
+	if err := runCommandInDir(tmpDir, "git", "init", "--initial-branch=dev"); err != nil {
+		t.Fatalf("Failed to init git: %v", err)
+	}
+
+	// First init WITHOUT --branch (creates config.yaml with commented sync-branch)
+	rootCmd.SetArgs([]string{"init", "--prefix", "test", "--quiet"})
+	if err := rootCmd.Execute(); err != nil {
+		t.Fatalf("First init failed: %v", err)
+	}
+
+	// Verify config.yaml has commented sync-branch initially
+	configPath := filepath.Join(tmpDir, ".beads", "config.yaml")
+	content, err := os.ReadFile(configPath)
+	if err != nil {
+		t.Fatalf("Failed to read config.yaml: %v", err)
+	}
+	if !strings.Contains(string(content), "# sync-branch:") {
+		t.Errorf("Initial config.yaml should have commented sync-branch")
+	}
+
+	// Reset Cobra flags for reinit
+	initCmd.Flags().Set("branch", "")
+	initCmd.Flags().Set("force", "false")
+
+	// Reinit WITH --branch (should update existing config.yaml)
+	rootCmd.SetArgs([]string{"init", "--prefix", "test", "--branch", "beads-sync", "--force", "--quiet"})
+	if err := rootCmd.Execute(); err != nil {
+		t.Fatalf("Reinit with --branch failed: %v", err)
+	}
+
+	// Verify config.yaml now has uncommented sync-branch
+	content, err = os.ReadFile(configPath)
+	if err != nil {
+		t.Fatalf("Failed to read config.yaml after reinit: %v", err)
+	}
+
+	configStr := string(content)
+	if !strings.Contains(configStr, "sync-branch: \"beads-sync\"") {
+		t.Errorf("After reinit with --branch, config.yaml should contain uncommented 'sync-branch: \"beads-sync\"', got:\n%s", configStr)
+	}
+}
+
 // TestSetupGlobalGitIgnore_ReadOnly verifies graceful handling when the
 // gitignore file cannot be written (prints manual instructions instead of failing).
 func TestSetupGlobalGitIgnore_ReadOnly(t *testing.T) {

internal/syncbranch/syncbranch.go

@@ -193,13 +193,29 @@ func getConfigFromDB(dbPath string, key string) string {
 	return value
 }
 
-// Set stores the sync branch configuration in the database
+// Set stores the sync branch configuration in both config.yaml AND the database.
+// GH#909: Writing to both ensures bd doctor and migrate detection work correctly.
+//
+// Config precedence on read (from Get function):
+//   1. BEADS_SYNC_BRANCH env var
+//   2. sync-branch in config.yaml (recommended, version controlled)
+//   3. sync.branch in database (legacy, for backward compatibility)
 func Set(ctx context.Context, store storage.Storage, branch string) error {
 	// GH#807: Use sync-specific validation that rejects main/master
 	if err := ValidateSyncBranchName(branch); err != nil {
 		return err
 	}
 
+	// GH#909: Write to config.yaml first (primary source for doctor/migration checks)
+	// This also handles uncommenting if the key was commented out
+	if err := config.SetYamlConfig(ConfigYAMLKey, branch); err != nil {
+		// Log warning but don't fail - database write is still valuable
+		// This can fail if config.yaml doesn't exist yet (pre-init state)
+		// In that case, the database config still works for backward compatibility
+		fmt.Fprintf(os.Stderr, "Warning: could not update config.yaml: %v\n", err)
+	}
+
+	// Write to database for backward compatibility
 	return store.SetConfig(ctx, ConfigKey, branch)
 }
 

internal/syncbranch/syncbranch_test.go

@@ -252,6 +252,78 @@ func TestSet(t *testing.T) {
 	})
 }
 
+// TestSetUpdatesConfigYAML verifies GH#909 fix: Set() writes to config.yaml
+func TestSetUpdatesConfigYAML(t *testing.T) {
+	ctx := context.Background()
+
+	t.Run("updates config.yaml when it exists", func(t *testing.T) {
+		// Create temp directory with .beads/config.yaml
+		tmpDir, err := os.MkdirTemp("", "test-syncbranch-yaml-*")
+		if err != nil {
+			t.Fatalf("Failed to create temp dir: %v", err)
+		}
+		defer os.RemoveAll(tmpDir)
+
+		beadsDir := tmpDir + "/.beads"
+		if err := os.MkdirAll(beadsDir, 0750); err != nil {
+			t.Fatalf("Failed to create .beads dir: %v", err)
+		}
+
+		// Create initial config.yaml with sync-branch commented out
+		configPath := beadsDir + "/config.yaml"
+		initialConfig := `# beads configuration
+# sync-branch: ""
+auto-start-daemon: true
+`
+		if err := os.WriteFile(configPath, []byte(initialConfig), 0600); err != nil {
+			t.Fatalf("Failed to create config.yaml: %v", err)
+		}
+
+		// Change to temp dir so findProjectConfigYaml can find it
+		origWd, _ := os.Getwd()
+		if err := os.Chdir(tmpDir); err != nil {
+			t.Fatalf("Failed to chdir: %v", err)
+		}
+		defer os.Chdir(origWd)
+
+		// Create test store
+		store := newTestStore(t)
+		defer store.Close()
+
+		// Call Set() which should update both database and config.yaml
+		if err := Set(ctx, store, "beads-sync"); err != nil {
+			t.Fatalf("Set() error = %v", err)
+		}
+
+		// Verify database was updated
+		dbValue, err := store.GetConfig(ctx, ConfigKey)
+		if err != nil {
+			t.Fatalf("GetConfig() error = %v", err)
+		}
+		if dbValue != "beads-sync" {
+			t.Errorf("Database value = %q, want %q", dbValue, "beads-sync")
+		}
+
+		// Verify config.yaml was updated (key uncommented and value set)
+		yamlContent, err := os.ReadFile(configPath)
+		if err != nil {
+			t.Fatalf("Failed to read config.yaml: %v", err)
+		}
+
+		yamlStr := string(yamlContent)
+		if !strings.Contains(yamlStr, "sync-branch:") {
+			t.Error("config.yaml should contain 'sync-branch:' (uncommented)")
+		}
+		if !strings.Contains(yamlStr, "beads-sync") {
+			t.Errorf("config.yaml should contain 'beads-sync', got:\n%s", yamlStr)
+		}
+		// Should NOT contain the commented version anymore
+		if strings.Contains(yamlStr, "# sync-branch:") {
+			t.Error("config.yaml still has commented '# sync-branch:', should be uncommented")
+		}
+	})
+}
+
 func TestUnset(t *testing.T) {
 	ctx := context.Background()