beads/cmd/bd/main.go

package main

import (
	"bufio"
	"bytes"
	"context"
	"crypto/sha256"
	"encoding/hex"
	"encoding/json"
	"fmt"
	"os"
	"os/exec"
	"path/filepath"
	"sort"
	"strconv"
	"strings"
	"sync"
	"time"

	"github.com/fatih/color"
	"github.com/spf13/cobra"
	"github.com/steveyegge/beads"
	"github.com/steveyegge/beads/internal/rpc"
	"github.com/steveyegge/beads/internal/storage"
	"github.com/steveyegge/beads/internal/storage/sqlite"
	"github.com/steveyegge/beads/internal/types"
	"golang.org/x/mod/semver"
)

// DaemonStatus captures daemon connection state for the current command
type DaemonStatus struct {
	Mode               string `json:"mode"` // "daemon" or "direct"
	Connected          bool   `json:"connected"`
	Degraded           bool   `json:"degraded"`
	SocketPath         string `json:"socket_path,omitempty"`
	AutoStartEnabled   bool   `json:"auto_start_enabled"`
	AutoStartAttempted bool   `json:"auto_start_attempted"`
	AutoStartSucceeded bool   `json:"auto_start_succeeded"`
	FallbackReason     string `json:"fallback_reason,omitempty"` // "none","flag_no_daemon","connect_failed","health_failed","auto_start_disabled","auto_start_failed"
	Detail             string `json:"detail,omitempty"`          // short diagnostic
	Health             string `json:"health,omitempty"`          // "healthy","degraded","unhealthy"
}

// Fallback reason constants
const (
	FallbackNone              = "none"
	FallbackFlagNoDaemon      = "flag_no_daemon"
	FallbackConnectFailed     = "connect_failed"
	FallbackHealthFailed      = "health_failed"
	FallbackAutoStartDisabled = "auto_start_disabled"
	FallbackAutoStartFailed   = "auto_start_failed"
	FallbackDaemonUnsupported = "daemon_unsupported"
)

var (
	dbPath       string
	actor        string
	store        storage.Storage
	jsonOutput   bool
	daemonStatus DaemonStatus // Tracks daemon connection state for current command

	// Daemon mode
	daemonClient *rpc.Client // RPC client when daemon is running
	noDaemon     bool        // Force direct mode (no daemon)

	// Auto-flush state
	autoFlushEnabled  = true  // Can be disabled with --no-auto-flush
	isDirty           = false // Tracks if DB has changes needing export
	needsFullExport   = false // Set to true when IDs change (renumber, rename-prefix)
	flushMutex        sync.Mutex
	flushTimer        *time.Timer
	storeMutex        sync.Mutex // Protects store access from background goroutine
	storeActive       = false    // Tracks if store is available
	flushFailureCount = 0        // Consecutive flush failures
	lastFlushError    error      // Last flush error for debugging

	// Auto-import state
	autoImportEnabled = true // Can be disabled with --no-auto-import
)

var rootCmd = &cobra.Command{
	Use:   "bd",
	Short: "bd - Dependency-aware issue tracker",
	Long:  `Issues chained together like beads. A lightweight issue tracker with first-class dependency support.`,
	PersistentPreRun: func(cmd *cobra.Command, args []string) {
		// Skip database initialization for commands that don't need a database
		if cmd.Name() == "init" || cmd.Name() == "daemon" || cmd.Name() == "help" || cmd.Name() == "version" || cmd.Name() == "quickstart" {
			return
		}

		// Set auto-flush based on flag (invert no-auto-flush)
		autoFlushEnabled = !noAutoFlush

		// Set auto-import based on flag (invert no-auto-import)
		autoImportEnabled = !noAutoImport

		// Initialize database path
		if dbPath == "" {
			cwd, err := os.Getwd()
			localBeadsDir := ""
			if err == nil {
				localBeadsDir = filepath.Join(cwd, ".beads")
			}
			
			// Use public API to find database (same logic as extensions)
			if foundDB := beads.FindDatabasePath(); foundDB != "" {
				dbPath = foundDB
				
				// Special case for import: if we found a database but there's a local .beads/
				// directory without a database, prefer creating a local database
				if cmd.Name() == "import" && localBeadsDir != "" {
					if _, err := os.Stat(localBeadsDir); err == nil {
						// Check if found database is NOT in the local .beads/ directory
						if !strings.HasPrefix(dbPath, localBeadsDir+string(filepath.Separator)) {
							// Use local .beads/vc.db instead for import
							dbPath = filepath.Join(localBeadsDir, "vc.db")
						}
					}
				}
			} else {
				// For import command, allow creating database if .beads/ directory exists
				if cmd.Name() == "import" && localBeadsDir != "" {
					if _, err := os.Stat(localBeadsDir); err == nil {
						// .beads/ directory exists - set dbPath for import to create
						dbPath = filepath.Join(localBeadsDir, "vc.db")
					}
				}
				
				// If dbPath still not set, error out
				if dbPath == "" {
					// No database found - error out instead of falling back to ~/.beads
					fmt.Fprintf(os.Stderr, "Error: no beads database found\n")
					fmt.Fprintf(os.Stderr, "Hint: run 'bd init' to create a database in the current directory\n")
					fmt.Fprintf(os.Stderr, "      or set BEADS_DB environment variable to specify a database\n")
					os.Exit(1)
				}
			}
		}

		// Set actor from flag, env, or default
		// Priority: --actor flag > BD_ACTOR env > USER env > "unknown"
		if actor == "" {
			if bdActor := os.Getenv("BD_ACTOR"); bdActor != "" {
				actor = bdActor
			} else if user := os.Getenv("USER"); user != "" {
				actor = user
			} else {
				actor = "unknown"
			}
		}

		// Initialize daemon status
		socketPath := getSocketPath()
		daemonStatus = DaemonStatus{
			Mode:             "direct",
			Connected:        false,
			Degraded:         true,
			SocketPath:       socketPath,
			AutoStartEnabled: shouldAutoStartDaemon(),
			FallbackReason:   FallbackNone,
		}

		// Try to connect to daemon first (unless --no-daemon flag is set)
		if noDaemon {
			daemonStatus.FallbackReason = FallbackFlagNoDaemon
			if os.Getenv("BD_DEBUG") != "" {
				fmt.Fprintf(os.Stderr, "Debug: --no-daemon flag set, using direct mode\n")
			}
		} else {
			// Attempt daemon connection
			client, err := rpc.TryConnect(socketPath)
			if err == nil && client != nil {
				// Set expected database path for validation
				if dbPath != "" {
					absDBPath, _ := filepath.Abs(dbPath)
					client.SetDatabasePath(absDBPath)
				}
				
				// Perform health check
				health, healthErr := client.Health()
				if healthErr == nil && health.Status == "healthy" {
					// Daemon is healthy - use it
					daemonClient = client
					daemonStatus.Mode = "daemon"
					daemonStatus.Connected = true
					daemonStatus.Degraded = false
					daemonStatus.Health = health.Status
					if os.Getenv("BD_DEBUG") != "" {
						fmt.Fprintf(os.Stderr, "Debug: connected to daemon at %s (health: %s)\n", socketPath, health.Status)
					}
					return // Skip direct storage initialization
				} else {
					// Health check failed or daemon unhealthy
					client.Close()
					daemonStatus.FallbackReason = FallbackHealthFailed
					if healthErr != nil {
						daemonStatus.Detail = healthErr.Error()
						if os.Getenv("BD_DEBUG") != "" {
							fmt.Fprintf(os.Stderr, "Debug: daemon health check failed: %v\n", healthErr)
						}
					} else {
						daemonStatus.Health = health.Status
						daemonStatus.Detail = health.Error
						if os.Getenv("BD_DEBUG") != "" {
							fmt.Fprintf(os.Stderr, "Debug: daemon unhealthy (status=%s): %s\n", health.Status, health.Error)
						}
					}
				}
			} else {
				// Connection failed
				daemonStatus.FallbackReason = FallbackConnectFailed
				if err != nil {
					daemonStatus.Detail = err.Error()
					if os.Getenv("BD_DEBUG") != "" {
						fmt.Fprintf(os.Stderr, "Debug: daemon connect failed at %s: %v\n", socketPath, err)
					}
				}
			}

			// Daemon not running or unhealthy - try auto-start if enabled
			if daemonStatus.AutoStartEnabled {
				daemonStatus.AutoStartAttempted = true
				if os.Getenv("BD_DEBUG") != "" {
					fmt.Fprintf(os.Stderr, "Debug: attempting to auto-start daemon\n")
				}
				startTime := time.Now()
				if tryAutoStartDaemon(socketPath) {
					// Retry connection after auto-start
					client, err := rpc.TryConnect(socketPath)
					if err == nil && client != nil {
						// Set expected database path for validation
						if dbPath != "" {
							absDBPath, _ := filepath.Abs(dbPath)
							client.SetDatabasePath(absDBPath)
						}
						
						// Check health of auto-started daemon
						health, healthErr := client.Health()
						if healthErr == nil && health.Status == "healthy" {
							daemonClient = client
							daemonStatus.Mode = "daemon"
							daemonStatus.Connected = true
							daemonStatus.Degraded = false
							daemonStatus.AutoStartSucceeded = true
							daemonStatus.Health = health.Status
							daemonStatus.FallbackReason = FallbackNone
							if os.Getenv("BD_DEBUG") != "" {
								elapsed := time.Since(startTime).Milliseconds()
								fmt.Fprintf(os.Stderr, "Debug: auto-start succeeded; connected at %s in %dms\n", socketPath, elapsed)
							}
							return // Skip direct storage initialization
						} else {
							// Auto-started daemon is unhealthy
							client.Close()
							daemonStatus.FallbackReason = FallbackHealthFailed
							if healthErr != nil {
								daemonStatus.Detail = healthErr.Error()
							} else {
								daemonStatus.Health = health.Status
								daemonStatus.Detail = health.Error
							}
							if os.Getenv("BD_DEBUG") != "" {
								fmt.Fprintf(os.Stderr, "Debug: auto-started daemon is unhealthy; falling back to direct mode\n")
							}
						}
					} else {
						// Auto-start completed but connection still failed
						daemonStatus.FallbackReason = FallbackAutoStartFailed
						if err != nil {
							daemonStatus.Detail = err.Error()
						}
						if os.Getenv("BD_DEBUG") != "" {
							fmt.Fprintf(os.Stderr, "Debug: auto-start did not yield a running daemon; falling back to direct mode\n")
						}
					}
				} else {
					// Auto-start itself failed
					daemonStatus.FallbackReason = FallbackAutoStartFailed
					if os.Getenv("BD_DEBUG") != "" {
						fmt.Fprintf(os.Stderr, "Debug: auto-start failed; falling back to direct mode\n")
					}
				}
			} else {
				// Auto-start disabled - only override if we don't already have a health failure
				if daemonStatus.FallbackReason != FallbackHealthFailed {
					// For connect failures, mention that auto-start was disabled
					if daemonStatus.FallbackReason == FallbackConnectFailed {
						daemonStatus.FallbackReason = FallbackAutoStartDisabled
					}
				}
				if os.Getenv("BD_DEBUG") != "" {
					fmt.Fprintf(os.Stderr, "Debug: auto-start disabled by BEADS_AUTO_START_DAEMON\n")
				}
			}

			// Emit BD_VERBOSE warning if falling back to direct mode
			if os.Getenv("BD_VERBOSE") != "" {
				emitVerboseWarning()
			}

			if os.Getenv("BD_DEBUG") != "" {
				fmt.Fprintf(os.Stderr, "Debug: using direct mode (reason: %s)\n", daemonStatus.FallbackReason)
			}
		}

		// Fall back to direct storage access
		var err error
		store, err = sqlite.New(dbPath)
		if err != nil {
			fmt.Fprintf(os.Stderr, "Error: failed to open database: %v\n", err)
			os.Exit(1)
		}

		// Mark store as active for flush goroutine safety
		storeMutex.Lock()
		storeActive = true
		storeMutex.Unlock()

		// Check for version mismatch (warn if binary is older than DB)
		checkVersionMismatch()

		// Auto-import if JSONL is newer than DB (e.g., after git pull)
		// Skip for import command itself to avoid recursion
		if cmd.Name() != "import" && autoImportEnabled {
			autoImportIfNewer()
		}
	},
	PersistentPostRun: func(cmd *cobra.Command, args []string) {
		// Close daemon client if we're using it
		if daemonClient != nil {
			_ = daemonClient.Close()
			return
		}

		// Otherwise, handle direct mode cleanup
		// Flush any pending changes before closing
		flushMutex.Lock()
		needsFlush := isDirty && autoFlushEnabled
		if needsFlush {
			// Cancel timer and flush immediately
			if flushTimer != nil {
				flushTimer.Stop()
				flushTimer = nil
			}
			// Don't clear isDirty or needsFullExport here - let flushToJSONL do it
		}
		flushMutex.Unlock()

		if needsFlush {
			// Call the shared flush function (handles both incremental and full export)
			flushToJSONL()
		}

		// Signal that store is closing (prevents background flush from accessing closed store)
		storeMutex.Lock()
		storeActive = false
		storeMutex.Unlock()

		if store != nil {
			_ = store.Close()
		}
	},
}

// getDebounceDuration returns the auto-flush debounce duration
// Configurable via BEADS_FLUSH_DEBOUNCE (e.g., "500ms", "10s")
// Defaults to 5 seconds if not set or invalid
func getDebounceDuration() time.Duration {
	envVal := os.Getenv("BEADS_FLUSH_DEBOUNCE")
	if envVal == "" {
		return 5 * time.Second
	}

	duration, err := time.ParseDuration(envVal)
	if err != nil {
		fmt.Fprintf(os.Stderr, "Warning: invalid BEADS_FLUSH_DEBOUNCE value '%s', using default 5s\n", envVal)
		return 5 * time.Second
	}

	return duration
}

// shouldAutoStartDaemon checks if daemon auto-start is enabled
// emitVerboseWarning prints a one-line warning when falling back to direct mode
func emitVerboseWarning() {
	switch daemonStatus.FallbackReason {
	case FallbackConnectFailed:
		fmt.Fprintf(os.Stderr, "Warning: Daemon unreachable at %s. Running in direct mode. Hint: bd daemon --status\n", daemonStatus.SocketPath)
	case FallbackHealthFailed:
		fmt.Fprintf(os.Stderr, "Warning: Daemon unhealthy. Falling back to direct mode. Hint: bd daemon --health\n")
	case FallbackAutoStartDisabled:
		fmt.Fprintf(os.Stderr, "Warning: Auto-start disabled (BEADS_AUTO_START_DAEMON=false). Running in direct mode. Hint: bd daemon\n")
	case FallbackAutoStartFailed:
		fmt.Fprintf(os.Stderr, "Warning: Failed to auto-start daemon. Running in direct mode. Hint: bd daemon --status\n")
	case FallbackDaemonUnsupported:
		fmt.Fprintf(os.Stderr, "Warning: Daemon does not support this command yet. Running in direct mode. Hint: update daemon or use local mode.\n")
	case FallbackFlagNoDaemon:
		// Don't warn when user explicitly requested --no-daemon
		return
	}
}

func shouldAutoStartDaemon() bool {
	// Check BEADS_NO_DAEMON first (escape hatch for single-user workflows)
	noDaemon := strings.ToLower(strings.TrimSpace(os.Getenv("BEADS_NO_DAEMON")))
	if noDaemon == "1" || noDaemon == "true" || noDaemon == "yes" || noDaemon == "on" {
		return false // Explicit opt-out
	}

	// Check legacy BEADS_AUTO_START_DAEMON for backward compatibility
	autoStart := strings.ToLower(strings.TrimSpace(os.Getenv("BEADS_AUTO_START_DAEMON")))
	if autoStart != "" {
		// Accept common falsy values
		return autoStart != "false" && autoStart != "0" && autoStart != "no" && autoStart != "off"
	}
	return true // Default to enabled (always-daemon mode)
}

// shouldUseGlobalDaemon determines if global daemon should be preferred
// based on environment variables, config, or heuristics (multi-repo detection)
func shouldUseGlobalDaemon() bool {
	// Check explicit environment variable first
	if pref := os.Getenv("BEADS_PREFER_GLOBAL_DAEMON"); pref != "" {
		return pref == "1" || strings.ToLower(pref) == "true"
	}

	// Heuristic: detect multiple beads repositories
	home, err := os.UserHomeDir()
	if err != nil {
		return false
	}

	// Count .beads directories under home
	repoCount := 0
	maxDepth := 5 // Don't scan too deep

	var countRepos func(string, int) error
	countRepos = func(dir string, depth int) error {
		if depth > maxDepth || repoCount > 1 {
			return filepath.SkipDir
		}

		entries, err := os.ReadDir(dir)
		if err != nil {
			return nil // Skip directories we can't read
		}

		for _, entry := range entries {
			if !entry.IsDir() {
				continue
			}

			name := entry.Name()

			// Skip hidden dirs except .beads
			if strings.HasPrefix(name, ".") && name != ".beads" {
				continue
			}

			// Skip common large directories
			if name == "node_modules" || name == "vendor" || name == "target" || name == ".git" {
				continue
			}

			path := filepath.Join(dir, name)

			// Check if this is a .beads directory with a database
			if name == ".beads" {
				dbPath := filepath.Join(path, "db.sqlite")
				if _, err := os.Stat(dbPath); err == nil {
					repoCount++
					if repoCount > 1 {
						return filepath.SkipDir
					}
				}
				continue
			}

			// Recurse into subdirectories
			if depth < maxDepth {
				countRepos(path, depth+1)
			}
		}
		return nil
	}

	// Scan common project directories
	projectDirs := []string{
		filepath.Join(home, "src"),
		filepath.Join(home, "projects"),
		filepath.Join(home, "code"),
		filepath.Join(home, "workspace"),
		filepath.Join(home, "dev"),
	}

	for _, dir := range projectDirs {
		if _, err := os.Stat(dir); err == nil {
			countRepos(dir, 0)
			if repoCount > 1 {
				break
			}
		}
	}

	if os.Getenv("BD_DEBUG") != "" {
		fmt.Fprintf(os.Stderr, "Debug: found %d beads repositories, prefer global: %v\n", repoCount, repoCount > 1)
	}

	// Use global daemon if we found more than 1 repository (multi-repo workflow)
	// This prevents concurrency issues when multiple repos are being worked on
	return repoCount > 1
}

// tryAutoStartDaemon attempts to start the daemon in the background
// Returns true if daemon was started successfully and socket is ready
func tryAutoStartDaemon(socketPath string) bool {
	// Check if we've failed recently (exponential backoff)
	if !canRetryDaemonStart() {
		if os.Getenv("BD_DEBUG") != "" {
			fmt.Fprintf(os.Stderr, "Debug: skipping auto-start due to recent failures\n")
		}
		return false
	}

	// Fast path: check if daemon is already healthy
	client, err := rpc.TryConnect(socketPath)
	if err == nil && client != nil {
		client.Close()
		if os.Getenv("BD_DEBUG") != "" {
			fmt.Fprintf(os.Stderr, "Debug: daemon already running and healthy\n")
		}
		return true
	}

	// Use lockfile to prevent multiple processes from starting daemon simultaneously
	lockPath := socketPath + ".startlock"
	lockFile, err := os.OpenFile(lockPath, os.O_CREATE|os.O_EXCL|os.O_WRONLY, 0600)
	if err != nil {
		// Someone else is starting daemon, wait for socket readiness
		if os.Getenv("BD_DEBUG") != "" {
			fmt.Fprintf(os.Stderr, "Debug: another process is starting daemon, waiting for readiness\n")
		}
		if waitForSocketReadiness(socketPath, 5*time.Second) {
			return true
		}

		// Socket still not ready - check if lock is stale
		if lockPID, err := readPIDFromFile(lockPath); err == nil {
			if !isPIDAlive(lockPID) {
				if os.Getenv("BD_DEBUG") != "" {
					fmt.Fprintf(os.Stderr, "Debug: lock is stale (PID %d dead), removing and retrying\n", lockPID)
				}
				os.Remove(lockPath)
				// Retry once
				return tryAutoStartDaemon(socketPath)
			}
		}
		return false
	}

	// Write our PID to lockfile
	fmt.Fprintf(lockFile, "%d\n", os.Getpid())
	lockFile.Close()
	defer os.Remove(lockPath)

	// Under lock: check for stale socket and clean up if necessary
	if _, err := os.Stat(socketPath); err == nil {
		// Socket exists - check if it's truly stale by trying a quick connect
		if canDialSocket(socketPath, 200*time.Millisecond) {
			// Another daemon is running - it must have started between our check and lock acquisition
			if os.Getenv("BD_DEBUG") != "" {
				fmt.Fprintf(os.Stderr, "Debug: daemon started by another process\n")
			}
			return true
		}

		// Socket exists but not responding - check if PID is alive before removing
		pidFile := getPIDFileForSocket(socketPath)
		if pidFile != "" {
			if pid, err := readPIDFromFile(pidFile); err == nil && isPIDAlive(pid) {
				// Daemon process is alive but socket not responding - wait for it
				if os.Getenv("BD_DEBUG") != "" {
					fmt.Fprintf(os.Stderr, "Debug: daemon PID %d alive, waiting for socket\n", pid)
				}
				return waitForSocketReadiness(socketPath, 5*time.Second)
			}
		}

		// Socket is stale (connect failed and PID dead/missing) - safe to remove
		if os.Getenv("BD_DEBUG") != "" {
			fmt.Fprintf(os.Stderr, "Debug: socket is stale, cleaning up\n")
		}
		os.Remove(socketPath)
		if pidFile != "" {
			os.Remove(pidFile)
		}
	}

	// Determine if we should start global or local daemon
	// If requesting local socket, check if we should suggest global instead
	isGlobal := false
	if home, err := os.UserHomeDir(); err == nil {
		globalSocket := filepath.Join(home, ".beads", "bd.sock")
		if socketPath == globalSocket {
			isGlobal = true
		} else if shouldUseGlobalDaemon() {
			// User has multiple repos, but requested local daemon
			// Auto-start global daemon instead and log suggestion
			isGlobal = true
			socketPath = globalSocket
			if os.Getenv("BD_DEBUG") != "" {
				fmt.Fprintf(os.Stderr, "Debug: detected multiple repos, auto-starting global daemon\n")
			}
		}
	}

	// Build daemon command using absolute path for security
	binPath, err := os.Executable()
	if err != nil {
		binPath = os.Args[0] // Fallback
	}

	args := []string{"daemon"}
	if isGlobal {
		args = append(args, "--global")
	}

	// Start daemon in background with proper I/O redirection
	cmd := exec.Command(binPath, args...)

	// Redirect stdio to /dev/null to prevent daemon output in foreground
	devNull, err := os.OpenFile(os.DevNull, os.O_RDWR, 0)
	if err == nil {
		cmd.Stdout = devNull
		cmd.Stderr = devNull
		cmd.Stdin = devNull
		defer devNull.Close()
	}

	// Set working directory to database directory for local daemon
	if !isGlobal && dbPath != "" {
		cmd.Dir = filepath.Dir(dbPath)
	}

	// Detach from parent process
	configureDaemonProcess(cmd)
	if err := cmd.Start(); err != nil {
		recordDaemonStartFailure()
		if os.Getenv("BD_DEBUG") != "" {
			fmt.Fprintf(os.Stderr, "Debug: failed to start daemon: %v\n", err)
		}
		return false
	}

	// Reap the process to avoid zombies
	go cmd.Wait()

	// Wait for socket to be ready with actual connection test
	if waitForSocketReadiness(socketPath, 5*time.Second) {
		recordDaemonStartSuccess()
		return true
	}

	recordDaemonStartFailure()
	if os.Getenv("BD_DEBUG") != "" {
		fmt.Fprintf(os.Stderr, "Debug: daemon socket not ready after 5 seconds\n")
	}
	return false
}

// getPIDFileForSocket returns the PID file path for a given socket path
func getPIDFileForSocket(socketPath string) string {
	// PID file is in same directory as socket, named daemon.pid
	dir := filepath.Dir(socketPath)
	return filepath.Join(dir, "daemon.pid")
}

// readPIDFromFile reads a PID from a file
func readPIDFromFile(path string) (int, error) {
	data, err := os.ReadFile(path)
	if err != nil {
		return 0, err
	}
	pid, err := strconv.Atoi(strings.TrimSpace(string(data)))
	if err != nil {
		return 0, err
	}
	return pid, nil
}

// isPIDAlive checks if a process with the given PID is running
func isPIDAlive(pid int) bool {
	if pid <= 0 {
		return false
	}
	return isProcessRunning(pid)
}

// canDialSocket attempts a quick dial to the socket with a timeout
func canDialSocket(socketPath string, timeout time.Duration) bool {
	client, err := rpc.TryConnectWithTimeout(socketPath, timeout)
	if err != nil || client == nil {
		return false
	}
	client.Close()
	return true
}

// waitForSocketReadiness waits for daemon socket to be ready by testing actual connections
func waitForSocketReadiness(socketPath string, timeout time.Duration) bool {
	deadline := time.Now().Add(timeout)
	for time.Now().Before(deadline) {
		if canDialSocket(socketPath, 200*time.Millisecond) {
			return true
		}
		time.Sleep(100 * time.Millisecond)
	}
	return false
}

// Daemon start failure tracking for exponential backoff
var (
	lastDaemonStartAttempt time.Time
	daemonStartFailures    int
)

func canRetryDaemonStart() bool {
	if daemonStartFailures == 0 {
		return true
	}

	// Exponential backoff: 5s, 10s, 20s, 40s, 80s, 120s (capped at 120s)
	backoff := time.Duration(5*(1<<uint(daemonStartFailures-1))) * time.Second
	if backoff > 120*time.Second {
		backoff = 120 * time.Second
	}

	return time.Since(lastDaemonStartAttempt) > backoff
}

func recordDaemonStartSuccess() {
	daemonStartFailures = 0
}

func recordDaemonStartFailure() {
	lastDaemonStartAttempt = time.Now()
	daemonStartFailures++
	// No cap needed - backoff is capped at 120s in canRetryDaemonStart
}

// getSocketPath returns the daemon socket path based on the database location
// Always returns local socket path (.beads/bd.sock relative to database)
func getSocketPath() string {
	// Always use local socket (same directory as database: .beads/bd.sock)
	localSocket := filepath.Join(filepath.Dir(dbPath), "bd.sock")
	
	// Warn if old global socket exists
	if home, err := os.UserHomeDir(); err == nil {
		globalSocket := filepath.Join(home, ".beads", "bd.sock")
		if _, err := os.Stat(globalSocket); err == nil {
			fmt.Fprintf(os.Stderr, "Warning: Found old global daemon socket at %s\n", globalSocket)
			fmt.Fprintf(os.Stderr, "Global sockets are deprecated. Each project now uses its own local daemon.\n")
			fmt.Fprintf(os.Stderr, "To migrate: Stop the global daemon and restart with 'bd daemon' in each project.\n")
		}
	}
	
	return localSocket
}

// outputJSON outputs data as pretty-printed JSON
func outputJSON(v interface{}) {
	encoder := json.NewEncoder(os.Stdout)
	encoder.SetIndent("", "  ")
	if err := encoder.Encode(v); err != nil {
		fmt.Fprintf(os.Stderr, "Error encoding JSON: %v\n", err)
		os.Exit(1)
	}
}

// findJSONLPath finds the JSONL file path for the current database
// findJSONLPath discovers the JSONL file path for the current database and ensures
// the parent directory exists. Uses beads.FindJSONLPath() for discovery (checking
// BEADS_JSONL env var first, then using .beads/issues.jsonl next to the database).
//
// Creates the .beads directory if it doesn't exist (important for new databases).
// If directory creation fails, returns the path anyway - the subsequent write will
// fail with a clearer error message.
//
// Thread-safe: No shared state access.
func findJSONLPath() string {
	// Use public API for path discovery
	jsonlPath := beads.FindJSONLPath(dbPath)

	// Ensure the directory exists (important for new databases)
	// This is the only difference from the public API - we create the directory
	dbDir := filepath.Dir(dbPath)
	if err := os.MkdirAll(dbDir, 0755); err != nil {
		// If we can't create the directory, return discovered path anyway
		// (the subsequent write will fail with a clearer error)
		return jsonlPath
	}

	return jsonlPath
}

// autoImportIfNewer checks if JSONL content changed (via hash) and imports if so
// Fixes bd-84: Hash-based comparison is git-proof (mtime comparison fails after git pull)
// Fixes bd-228: Now uses collision detection to prevent silently overwriting local changes
func autoImportIfNewer() {
	// Find JSONL path
	jsonlPath := findJSONLPath()

	// Read JSONL file
	jsonlData, err := os.ReadFile(jsonlPath)
	if err != nil {
		// JSONL doesn't exist or can't be accessed, skip import
		if os.Getenv("BD_DEBUG") != "" {
			fmt.Fprintf(os.Stderr, "Debug: auto-import skipped, JSONL not found: %v\n", err)
		}
		return
	}

	// Compute current JSONL hash
	hasher := sha256.New()
	hasher.Write(jsonlData)
	currentHash := hex.EncodeToString(hasher.Sum(nil))

	// Get last import hash from DB metadata
	ctx := context.Background()
	lastHash, err := store.GetMetadata(ctx, "last_import_hash")
	if err != nil {
		// Metadata error - treat as first import rather than skipping (bd-663)
		// This allows auto-import to recover from corrupt/missing metadata
		if os.Getenv("BD_DEBUG") != "" {
			fmt.Fprintf(os.Stderr, "Debug: metadata read failed (%v), treating as first import\n", err)
		}
		lastHash = ""
	}

	// Compare hashes
	if currentHash == lastHash {
		// Content unchanged, skip import
		if os.Getenv("BD_DEBUG") != "" {
			fmt.Fprintf(os.Stderr, "Debug: auto-import skipped, JSONL unchanged (hash match)\n")
		}
		return
	}

	if os.Getenv("BD_DEBUG") != "" {
		fmt.Fprintf(os.Stderr, "Debug: auto-import triggered (hash changed)\n")
	}

	// Check for Git merge conflict markers (bd-270)
	// Only match if they appear as standalone lines (not embedded in JSON strings)
	lines := bytes.Split(jsonlData, []byte("\n"))
	for _, line := range lines {
		trimmed := bytes.TrimSpace(line)
		if bytes.HasPrefix(trimmed, []byte("<<<<<<< ")) ||
			bytes.Equal(trimmed, []byte("=======")) ||
			bytes.HasPrefix(trimmed, []byte(">>>>>>> ")) {
			fmt.Fprintf(os.Stderr, "\n❌ Git merge conflict detected in %s\n\n", jsonlPath)
			fmt.Fprintf(os.Stderr, "The JSONL file contains unresolved merge conflict markers.\n")
			fmt.Fprintf(os.Stderr, "This prevents auto-import from loading your issues.\n\n")
			fmt.Fprintf(os.Stderr, "To resolve:\n")
			fmt.Fprintf(os.Stderr, "  1. Resolve the merge conflict in your Git client, OR\n")
			fmt.Fprintf(os.Stderr, "  2. Export from database to regenerate clean JSONL:\n")
			fmt.Fprintf(os.Stderr, "     bd export -o %s\n\n", jsonlPath)
			fmt.Fprintf(os.Stderr, "After resolving, commit the fixed JSONL file.\n")
			return
		}
	}

	// Content changed - parse all issues
	scanner := bufio.NewScanner(bytes.NewReader(jsonlData))
	scanner.Buffer(make([]byte, 0, 1024), 2*1024*1024) // 2MB buffer for large JSON lines
	var allIssues []*types.Issue
	lineNo := 0

	for scanner.Scan() {
		lineNo++
		line := scanner.Text()
		if line == "" {
			continue
		}

		var issue types.Issue
		if err := json.Unmarshal([]byte(line), &issue); err != nil {
			// Parse error, skip this import
			snippet := line
			if len(snippet) > 80 {
				snippet = snippet[:80] + "..."
			}
			fmt.Fprintf(os.Stderr, "Auto-import skipped: parse error at line %d: %v\nSnippet: %s\n", lineNo, err, snippet)
			return
		}

		// Fix closed_at invariant: closed issues must have closed_at timestamp
		if issue.Status == types.StatusClosed && issue.ClosedAt == nil {
			now := time.Now()
			issue.ClosedAt = &now
		}

		allIssues = append(allIssues, &issue)
	}

	if err := scanner.Err(); err != nil {
		fmt.Fprintf(os.Stderr, "Auto-import skipped: scanner error: %v\n", err)
		return
	}

	// Use shared import logic (bd-157)
	opts := ImportOptions{
		ResolveCollisions:  true, // Auto-import always resolves collisions
		DryRun:             false,
		SkipUpdate:         false,
		Strict:             false,
		SkipPrefixValidation: true, // Auto-import is lenient about prefixes
	}

	result, err := importIssuesCore(ctx, dbPath, store, allIssues, opts)
	if err != nil {
		fmt.Fprintf(os.Stderr, "Auto-import failed: %v\n", err)
		return
	}

	// Show collision remapping notification if any occurred
	if len(result.IDMapping) > 0 {
		// Build title lookup map to avoid O(n^2) search
		titleByID := make(map[string]string)
		for _, issue := range allIssues {
			titleByID[issue.ID] = issue.Title
		}

		// Sort remappings by old ID for consistent output
		type mapping struct {
			oldID string
			newID string
		}
		mappings := make([]mapping, 0, len(result.IDMapping))
		for oldID, newID := range result.IDMapping {
			mappings = append(mappings, mapping{oldID, newID})
		}
		sort.Slice(mappings, func(i, j int) bool {
			return mappings[i].oldID < mappings[j].oldID
		})

		maxShow := 10
		numRemapped := len(mappings)
		if numRemapped < maxShow {
			maxShow = numRemapped
		}

		fmt.Fprintf(os.Stderr, "\nAuto-import: remapped %d colliding issue(s) to new IDs:\n", numRemapped)
		for i := 0; i < maxShow; i++ {
			m := mappings[i]
			title := titleByID[m.oldID]
			fmt.Fprintf(os.Stderr, "  %s → %s (%s)\n", m.oldID, m.newID, title)
		}
		if numRemapped > maxShow {
			fmt.Fprintf(os.Stderr, "  ... and %d more\n", numRemapped-maxShow)
		}
		fmt.Fprintf(os.Stderr, "\n")
	}

	// Schedule export to sync JSONL after successful import
	changed := (result.Created + result.Updated + len(result.IDMapping)) > 0
	if changed {
		if len(result.IDMapping) > 0 {
			// Remappings may affect many issues, do a full export
			markDirtyAndScheduleFullExport()
		} else {
			// Regular import, incremental export is fine
			markDirtyAndScheduleFlush()
		}
	}

	// Store new hash after successful import
	if err := store.SetMetadata(ctx, "last_import_hash", currentHash); err != nil {
		fmt.Fprintf(os.Stderr, "Warning: failed to update last_import_hash after import: %v\n", err)
		fmt.Fprintf(os.Stderr, "This may cause auto-import to retry the same import on next operation.\n")
	}
}

// checkVersionMismatch checks if the binary version matches the database version
// and warns the user if they're running an outdated binary
func checkVersionMismatch() {
	ctx := context.Background()

	// Get the database version (version that last wrote to this DB)
	dbVersion, err := store.GetMetadata(ctx, "bd_version")
	if err != nil {
		// Metadata error - skip check (shouldn't happen, but be defensive)
		if os.Getenv("BD_DEBUG") != "" {
			fmt.Fprintf(os.Stderr, "Debug: version check skipped, metadata error: %v\n", err)
		}
		return
	}

	// If no version stored, this is an old database - store current version and continue
	if dbVersion == "" {
		_ = store.SetMetadata(ctx, "bd_version", Version)
		return
	}

	// Compare versions: warn if binary is older than database
	if dbVersion != Version {
		yellow := color.New(color.FgYellow, color.Bold).SprintFunc()
		fmt.Fprintf(os.Stderr, "\n%s\n", yellow("⚠️  WARNING: Version mismatch detected!"))
		fmt.Fprintf(os.Stderr, "%s\n", yellow(fmt.Sprintf("⚠️  Your bd binary (v%s) differs from the database version (v%s)", Version, dbVersion)))

		// Use semantic version comparison (requires v prefix)
		binaryVer := "v" + Version
		dbVer := "v" + dbVersion

		// semver.Compare returns -1 if binaryVer < dbVer, 0 if equal, 1 if binaryVer > dbVer
		cmp := semver.Compare(binaryVer, dbVer)

		if cmp < 0 {
			// Binary is older than database
			fmt.Fprintf(os.Stderr, "%s\n", yellow("⚠️  Your binary appears to be OUTDATED."))
			fmt.Fprintf(os.Stderr, "%s\n\n", yellow("⚠️  Some features may not work correctly. Rebuild: go build -o bd ./cmd/bd"))
		} else if cmp > 0 {
			// Binary is newer than database
			fmt.Fprintf(os.Stderr, "%s\n", yellow("⚠️  Your binary appears NEWER than the database."))
			fmt.Fprintf(os.Stderr, "%s\n\n", yellow("⚠️  The database will be upgraded automatically."))
			// Update stored version to current
			_ = store.SetMetadata(ctx, "bd_version", Version)
		}
	}

	// Always update the version metadata to track last-used version
	// This is safe even if versions match (idempotent operation)
	_ = store.SetMetadata(ctx, "bd_version", Version)
}

// markDirtyAndScheduleFlush marks the database as dirty and schedules a flush
// markDirtyAndScheduleFlush marks the database as dirty and schedules a debounced
// export to JSONL. Uses a timer that resets on each call - flush occurs 5 seconds
// after the LAST database modification (not the first).
//
// Debouncing behavior: If multiple operations happen within 5 seconds, the timer
// resets each time, and only one flush occurs after the burst of activity completes.
// This prevents excessive writes during rapid issue creation/updates.
//
// Flush-on-exit guarantee: PersistentPostRun cancels the timer and flushes immediately
// before the command exits, ensuring no data is lost even if the timer hasn't fired.
//
// Thread-safe: Protected by flushMutex. Safe to call from multiple goroutines.
// No-op if auto-flush is disabled via --no-auto-flush flag.
func markDirtyAndScheduleFlush() {
	if !autoFlushEnabled {
		return
	}

	flushMutex.Lock()
	defer flushMutex.Unlock()

	isDirty = true

	// Cancel existing timer if any
	if flushTimer != nil {
		flushTimer.Stop()
		flushTimer = nil
	}

	// Schedule new flush
	flushTimer = time.AfterFunc(getDebounceDuration(), func() {
		flushToJSONL()
	})
}

// markDirtyAndScheduleFullExport marks DB as needing a full export (for ID-changing operations)
func markDirtyAndScheduleFullExport() {
	if !autoFlushEnabled {
		return
	}

	flushMutex.Lock()
	defer flushMutex.Unlock()

	isDirty = true
	needsFullExport = true // Force full export, not incremental

	// Cancel existing timer if any
	if flushTimer != nil {
		flushTimer.Stop()
		flushTimer = nil
	}

	// Schedule new flush
	flushTimer = time.AfterFunc(getDebounceDuration(), func() {
		flushToJSONL()
	})
}

// clearAutoFlushState cancels pending flush and marks DB as clean (after manual export)
func clearAutoFlushState() {
	flushMutex.Lock()
	defer flushMutex.Unlock()

	// Cancel pending timer
	if flushTimer != nil {
		flushTimer.Stop()
		flushTimer = nil
	}

	// Clear dirty flag
	isDirty = false

	// Reset failure counter (manual export succeeded)
	flushFailureCount = 0
	lastFlushError = nil
}

// flushToJSONL exports dirty issues to JSONL using incremental updates
// flushToJSONL exports dirty database changes to the JSONL file. Uses incremental
// export by default (only exports modified issues), or full export for ID-changing
// operations (renumber, resolve-collisions). Invoked by the debounce timer or
// immediately on command exit.
//
// Export modes:
//   - Incremental (default): Exports only GetDirtyIssues(), merges with existing JSONL
//   - Full (after renumber): Exports all issues, rebuilds JSONL from scratch
//
// Error handling: Tracks consecutive failures. After 3+ failures, displays prominent
// warning suggesting manual "bd export" to recover. Failure counter resets on success.
//
// Thread-safety:
//   - Protected by flushMutex for isDirty/needsFullExport access
//   - Checks storeActive flag (via storeMutex) to prevent use-after-close
//   - Safe to call from timer goroutine or main thread
//
// No-op conditions:
//   - Store already closed (storeActive=false)
//   - Database not dirty (isDirty=false)
//   - No dirty issues found (incremental mode only)
func flushToJSONL() {
	// Check if store is still active (not closed)
	storeMutex.Lock()
	if !storeActive {
		storeMutex.Unlock()
		return
	}
	storeMutex.Unlock()

	flushMutex.Lock()
	if !isDirty {
		flushMutex.Unlock()
		return
	}
	isDirty = false
	fullExport := needsFullExport
	needsFullExport = false // Reset flag
	flushMutex.Unlock()

	jsonlPath := findJSONLPath()

	// Double-check store is still active before accessing
	storeMutex.Lock()
	if !storeActive {
		storeMutex.Unlock()
		return
	}
	storeMutex.Unlock()

	// Helper to record failure
	recordFailure := func(err error) {
		flushMutex.Lock()
		flushFailureCount++
		lastFlushError = err
		failCount := flushFailureCount
		flushMutex.Unlock()

		// Always show the immediate warning
		fmt.Fprintf(os.Stderr, "Warning: auto-flush failed: %v\n", err)

		// Show prominent warning after 3+ consecutive failures
		if failCount >= 3 {
			red := color.New(color.FgRed, color.Bold).SprintFunc()
			fmt.Fprintf(os.Stderr, "\n%s\n", red("⚠️  CRITICAL: Auto-flush has failed "+fmt.Sprint(failCount)+" times consecutively!"))
			fmt.Fprintf(os.Stderr, "%s\n", red("⚠️  Your JSONL file may be out of sync with the database."))
			fmt.Fprintf(os.Stderr, "%s\n\n", red("⚠️  Run 'bd export -o .beads/issues.jsonl' manually to fix."))
		}
	}

	// Helper to record success
	recordSuccess := func() {
		flushMutex.Lock()
		flushFailureCount = 0
		lastFlushError = nil
		flushMutex.Unlock()
	}

	ctx := context.Background()

	// Determine which issues to export
	var dirtyIDs []string
	var err error

	if fullExport {
		// Full export: get ALL issues (needed after ID-changing operations like renumber)
		allIssues, err := store.SearchIssues(ctx, "", types.IssueFilter{})
		if err != nil {
			recordFailure(fmt.Errorf("failed to get all issues: %w", err))
			return
		}
		dirtyIDs = make([]string, len(allIssues))
		for i, issue := range allIssues {
			dirtyIDs[i] = issue.ID
		}
	} else {
		// Incremental export: get only dirty issue IDs (bd-39 optimization)
		dirtyIDs, err = store.GetDirtyIssues(ctx)
		if err != nil {
			recordFailure(fmt.Errorf("failed to get dirty issues: %w", err))
			return
		}

		// No dirty issues? Nothing to do!
		if len(dirtyIDs) == 0 {
			recordSuccess()
			return
		}
	}

	// Read existing JSONL into a map (skip for full export - we'll rebuild from scratch)
	issueMap := make(map[string]*types.Issue)
	if !fullExport {
		if existingFile, err := os.Open(jsonlPath); err == nil {
			scanner := bufio.NewScanner(existingFile)
			lineNum := 0
			for scanner.Scan() {
				lineNum++
				line := scanner.Text()
				if line == "" {
					continue
				}
				var issue types.Issue
				if err := json.Unmarshal([]byte(line), &issue); err == nil {
					issueMap[issue.ID] = &issue
				} else {
					// Warn about malformed JSONL lines
					fmt.Fprintf(os.Stderr, "Warning: skipping malformed JSONL line %d: %v\n", lineNum, err)
				}
			}
			existingFile.Close()
		}
	}

	// Fetch only dirty issues from DB
	for _, issueID := range dirtyIDs {
		issue, err := store.GetIssue(ctx, issueID)
		if err != nil {
			recordFailure(fmt.Errorf("failed to get issue %s: %w", issueID, err))
			return
		}
		if issue == nil {
			// Issue was deleted, remove from map
			delete(issueMap, issueID)
			continue
		}

		// Get dependencies for this issue
		deps, err := store.GetDependencyRecords(ctx, issueID)
		if err != nil {
			recordFailure(fmt.Errorf("failed to get dependencies for %s: %w", issueID, err))
			return
		}
		issue.Dependencies = deps

		// Update map
		issueMap[issueID] = issue
	}

	// Convert map to sorted slice
	issues := make([]*types.Issue, 0, len(issueMap))
	for _, issue := range issueMap {
		issues = append(issues, issue)
	}
	sort.Slice(issues, func(i, j int) bool {
		return issues[i].ID < issues[j].ID
	})

	// Write to temp file first, then rename (atomic)
	// Use PID in filename to avoid collisions between concurrent bd commands (bd-306)
	tempPath := fmt.Sprintf("%s.tmp.%d", jsonlPath, os.Getpid())
	f, err := os.Create(tempPath)
	if err != nil {
		recordFailure(fmt.Errorf("failed to create temp file: %w", err))
		return
	}

	encoder := json.NewEncoder(f)
	for _, issue := range issues {
		if err := encoder.Encode(issue); err != nil {
			f.Close()
			os.Remove(tempPath)
			recordFailure(fmt.Errorf("failed to encode issue %s: %w", issue.ID, err))
			return
		}
	}

	if err := f.Close(); err != nil {
		os.Remove(tempPath)
		recordFailure(fmt.Errorf("failed to close temp file: %w", err))
		return
	}

	// Atomic rename
	if err := os.Rename(tempPath, jsonlPath); err != nil {
		os.Remove(tempPath)
		recordFailure(fmt.Errorf("failed to rename file: %w", err))
		return
	}

	// Clear only the dirty issues that were actually exported (fixes bd-52 race condition)
	if err := store.ClearDirtyIssuesByID(ctx, dirtyIDs); err != nil {
		// Don't fail the whole flush for this, but warn
		fmt.Fprintf(os.Stderr, "Warning: failed to clear dirty issues: %v\n", err)
	}

	// Store hash of exported JSONL (fixes bd-84: enables hash-based auto-import)
	jsonlData, err := os.ReadFile(jsonlPath)
	if err == nil {
		hasher := sha256.New()
		hasher.Write(jsonlData)
		exportedHash := hex.EncodeToString(hasher.Sum(nil))
		if err := store.SetMetadata(ctx, "last_import_hash", exportedHash); err != nil {
			fmt.Fprintf(os.Stderr, "Warning: failed to update last_import_hash after export: %v\n", err)
		}
	}

	// Success!
	recordSuccess()
}

var (
	noAutoFlush  bool
	noAutoImport bool
)

func init() {
	rootCmd.PersistentFlags().StringVar(&dbPath, "db", "", "Database path (default: auto-discover .beads/*.db or ~/.beads/default.db)")
	rootCmd.PersistentFlags().StringVar(&actor, "actor", "", "Actor name for audit trail (default: $BD_ACTOR or $USER)")
	rootCmd.PersistentFlags().BoolVar(&jsonOutput, "json", false, "Output in JSON format")
	rootCmd.PersistentFlags().BoolVar(&noDaemon, "no-daemon", false, "Force direct storage mode, bypass daemon if running")
	rootCmd.PersistentFlags().BoolVar(&noAutoFlush, "no-auto-flush", false, "Disable automatic JSONL sync after CRUD operations")
	rootCmd.PersistentFlags().BoolVar(&noAutoImport, "no-auto-import", false, "Disable automatic JSONL import when newer than DB")
}

// createIssuesFromMarkdown parses a markdown file and creates multiple issues
func createIssuesFromMarkdown(cmd *cobra.Command, filepath string) {
	// Parse markdown file
	templates, err := parseMarkdownFile(filepath)
	if err != nil {
		fmt.Fprintf(os.Stderr, "Error parsing markdown file: %v\n", err)
		os.Exit(1)
	}

	if len(templates) == 0 {
		fmt.Fprintf(os.Stderr, "No issues found in markdown file\n")
		os.Exit(1)
	}

	ctx := context.Background()
	createdIssues := []*types.Issue{}
	failedIssues := []string{}

	// Create each issue
	for _, template := range templates {
		issue := &types.Issue{
			Title:              template.Title,
			Description:        template.Description,
			Design:             template.Design,
			AcceptanceCriteria: template.AcceptanceCriteria,
			Status:             types.StatusOpen,
			Priority:           template.Priority,
			IssueType:          template.IssueType,
			Assignee:           template.Assignee,
		}

		if err := store.CreateIssue(ctx, issue, actor); err != nil {
			fmt.Fprintf(os.Stderr, "Error creating issue '%s': %v\n", template.Title, err)
			failedIssues = append(failedIssues, template.Title)
			continue
		}

		// Add labels
		for _, label := range template.Labels {
			if err := store.AddLabel(ctx, issue.ID, label, actor); err != nil {
				fmt.Fprintf(os.Stderr, "Warning: failed to add label %s to %s: %v\n", label, issue.ID, err)
			}
		}

		// Add dependencies
		for _, depSpec := range template.Dependencies {
			depSpec = strings.TrimSpace(depSpec)
			if depSpec == "" {
				continue
			}

			var depType types.DependencyType
			var dependsOnID string

			// Parse format: "type:id" or just "id" (defaults to "blocks")
			if strings.Contains(depSpec, ":") {
				parts := strings.SplitN(depSpec, ":", 2)
				if len(parts) != 2 {
					fmt.Fprintf(os.Stderr, "Warning: invalid dependency format '%s' for %s\n", depSpec, issue.ID)
					continue
				}
				depType = types.DependencyType(strings.TrimSpace(parts[0]))
				dependsOnID = strings.TrimSpace(parts[1])
			} else {
				depType = types.DepBlocks
				dependsOnID = depSpec
			}

			if !depType.IsValid() {
				fmt.Fprintf(os.Stderr, "Warning: invalid dependency type '%s' for %s\n", depType, issue.ID)
				continue
			}

			dep := &types.Dependency{
				IssueID:     issue.ID,
				DependsOnID: dependsOnID,
				Type:        depType,
			}
			if err := store.AddDependency(ctx, dep, actor); err != nil {
				fmt.Fprintf(os.Stderr, "Warning: failed to add dependency %s -> %s: %v\n", issue.ID, dependsOnID, err)
			}
		}

		createdIssues = append(createdIssues, issue)
	}

	// Schedule auto-flush
	if len(createdIssues) > 0 {
		markDirtyAndScheduleFlush()
	}

	// Report failures if any
	if len(failedIssues) > 0 {
		red := color.New(color.FgRed).SprintFunc()
		fmt.Fprintf(os.Stderr, "\n%s Failed to create %d issues:\n", red("✗"), len(failedIssues))
		for _, title := range failedIssues {
			fmt.Fprintf(os.Stderr, "  - %s\n", title)
		}
	}

	if jsonOutput {
		outputJSON(createdIssues)
	} else {
		green := color.New(color.FgGreen).SprintFunc()
		fmt.Printf("%s Created %d issues from %s:\n", green("✓"), len(createdIssues), filepath)
		for _, issue := range createdIssues {
			fmt.Printf("  %s: %s [P%d, %s]\n", issue.ID, issue.Title, issue.Priority, issue.IssueType)
		}
	}
}

var createCmd = &cobra.Command{
	Use:   "create [title]",
	Short: "Create a new issue (or multiple issues from markdown file)",
	Args:  cobra.MinimumNArgs(0), // Changed to allow no args when using -f
	Run: func(cmd *cobra.Command, args []string) {
		file, _ := cmd.Flags().GetString("file")

		// If file flag is provided, parse markdown and create multiple issues
		if file != "" {
			if len(args) > 0 {
				fmt.Fprintf(os.Stderr, "Error: cannot specify both title and --file flag\n")
				os.Exit(1)
			}
			createIssuesFromMarkdown(cmd, file)
			return
		}

		// Original single-issue creation logic
		if len(args) == 0 {
			fmt.Fprintf(os.Stderr, "Error: title required (or use --file to create from markdown)\n")
			os.Exit(1)
		}

		title := args[0]
		description, _ := cmd.Flags().GetString("description")
		design, _ := cmd.Flags().GetString("design")
		acceptance, _ := cmd.Flags().GetString("acceptance")
		priority, _ := cmd.Flags().GetInt("priority")
		issueType, _ := cmd.Flags().GetString("type")
		assignee, _ := cmd.Flags().GetString("assignee")
		labels, _ := cmd.Flags().GetStringSlice("labels")
		explicitID, _ := cmd.Flags().GetString("id")
		externalRef, _ := cmd.Flags().GetString("external-ref")
		deps, _ := cmd.Flags().GetStringSlice("deps")
		forceCreate, _ := cmd.Flags().GetBool("force")

		// Validate explicit ID format if provided (prefix-number)
		if explicitID != "" {
			// Check format: must contain hyphen and have numeric suffix
			parts := strings.Split(explicitID, "-")
			if len(parts) != 2 {
				fmt.Fprintf(os.Stderr, "Error: invalid ID format '%s' (expected format: prefix-number, e.g., 'bd-42')\n", explicitID)
				os.Exit(1)
			}
			// Validate numeric suffix
			if _, err := fmt.Sscanf(parts[1], "%d", new(int)); err != nil {
				fmt.Fprintf(os.Stderr, "Error: invalid ID format '%s' (numeric suffix required, e.g., 'bd-42')\n", explicitID)
				os.Exit(1)
			}

			// Validate prefix matches database prefix (unless --force is used)
			if !forceCreate {
				requestedPrefix := parts[0]
				ctx := context.Background()

				// Get database prefix from config
				var dbPrefix string
				if daemonClient != nil {
					// Using daemon - need to get config via RPC
					// For now, skip validation in daemon mode (needs RPC enhancement)
				} else {
					// Direct mode - check config
					dbPrefix, _ = store.GetConfig(ctx, "issue_prefix")
				}

				if dbPrefix != "" && dbPrefix != requestedPrefix {
					fmt.Fprintf(os.Stderr, "Error: prefix mismatch detected\n")
					fmt.Fprintf(os.Stderr, "  This database uses prefix '%s-', but you specified '%s-'\n", dbPrefix, requestedPrefix)
					fmt.Fprintf(os.Stderr, "  Did you mean to create '%s-%s'?\n", dbPrefix, parts[1])
					fmt.Fprintf(os.Stderr, "  Use --force to create with mismatched prefix anyway\n")
					os.Exit(1)
				}
			}
		}

		var externalRefPtr *string
		if externalRef != "" {
			externalRefPtr = &externalRef
		}

		// If daemon is running, use RPC
		if daemonClient != nil {
			createArgs := &rpc.CreateArgs{
				ID:                 explicitID,
				Title:              title,
				Description:        description,
				IssueType:          issueType,
				Priority:           priority,
				Design:             design,
				AcceptanceCriteria: acceptance,
				Assignee:           assignee,
				Labels:             labels,
				Dependencies:       deps,
			}

			resp, err := daemonClient.Create(createArgs)
			if err != nil {
				fmt.Fprintf(os.Stderr, "Error: %v\n", err)
				os.Exit(1)
			}

			if jsonOutput {
				fmt.Println(string(resp.Data))
			} else {
				var issue types.Issue
				if err := json.Unmarshal(resp.Data, &issue); err != nil {
					fmt.Fprintf(os.Stderr, "Error parsing response: %v\n", err)
					os.Exit(1)
				}
				green := color.New(color.FgGreen).SprintFunc()
				fmt.Printf("%s Created issue: %s\n", green("✓"), issue.ID)
				fmt.Printf("  Title: %s\n", issue.Title)
				fmt.Printf("  Priority: P%d\n", issue.Priority)
				fmt.Printf("  Status: %s\n", issue.Status)
			}
			return
		}

		// Direct mode
		issue := &types.Issue{
			ID:                 explicitID, // Set explicit ID if provided (empty string if not)
			Title:              title,
			Description:        description,
			Design:             design,
			AcceptanceCriteria: acceptance,
			Status:             types.StatusOpen,
			Priority:           priority,
			IssueType:          types.IssueType(issueType),
			Assignee:           assignee,
			ExternalRef:        externalRefPtr,
		}

		ctx := context.Background()
		if err := store.CreateIssue(ctx, issue, actor); err != nil {
			fmt.Fprintf(os.Stderr, "Error: %v\n", err)
			os.Exit(1)
		}

		// Add labels if specified
		for _, label := range labels {
			if err := store.AddLabel(ctx, issue.ID, label, actor); err != nil {
				fmt.Fprintf(os.Stderr, "Warning: failed to add label %s: %v\n", label, err)
			}
		}

		// Add dependencies if specified (format: type:id or just id for default "blocks" type)
		for _, depSpec := range deps {
			// Skip empty specs (e.g., from trailing commas)
			depSpec = strings.TrimSpace(depSpec)
			if depSpec == "" {
				continue
			}

			var depType types.DependencyType
			var dependsOnID string

			// Parse format: "type:id" or just "id" (defaults to "blocks")
			if strings.Contains(depSpec, ":") {
				parts := strings.SplitN(depSpec, ":", 2)
				if len(parts) != 2 {
					fmt.Fprintf(os.Stderr, "Warning: invalid dependency format '%s', expected 'type:id' or 'id'\n", depSpec)
					continue
				}
				depType = types.DependencyType(strings.TrimSpace(parts[0]))
				dependsOnID = strings.TrimSpace(parts[1])
			} else {
				// Default to "blocks" if no type specified
				depType = types.DepBlocks
				dependsOnID = depSpec
			}

			// Validate dependency type
			if !depType.IsValid() {
				fmt.Fprintf(os.Stderr, "Warning: invalid dependency type '%s' (valid: blocks, related, parent-child, discovered-from)\n", depType)
				continue
			}

			// Add the dependency
			dep := &types.Dependency{
				IssueID:     issue.ID,
				DependsOnID: dependsOnID,
				Type:        depType,
			}
			if err := store.AddDependency(ctx, dep, actor); err != nil {
				fmt.Fprintf(os.Stderr, "Warning: failed to add dependency %s -> %s: %v\n", issue.ID, dependsOnID, err)
			}
		}

		// Schedule auto-flush
		markDirtyAndScheduleFlush()

		if jsonOutput {
			outputJSON(issue)
		} else {
			green := color.New(color.FgGreen).SprintFunc()
			fmt.Printf("%s Created issue: %s\n", green("✓"), issue.ID)
			fmt.Printf("  Title: %s\n", issue.Title)
			fmt.Printf("  Priority: P%d\n", issue.Priority)
			fmt.Printf("  Status: %s\n", issue.Status)
		}
	},
}

func init() {
	createCmd.Flags().StringP("file", "f", "", "Create multiple issues from markdown file")
	createCmd.Flags().StringP("description", "d", "", "Issue description")
	createCmd.Flags().String("design", "", "Design notes")
	createCmd.Flags().String("acceptance", "", "Acceptance criteria")
	createCmd.Flags().IntP("priority", "p", 2, "Priority (0-4, 0=highest)")
	createCmd.Flags().StringP("type", "t", "task", "Issue type (bug|feature|task|epic|chore)")
	createCmd.Flags().StringP("assignee", "a", "", "Assignee")
	createCmd.Flags().StringSliceP("labels", "l", []string{}, "Labels (comma-separated)")
	createCmd.Flags().String("id", "", "Explicit issue ID (e.g., 'bd-42' for partitioning)")
	createCmd.Flags().String("external-ref", "", "External reference (e.g., 'gh-9', 'jira-ABC')")
	createCmd.Flags().StringSlice("deps", []string{}, "Dependencies in format 'type:id' or 'id' (e.g., 'discovered-from:bd-20,blocks:bd-15' or 'bd-20')")
	createCmd.Flags().Bool("force", false, "Force creation even if prefix doesn't match database prefix")
	rootCmd.AddCommand(createCmd)
}

var showCmd = &cobra.Command{
	Use:   "show [id...]",
	Short: "Show issue details",
	Args:  cobra.MinimumNArgs(1),
	Run: func(cmd *cobra.Command, args []string) {
		// If daemon is running, use RPC
		if daemonClient != nil {
			allDetails := []interface{}{}
			for idx, id := range args {
				showArgs := &rpc.ShowArgs{ID: id}
				resp, err := daemonClient.Show(showArgs)
				if err != nil {
					fmt.Fprintf(os.Stderr, "Error fetching %s: %v\n", id, err)
					continue
				}

				if jsonOutput {
					type IssueDetails struct {
						types.Issue
						Labels       []string       `json:"labels,omitempty"`
						Dependencies []*types.Issue `json:"dependencies,omitempty"`
						Dependents   []*types.Issue `json:"dependents,omitempty"`
					}
					var details IssueDetails
					if err := json.Unmarshal(resp.Data, &details); err == nil {
						allDetails = append(allDetails, details)
					}
				} else {
					// Check if issue exists (daemon returns null for non-existent issues)
					if string(resp.Data) == "null" || len(resp.Data) == 0 {
						fmt.Fprintf(os.Stderr, "Issue %s not found\n", id)
						continue
					}
					if idx > 0 {
						fmt.Println("\n" + strings.Repeat("─", 60))
					}

				// Parse response and use existing formatting code
				type IssueDetails struct {
					types.Issue
					Labels       []string       `json:"labels,omitempty"`
					Dependencies []*types.Issue `json:"dependencies,omitempty"`
					Dependents   []*types.Issue `json:"dependents,omitempty"`
				}
				var details IssueDetails
				if err := json.Unmarshal(resp.Data, &details); err != nil {
					fmt.Fprintf(os.Stderr, "Error parsing response: %v\n", err)
					os.Exit(1)
				}
				issue := &details.Issue

				cyan := color.New(color.FgCyan).SprintFunc()

				// Format output (same as direct mode below)
				tierEmoji := ""
				statusSuffix := ""
				if issue.CompactionLevel == 1 {
					tierEmoji = " 🗜️"
				} else if issue.CompactionLevel == 2 {
					tierEmoji = " 📦"
				}
				if issue.CompactionLevel > 0 {
					statusSuffix = fmt.Sprintf(" (compacted L%d)", issue.CompactionLevel)
				}

				fmt.Printf("\n%s: %s%s\n", cyan(issue.ID), issue.Title, tierEmoji)
				fmt.Printf("Status: %s%s\n", issue.Status, statusSuffix)
				fmt.Printf("Priority: P%d\n", issue.Priority)
				fmt.Printf("Type: %s\n", issue.IssueType)
				if issue.Assignee != "" {
					fmt.Printf("Assignee: %s\n", issue.Assignee)
				}
				if issue.EstimatedMinutes != nil {
					fmt.Printf("Estimated: %d minutes\n", *issue.EstimatedMinutes)
				}
				fmt.Printf("Created: %s\n", issue.CreatedAt.Format("2006-01-02 15:04"))
				fmt.Printf("Updated: %s\n", issue.UpdatedAt.Format("2006-01-02 15:04"))

				// Show compaction status
				if issue.CompactionLevel > 0 {
					fmt.Println()
					if issue.OriginalSize > 0 {
						currentSize := len(issue.Description) + len(issue.Design) + len(issue.Notes) + len(issue.AcceptanceCriteria)
						saved := issue.OriginalSize - currentSize
						if saved > 0 {
							reduction := float64(saved) / float64(issue.OriginalSize) * 100
							fmt.Printf("📊 Original: %d bytes | Compressed: %d bytes (%.0f%% reduction)\n",
								issue.OriginalSize, currentSize, reduction)
						}
					}
					tierEmoji2 := "🗜️"
					if issue.CompactionLevel == 2 {
						tierEmoji2 = "📦"
					}
					compactedDate := ""
					if issue.CompactedAt != nil {
						compactedDate = issue.CompactedAt.Format("2006-01-02")
					}
					fmt.Printf("%s Compacted: %s (Tier %d)\n", tierEmoji2, compactedDate, issue.CompactionLevel)
				}

				if issue.Description != "" {
					fmt.Printf("\nDescription:\n%s\n", issue.Description)
				}
				if issue.Design != "" {
					fmt.Printf("\nDesign:\n%s\n", issue.Design)
				}
				if issue.Notes != "" {
					fmt.Printf("\nNotes:\n%s\n", issue.Notes)
				}
				if issue.AcceptanceCriteria != "" {
					fmt.Printf("\nAcceptance Criteria:\n%s\n", issue.AcceptanceCriteria)
				}

				if len(details.Labels) > 0 {
					fmt.Printf("\nLabels: %v\n", details.Labels)
				}

				if len(details.Dependencies) > 0 {
					fmt.Printf("\nDepends on (%d):\n", len(details.Dependencies))
					for _, dep := range details.Dependencies {
						fmt.Printf("  → %s: %s [P%d]\n", dep.ID, dep.Title, dep.Priority)
					}
				}

				if len(details.Dependents) > 0 {
					fmt.Printf("\nBlocks (%d):\n", len(details.Dependents))
					for _, dep := range details.Dependents {
						fmt.Printf("  ← %s: %s [P%d]\n", dep.ID, dep.Title, dep.Priority)
					}
				}

					fmt.Println()
				}
			}

			if jsonOutput && len(allDetails) > 0 {
				outputJSON(allDetails)
			}
			return
		}

		// Direct mode
		ctx := context.Background()
		allDetails := []interface{}{}
		for idx, id := range args {
			issue, err := store.GetIssue(ctx, id)
			if err != nil {
				fmt.Fprintf(os.Stderr, "Error fetching %s: %v\n", id, err)
				continue
			}
			if issue == nil {
				fmt.Fprintf(os.Stderr, "Issue %s not found\n", id)
				continue
			}

			if jsonOutput {
				// Include labels, dependencies, and comments in JSON output
				type IssueDetails struct {
					*types.Issue
					Labels       []string         `json:"labels,omitempty"`
					Dependencies []*types.Issue   `json:"dependencies,omitempty"`
					Dependents   []*types.Issue   `json:"dependents,omitempty"`
					Comments     []*types.Comment `json:"comments,omitempty"`
				}
				details := &IssueDetails{Issue: issue}
				details.Labels, _ = store.GetLabels(ctx, issue.ID)
				details.Dependencies, _ = store.GetDependencies(ctx, issue.ID)
				details.Dependents, _ = store.GetDependents(ctx, issue.ID)
				details.Comments, _ = store.GetIssueComments(ctx, issue.ID)
				allDetails = append(allDetails, details)
				continue
			}

			if idx > 0 {
				fmt.Println("\n" + strings.Repeat("─", 60))
			}

		cyan := color.New(color.FgCyan).SprintFunc()

		// Add compaction emoji to title line
		tierEmoji := ""
		statusSuffix := ""
		if issue.CompactionLevel == 1 {
			tierEmoji = " 🗜️"
		} else if issue.CompactionLevel == 2 {
			tierEmoji = " 📦"
		}
		if issue.CompactionLevel > 0 {
			statusSuffix = fmt.Sprintf(" (compacted L%d)", issue.CompactionLevel)
		}

		fmt.Printf("\n%s: %s%s\n", cyan(issue.ID), issue.Title, tierEmoji)
		fmt.Printf("Status: %s%s\n", issue.Status, statusSuffix)
		fmt.Printf("Priority: P%d\n", issue.Priority)
		fmt.Printf("Type: %s\n", issue.IssueType)
		if issue.Assignee != "" {
			fmt.Printf("Assignee: %s\n", issue.Assignee)
		}
		if issue.EstimatedMinutes != nil {
			fmt.Printf("Estimated: %d minutes\n", *issue.EstimatedMinutes)
		}
		fmt.Printf("Created: %s\n", issue.CreatedAt.Format("2006-01-02 15:04"))
		fmt.Printf("Updated: %s\n", issue.UpdatedAt.Format("2006-01-02 15:04"))

		// Show compaction status footer
		if issue.CompactionLevel > 0 {
			tierEmoji := "🗜️"
			if issue.CompactionLevel == 2 {
				tierEmoji = "📦"
			}
			tierName := fmt.Sprintf("Tier %d", issue.CompactionLevel)

			fmt.Println()
			if issue.OriginalSize > 0 {
				currentSize := len(issue.Description) + len(issue.Design) + len(issue.Notes) + len(issue.AcceptanceCriteria)
				saved := issue.OriginalSize - currentSize
				if saved > 0 {
					reduction := float64(saved) / float64(issue.OriginalSize) * 100
					fmt.Printf("📊 Original: %d bytes | Compressed: %d bytes (%.0f%% reduction)\n",
						issue.OriginalSize, currentSize, reduction)
				}
			}
			compactedDate := ""
			if issue.CompactedAt != nil {
				compactedDate = issue.CompactedAt.Format("2006-01-02")
			}
			fmt.Printf("%s Compacted: %s (%s)\n", tierEmoji, compactedDate, tierName)
		}

		if issue.Description != "" {
			fmt.Printf("\nDescription:\n%s\n", issue.Description)
		}
		if issue.Design != "" {
			fmt.Printf("\nDesign:\n%s\n", issue.Design)
		}
		if issue.Notes != "" {
			fmt.Printf("\nNotes:\n%s\n", issue.Notes)
		}
		if issue.AcceptanceCriteria != "" {
			fmt.Printf("\nAcceptance Criteria:\n%s\n", issue.AcceptanceCriteria)
		}

		// Show labels
		labels, _ := store.GetLabels(ctx, issue.ID)
		if len(labels) > 0 {
			fmt.Printf("\nLabels: %v\n", labels)
		}

		// Show dependencies
		deps, _ := store.GetDependencies(ctx, issue.ID)
		if len(deps) > 0 {
			fmt.Printf("\nDepends on (%d):\n", len(deps))
			for _, dep := range deps {
				fmt.Printf("  → %s: %s [P%d]\n", dep.ID, dep.Title, dep.Priority)
			}
		}

		// Show dependents
		dependents, _ := store.GetDependents(ctx, issue.ID)
		if len(dependents) > 0 {
			fmt.Printf("\nBlocks (%d):\n", len(dependents))
			for _, dep := range dependents {
				fmt.Printf("  ← %s: %s [P%d]\n", dep.ID, dep.Title, dep.Priority)
			}
		}

			// Show comments
			comments, _ := store.GetIssueComments(ctx, issue.ID)
			if len(comments) > 0 {
				fmt.Printf("\nComments (%d):\n", len(comments))
				for _, comment := range comments {
					fmt.Printf("  [%s at %s]\n  %s\n\n", comment.Author, comment.CreatedAt.Format("2006-01-02 15:04"), comment.Text)
				}
			}

			fmt.Println()
		}

		if jsonOutput && len(allDetails) > 0 {
			outputJSON(allDetails)
		}
	},
}

func init() {
	rootCmd.AddCommand(showCmd)
}

var updateCmd = &cobra.Command{
	Use:   "update [id...]",
	Short: "Update one or more issues",
	Args:  cobra.MinimumNArgs(1),
	Run: func(cmd *cobra.Command, args []string) {
		updates := make(map[string]interface{})

		if cmd.Flags().Changed("status") {
			status, _ := cmd.Flags().GetString("status")
			updates["status"] = status
		}
		if cmd.Flags().Changed("priority") {
			priority, _ := cmd.Flags().GetInt("priority")
			updates["priority"] = priority
		}
		if cmd.Flags().Changed("title") {
			title, _ := cmd.Flags().GetString("title")
			updates["title"] = title
		}
		if cmd.Flags().Changed("assignee") {
			assignee, _ := cmd.Flags().GetString("assignee")
			updates["assignee"] = assignee
		}
		if cmd.Flags().Changed("design") {
			design, _ := cmd.Flags().GetString("design")
			updates["design"] = design
		}
		if cmd.Flags().Changed("notes") {
			notes, _ := cmd.Flags().GetString("notes")
			updates["notes"] = notes
		}
		if cmd.Flags().Changed("acceptance") || cmd.Flags().Changed("acceptance-criteria") {
		var acceptanceCriteria string
		if cmd.Flags().Changed("acceptance") {
		  acceptanceCriteria, _ = cmd.Flags().GetString("acceptance")
		} else {
			acceptanceCriteria, _ = cmd.Flags().GetString("acceptance-criteria")
		}
		updates["acceptance_criteria"] = acceptanceCriteria
	}
		if cmd.Flags().Changed("external-ref") {
			externalRef, _ := cmd.Flags().GetString("external-ref")
			updates["external_ref"] = externalRef
		}

		if len(updates) == 0 {
			fmt.Println("No updates specified")
			return
		}

		// If daemon is running, use RPC
		if daemonClient != nil {
			updatedIssues := []*types.Issue{}
			for _, id := range args {
				updateArgs := &rpc.UpdateArgs{ID: id}

				// Map updates to RPC args
				if status, ok := updates["status"].(string); ok {
					updateArgs.Status = &status
				}
				if priority, ok := updates["priority"].(int); ok {
					updateArgs.Priority = &priority
				}
				if title, ok := updates["title"].(string); ok {
					updateArgs.Title = &title
				}
				if assignee, ok := updates["assignee"].(string); ok {
					updateArgs.Assignee = &assignee
				}
				if design, ok := updates["design"].(string); ok {
					updateArgs.Design = &design
				}
				if notes, ok := updates["notes"].(string); ok {
					updateArgs.Notes = &notes
				}
				if acceptanceCriteria, ok := updates["acceptance_criteria"].(string); ok {
					updateArgs.AcceptanceCriteria = &acceptanceCriteria
				}

				resp, err := daemonClient.Update(updateArgs)
				if err != nil {
					fmt.Fprintf(os.Stderr, "Error updating %s: %v\n", id, err)
					continue
				}

				if jsonOutput {
					var issue types.Issue
					if err := json.Unmarshal(resp.Data, &issue); err == nil {
						updatedIssues = append(updatedIssues, &issue)
					}
				} else {
					green := color.New(color.FgGreen).SprintFunc()
					fmt.Printf("%s Updated issue: %s\n", green("✓"), id)
				}
			}

			if jsonOutput && len(updatedIssues) > 0 {
				outputJSON(updatedIssues)
			}
			return
		}

		// Direct mode
		ctx := context.Background()
		updatedIssues := []*types.Issue{}
		for _, id := range args {
			if err := store.UpdateIssue(ctx, id, updates, actor); err != nil {
				fmt.Fprintf(os.Stderr, "Error updating %s: %v\n", id, err)
				continue
			}

			if jsonOutput {
				issue, _ := store.GetIssue(ctx, id)
				if issue != nil {
					updatedIssues = append(updatedIssues, issue)
				}
			} else {
				green := color.New(color.FgGreen).SprintFunc()
				fmt.Printf("%s Updated issue: %s\n", green("✓"), id)
			}
		}

		// Schedule auto-flush if any issues were updated
		if len(args) > 0 {
			markDirtyAndScheduleFlush()
		}

		if jsonOutput && len(updatedIssues) > 0 {
			outputJSON(updatedIssues)
		}
	},
}

func init() {
	updateCmd.Flags().StringP("status", "s", "", "New status")
	updateCmd.Flags().IntP("priority", "p", 0, "New priority")
	updateCmd.Flags().String("title", "", "New title")
	updateCmd.Flags().StringP("assignee", "a", "", "New assignee")
	updateCmd.Flags().String("design", "", "Design notes")
	updateCmd.Flags().String("notes", "", "Additional notes")
	updateCmd.Flags().String("acceptance", "", "Acceptance criteria")
	updateCmd.Flags().String("acceptance-criteria", "", "DEPRECATED: use --acceptance")
	_ = updateCmd.Flags().MarkHidden("acceptance-criteria")
	updateCmd.Flags().String("external-ref", "", "External reference (e.g., 'gh-9', 'jira-ABC')")
	rootCmd.AddCommand(updateCmd)
}

var closeCmd = &cobra.Command{
	Use:   "close [id...]",
	Short: "Close one or more issues",
	Args:  cobra.MinimumNArgs(1),
	Run: func(cmd *cobra.Command, args []string) {
		reason, _ := cmd.Flags().GetString("reason")
		if reason == "" {
			reason = "Closed"
		}

		// If daemon is running, use RPC
		if daemonClient != nil {
			closedIssues := []*types.Issue{}
			for _, id := range args {
				closeArgs := &rpc.CloseArgs{
					ID:     id,
					Reason: reason,
				}
				resp, err := daemonClient.CloseIssue(closeArgs)
				if err != nil {
					fmt.Fprintf(os.Stderr, "Error closing %s: %v\n", id, err)
					continue
				}

				if jsonOutput {
					var issue types.Issue
					if err := json.Unmarshal(resp.Data, &issue); err == nil {
						closedIssues = append(closedIssues, &issue)
					}
				} else {
					green := color.New(color.FgGreen).SprintFunc()
					fmt.Printf("%s Closed %s: %s\n", green("✓"), id, reason)
				}
			}

			if jsonOutput && len(closedIssues) > 0 {
				outputJSON(closedIssues)
			}
			return
		}

		// Direct mode
		ctx := context.Background()
		closedIssues := []*types.Issue{}
		for _, id := range args {
			if err := store.CloseIssue(ctx, id, reason, actor); err != nil {
				fmt.Fprintf(os.Stderr, "Error closing %s: %v\n", id, err)
				continue
			}
			if jsonOutput {
				issue, _ := store.GetIssue(ctx, id)
				if issue != nil {
					closedIssues = append(closedIssues, issue)
				}
			} else {
				green := color.New(color.FgGreen).SprintFunc()
				fmt.Printf("%s Closed %s: %s\n", green("✓"), id, reason)
			}
		}

		// Schedule auto-flush if any issues were closed
		if len(args) > 0 {
			markDirtyAndScheduleFlush()
		}

		if jsonOutput && len(closedIssues) > 0 {
			outputJSON(closedIssues)
		}
	},
}

func init() {
	closeCmd.Flags().StringP("reason", "r", "", "Reason for closing")
	rootCmd.AddCommand(closeCmd)
}

func main() {
	if err := rootCmd.Execute(); err != nil {
		os.Exit(1)
	}
}