refactor: remove embedded Dolt server code entirely

Remove all embedded Dolt server spawning, watchdog auto-recovery, and
process management code. Beads now requires a standalone dolt sql-server
(per Tim Sehn's recommendation). The embedded code caused port-hijacking
chaos where watchdog loops respawned rogue servers from .beads/dolt/.

Deleted (6 implementation files):
- internal/storage/dolt/server.go (process spawning)
- internal/storage/dolt/watchdog.go (auto-restart loop)
- internal/storage/dolt/procattr_{unix,windows}.go
- internal/storage/dolt/process_{unix,windows}.go

Deleted (8 test files):
- server_test.go, server_integration_test.go, server_dependency_test.go
- watchdog_test.go, nested_query_test.go
- hub_spokes_integration_test.go, peer_sync_integration_test.go
- cmd/bd/test_dolt_server_test.go

Simplified:
- store.go: removed watchdog fields and start/stop calls
- cmd/bd/dolt.go: removed bd dolt start/stop commands
- doctor/federation.go: replaced GetRunningServerPID with TCP check

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: steveyegge

cmd/bd/doctor/federation.go

@@ -51,9 +51,10 @@ func CheckFederationRemotesAPI(path string) DoctorCheck {
 
 	// Check if server PID file exists (indicates server mode might be running)
 	pidFile := filepath.Join(doltPath, "dolt-server.pid")
-	serverPID := dolt.GetRunningServerPID(doltPath)
+	_, pidFileErr := os.Stat(pidFile)
+	serverRunning := pidFileErr == nil
 
-	if serverPID == 0 {
+	if !serverRunning {
 		// No server running - check if we have remotes configured
 		ctx := context.Background()
 		store, err := dolt.New(ctx, &dolt.Config{Path: doltPath, ReadOnly: true, Database: doltDatabaseName(beadsDir)})
@@ -90,7 +91,7 @@ func CheckFederationRemotesAPI(path string) DoctorCheck {
 
 	// Server is running - check if remotesapi port is accessible
 	// Default remotesapi port is 8080
-	remotesAPIPort := dolt.DefaultRemotesAPIPort
+	remotesAPIPort := 8080 // default dolt remotesapi port
 	host := "127.0.0.1"
 
 	addr := net.JoinHostPort(host, fmt.Sprintf("%d", remotesAPIPort))
@@ -100,7 +101,7 @@ func CheckFederationRemotesAPI(path string) DoctorCheck {
 			Name:     "Federation remotesapi",
 			Status:   StatusError,
 			Message:  fmt.Sprintf("remotesapi port %d not accessible", remotesAPIPort),
-			Detail:   fmt.Sprintf("Server PID %d found in %s but port unreachable: %v", serverPID, pidFile, err),
+			Detail:   fmt.Sprintf("PID file %s exists but port unreachable: %v", pidFile, err),
 			Fix:      "Check if dolt sql-server is running with --remotesapi-port flag",
 			Category: CategoryFederation,
 		}
@@ -441,25 +442,24 @@ func CheckDoltServerModeMismatch(path string) DoctorCheck {
 		}
 	}
 
-	// Check for server PID file
-	serverPID := dolt.GetRunningServerPID(doltPath)
+	// Check if server is reachable by trying to connect
+	cfg, _ := configfile.Load(beadsDir)
+	serverReachable := false
+	if cfg != nil {
+		host := cfg.GetDoltServerHost()
+		port := cfg.GetDoltServerPort()
+		addr := net.JoinHostPort(host, fmt.Sprintf("%d", port))
+		conn, err := net.DialTimeout("tcp", addr, 2*time.Second)
+		if err == nil {
+			_ = conn.Close()
+			serverReachable = true
+		}
+	}
 
 	// Open storage to check for remotes
 	ctx := context.Background()
 	store, err := dolt.New(ctx, &dolt.Config{Path: doltPath, ReadOnly: true, Database: doltDatabaseName(beadsDir)})
 	if err != nil {
-		// If we can't open the store, check if there's a lock file indicating embedded mode
-		lockFile := filepath.Join(doltPath, ".dolt", "lock")
-		if _, lockErr := os.Stat(lockFile); lockErr == nil && serverPID == 0 {
-			return DoctorCheck{
-				Name:     "Dolt Mode",
-				Status:   StatusWarning,
-				Message:  "Embedded mode with lock file",
-				Detail:   "Another process may be using the database in embedded mode",
-				Fix:      "Close other bd processes or switch to server mode",
-				Category: CategoryFederation,
-			}
-		}
 		return DoctorCheck{
 			Name:     "Dolt Mode",
 			Status:   StatusWarning,
@@ -491,22 +491,22 @@ func CheckDoltServerModeMismatch(path string) DoctorCheck {
 	}
 
 	// Determine expected vs actual mode
-	if peerCount > 0 && serverPID == 0 {
+	if peerCount > 0 && !serverReachable {
 		return DoctorCheck{
 			Name:     "Dolt Mode",
 			Status:   StatusWarning,
-			Message:  fmt.Sprintf("Embedded mode with %d peers configured", peerCount),
-			Detail:   "Federation with peers requires server mode for multi-writer support",
-			Fix:      "Switch to server mode: gt dolt start && bd config set dolt.mode server",
+			Message:  fmt.Sprintf("Server not reachable with %d peers configured", peerCount),
+			Detail:   "Federation with peers requires a running dolt sql-server",
+			Fix:      "Start dolt sql-server manually",
 			Category: CategoryFederation,
 		}
 	}
 
-	if serverPID > 0 {
+	if serverReachable {
 		return DoctorCheck{
 			Name:     "Dolt Mode",
 			Status:   StatusOK,
-			Message:  fmt.Sprintf("Server mode (PID %d)", serverPID),
+			Message:  "Server mode (connected)",
 			Detail:   fmt.Sprintf("%d peers configured", peerCount),
 			Category: CategoryFederation,
 		}

cmd/bd/dolt.go

@@ -14,7 +14,6 @@ import (
 	"github.com/steveyegge/beads/internal/beads"
 	"github.com/steveyegge/beads/internal/config"
 	"github.com/steveyegge/beads/internal/configfile"
-	dolt "github.com/steveyegge/beads/internal/storage/dolt"
 	"github.com/steveyegge/beads/internal/ui"
 )
 
@@ -30,8 +29,6 @@ Commands:
   bd dolt show         Show current Dolt configuration with connection test
   bd dolt set <k> <v>  Set a configuration value
   bd dolt test         Test server connection
-  bd dolt start        Start a Dolt SQL server (background process)
-  bd dolt stop         Stop the running Dolt SQL server
   bd dolt commit       Commit pending changes
   bd dolt push         Push commits to Dolt remote
   bd dolt pull         Pull commits from Dolt remote
@@ -46,8 +43,6 @@ Flags for 'bd dolt set':
   --update-config  Also write to config.yaml for team-wide defaults
 
 Examples:
-  bd dolt start                              Start server with configured settings
-  bd dolt stop                               Stop the running server
   bd dolt set database myproject
   bd dolt set host 192.168.1.100 --update-config
   bd dolt test`,
@@ -102,35 +97,6 @@ Use this before switching to server mode to ensure the server is running.`,
 	},
 }
 
-var doltStartCmd = &cobra.Command{
-	Use:   "start",
-	Short: "Start a Dolt SQL server using configured settings",
-	Long: `Start a Dolt SQL server as a background process.
-
-Uses the host, port, and user from your Dolt configuration (see 'bd dolt show').
-The server runs in the background and persists after bd exits.
-
-Configuration sources (priority order):
-  1. Environment variables (BEADS_DOLT_*)
-  2. metadata.json (bd dolt set)
-  3. config.yaml (team defaults)`,
-	Run: func(cmd *cobra.Command, args []string) {
-		startDoltServer()
-	},
-}
-
-var doltStopCmd = &cobra.Command{
-	Use:   "stop",
-	Short: "Stop the running Dolt SQL server",
-	Long: `Stop the Dolt SQL server started by 'bd dolt start'.
-
-Sends a graceful shutdown signal (SIGTERM). If the server doesn't stop
-within 10 seconds, it is forcefully terminated.`,
-	Run: func(cmd *cobra.Command, args []string) {
-		stopDoltServer()
-	},
-}
-
 var doltPushCmd = &cobra.Command{
 	Use:   "push",
 	Short: "Push commits to Dolt remote",
@@ -246,8 +212,6 @@ func init() {
 	doltCmd.AddCommand(doltShowCmd)
 	doltCmd.AddCommand(doltSetCmd)
 	doltCmd.AddCommand(doltTestCmd)
-	doltCmd.AddCommand(doltStartCmd)
-	doltCmd.AddCommand(doltStopCmd)
 	doltCmd.AddCommand(doltCommitCmd)
 	doltCmd.AddCommand(doltPushCmd)
 	doltCmd.AddCommand(doltPullCmd)
@@ -483,178 +447,6 @@ func testServerConnection(cfg *configfile.Config) bool {
 	return true
 }
 
-func startDoltServer() {
-	beadsDir := beads.FindBeadsDir()
-	if beadsDir == "" {
-		fmt.Fprintf(os.Stderr, "Error: not in a beads repository (no .beads directory found)\n")
-		os.Exit(1)
-	}
-
-	cfg, err := configfile.Load(beadsDir)
-	if err != nil {
-		fmt.Fprintf(os.Stderr, "Error loading config: %v\n", err)
-		os.Exit(1)
-	}
-	if cfg == nil {
-		cfg = configfile.DefaultConfig()
-	}
-
-	dataDir := filepath.Join(beadsDir, "dolt")
-	logFile := filepath.Join(beadsDir, "dolt-server.log")
-	host := cfg.GetDoltServerHost()
-	port := cfg.GetDoltServerPort()
-	user := cfg.GetDoltServerUser()
-	database := cfg.GetDoltDatabase()
-
-	// Check if server is already running
-	if pid := dolt.GetRunningServerPID(dataDir); pid > 0 {
-		if jsonOutput {
-			outputJSON(map[string]interface{}{
-				"error":   "server_already_running",
-				"message": fmt.Sprintf("Dolt server already running (PID %d)", pid),
-				"pid":     pid,
-				"host":    host,
-				"port":    port,
-			})
-		} else {
-			fmt.Fprintf(os.Stderr, "Error: Dolt server already running (PID %d)\n", pid)
-			fmt.Fprintf(os.Stderr, "Stop it first: bd dolt stop\n")
-		}
-		os.Exit(1)
-	}
-
-	// Check if data directory exists
-	if _, err := os.Stat(dataDir); os.IsNotExist(err) {
-		if jsonOutput {
-			outputJSON(map[string]interface{}{
-				"error":   "data_dir_not_found",
-				"message": fmt.Sprintf("Dolt data directory not found: %s", dataDir),
-			})
-		} else {
-			fmt.Fprintf(os.Stderr, "Error: Dolt data directory not found: %s\n", dataDir)
-			fmt.Fprintf(os.Stderr, "Run 'bd init' first to create the database.\n")
-		}
-		os.Exit(1)
-	}
-
-	if !jsonOutput {
-		fmt.Println("Starting Dolt SQL server...")
-		fmt.Printf("  Host:     %s\n", host)
-		fmt.Printf("  Port:     %d\n", port)
-		fmt.Printf("  User:     %s\n", user)
-		fmt.Printf("  Database: %s\n", database)
-		fmt.Printf("  Data dir: %s\n", dataDir)
-		fmt.Printf("  Log file: %s\n", logFile)
-		fmt.Println()
-		fmt.Print("Waiting for server to accept connections...")
-	}
-
-	server := dolt.NewServer(dolt.ServerConfig{
-		DataDir:           dataDir,
-		SQLPort:           port,
-		Host:              host,
-		LogFile:           logFile,
-		User:              user,
-		DisableRemotesAPI: true, // remotesapi only needed for federation
-	})
-
-	if err := server.Start(context.Background()); err != nil {
-		if jsonOutput {
-			outputJSON(map[string]interface{}{
-				"error":   "start_failed",
-				"message": err.Error(),
-			})
-		} else {
-			fmt.Println() // finish the "Waiting..." line
-			fmt.Fprintf(os.Stderr, "Error: %v\n", err)
-			fmt.Fprintf(os.Stderr, "Check the log file for details: %s\n", logFile)
-		}
-		os.Exit(1)
-	}
-	if !jsonOutput {
-		fmt.Println() // finish the "Waiting..." line
-	}
-
-	pid := dolt.GetRunningServerPID(dataDir)
-
-	if jsonOutput {
-		outputJSON(map[string]interface{}{
-			"status":   "started",
-			"pid":      pid,
-			"host":     host,
-			"port":     port,
-			"user":     user,
-			"database": database,
-			"data_dir": dataDir,
-			"log_file": logFile,
-		})
-		return
-	}
-
-	fmt.Printf("  %s\n", ui.RenderPass(fmt.Sprintf("✓ Server started (PID %d)", pid)))
-	fmt.Println()
-	fmt.Println("To stop the server:")
-	fmt.Println("  bd dolt stop")
-}
-
-func stopDoltServer() {
-	beadsDir := beads.FindBeadsDir()
-	if beadsDir == "" {
-		fmt.Fprintf(os.Stderr, "Error: not in a beads repository (no .beads directory found)\n")
-		os.Exit(1)
-	}
-
-	dataDir := filepath.Join(beadsDir, "dolt")
-
-	pid := dolt.GetRunningServerPID(dataDir)
-	if pid == 0 {
-		if jsonOutput {
-			outputJSON(map[string]interface{}{
-				"status":  "not_running",
-				"message": "No Dolt server is running",
-			})
-		} else {
-			fmt.Println("No Dolt server is running.")
-		}
-		return
-	}
-
-	if !jsonOutput {
-		fmt.Printf("Stopping Dolt SQL server (PID %d)...\n", pid)
-	}
-
-	if err := dolt.StopServerByPID(pid); err != nil {
-		if jsonOutput {
-			outputJSON(map[string]interface{}{
-				"error":   "stop_failed",
-				"message": err.Error(),
-				"pid":     pid,
-			})
-		} else {
-			fmt.Fprintf(os.Stderr, "Error stopping server: %v\n", err)
-		}
-		os.Exit(1)
-	}
-
-	// Clean up PID file
-	pidFile := filepath.Join(dataDir, "dolt-server.pid")
-	_ = os.Remove(pidFile)
-
-	if jsonOutput {
-		outputJSON(map[string]interface{}{
-			"status": "stopped",
-			"pid":    pid,
-		})
-		return
-	}
-
-	fmt.Printf("%s\n", ui.RenderPass("✓ Server stopped"))
-
-	fmt.Println()
-	fmt.Println("Note: bd commands require a running server.")
-	fmt.Println("Restart with: bd dolt start")
-}
-
 // logDoltConfigChange appends an audit entry to .beads/dolt-config.log.
 // Includes the beadsDir path for debugging worktree config pollution (bd-la2cl).
 func logDoltConfigChange(beadsDir, key, value string) {