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/config"
	"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"
	cmdDaemon                 = "daemon"
	cmdImport                 = "import"
	statusHealthy             = "healthy"
	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) {
		// Apply viper configuration if flags weren't explicitly set
		// Priority: flags > viper (config file + env vars) > defaults
		// Do this BEFORE early-return so init/version/help respect config

		// If flag wasn't explicitly set, use viper value
		if !cmd.Flags().Changed("json") {
			jsonOutput = config.GetBool("json")
		}
		if !cmd.Flags().Changed("no-daemon") {
			noDaemon = config.GetBool("no-daemon")
		}
		if !cmd.Flags().Changed("no-auto-flush") {
			noAutoFlush = config.GetBool("no-auto-flush")
		}
		if !cmd.Flags().Changed("no-auto-import") {
			noAutoImport = config.GetBool("no-auto-import")
		}
		if !cmd.Flags().Changed("db") && dbPath == "" {
			dbPath = config.GetString("db")
		}
		if !cmd.Flags().Changed("actor") && actor == "" {
			actor = config.GetString("actor")
		}

		// Skip database initialization for commands that don't need a database
		if cmd.Name() == "init" || cmd.Name() == cmdDaemon || cmd.Name() == "help" || cmd.Name() == "version" || cmd.Name() == "quickstart" {
			return
		}

		// If sandbox mode is set, enable all sandbox flags
		if sandboxMode {
			noDaemon = true
			noAutoFlush = true
			noAutoImport = true
		}

		// 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() == cmdImport && 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() == cmdImport && 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, viper (env), or default
		// Priority: --actor flag > viper (config + BD_ACTOR env) > USER env > "unknown"
		// Note: Viper handles BD_ACTOR automatically via AutomaticEnv()
		if actor == "" {
			// Viper already populated from config file or BD_ACTOR env
			// Fall back to USER env if still empty
			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 == statusHealthy {
					// Check version compatibility
					if !health.Compatible {
						if os.Getenv("BD_DEBUG") != "" {
							fmt.Fprintf(os.Stderr, "Debug: daemon version mismatch (daemon: %s, client: %s), restarting daemon\n",
								health.Version, Version)
						}
						client.Close()

						// Kill old daemon and restart with new version
						if restartDaemonForVersionMismatch() {
							// Retry connection after restart
							client, err = rpc.TryConnect(socketPath)
							if err == nil && client != nil {
								if dbPath != "" {
									absDBPath, _ := filepath.Abs(dbPath)
									client.SetDatabasePath(absDBPath)
								}
								health, healthErr = client.Health()
								if healthErr == nil && health.Status == statusHealthy {
									daemonClient = client
									daemonStatus.Mode = cmdDaemon
									daemonStatus.Connected = true
									daemonStatus.Degraded = false
									daemonStatus.Health = health.Status
									if os.Getenv("BD_DEBUG") != "" {
										fmt.Fprintf(os.Stderr, "Debug: connected to restarted daemon (version: %s)\n", health.Version)
									}
									warnWorktreeDaemon(dbPath)
									return
								}
							}
						}
						// If restart failed, fall through to direct mode
						daemonStatus.FallbackReason = FallbackHealthFailed
						daemonStatus.Detail = fmt.Sprintf("version mismatch (daemon: %s, client: %s) and restart failed",
							health.Version, Version)
					} else {
						// Daemon is healthy and compatible - use it
						daemonClient = client
						daemonStatus.Mode = cmdDaemon
						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)
						}
						// Warn if using daemon with git worktrees
						warnWorktreeDaemon(dbPath)
						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 == statusHealthy {
							daemonClient = client
							daemonStatus.Mode = cmdDaemon
							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)
							}
							// Warn if using daemon with git worktrees
							warnWorktreeDaemon(dbPath)
							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 config file or BEADS_FLUSH_DEBOUNCE env var (e.g., "500ms", "10s")
// Defaults to 5 seconds if not set or invalid
func getDebounceDuration() time.Duration {
	duration := config.GetDuration("flush-debounce")
	if duration == 0 {
		// If parsing failed, use default
		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
	}

	// Use viper to read from config file or BEADS_AUTO_START_DAEMON env var
	// Viper handles BEADS_AUTO_START_DAEMON automatically via BindEnv
	return config.GetBool("auto-start-daemon") // Defaults to true
}

// shouldUseGlobalDaemon determines if global daemon should be preferred
// based on heuristics (multi-repo detection)
// Note: Global daemon is deprecated; this always returns false for now
func shouldUseGlobalDaemon() bool {
	// Global daemon support is deprecated
	// Always use local daemon (per-project .beads/ socket)
	// Previously supported BEADS_PREFER_GLOBAL_DAEMON env var, but global
	// daemon has issues with multi-workspace git workflows
	return false
}

// restartDaemonForVersionMismatch stops the old daemon and starts a new one
// Returns true if restart was successful
func restartDaemonForVersionMismatch() bool {
	// Use local daemon (global is deprecated)
	pidFile, err := getPIDFilePath(false)
	if err != nil {
		if os.Getenv("BD_DEBUG") != "" {
			fmt.Fprintf(os.Stderr, "Debug: failed to get PID file path: %v\n", err)
		}
		return false
	}

	socketPath := getSocketPath()

	// Check if daemon is running and stop it
	forcedKill := false
	if isRunning, pid := isDaemonRunning(pidFile); isRunning {
		if os.Getenv("BD_DEBUG") != "" {
			fmt.Fprintf(os.Stderr, "Debug: stopping old daemon (PID %d)\n", pid)
		}

		process, err := os.FindProcess(pid)
		if err != nil {
			if os.Getenv("BD_DEBUG") != "" {
				fmt.Fprintf(os.Stderr, "Debug: failed to find process: %v\n", err)
			}
			return false
		}

		// Send stop signal
		if err := sendStopSignal(process); err != nil {
			if os.Getenv("BD_DEBUG") != "" {
				fmt.Fprintf(os.Stderr, "Debug: failed to signal daemon: %v\n", err)
			}
			return false
		}

		// Wait for daemon to stop (up to 5 seconds)
		for i := 0; i < 50; i++ {
			time.Sleep(100 * time.Millisecond)
			if isRunning, _ := isDaemonRunning(pidFile); !isRunning {
				if os.Getenv("BD_DEBUG") != "" {
					fmt.Fprintf(os.Stderr, "Debug: old daemon stopped successfully\n")
				}
				break
			}
		}

		// Force kill if still running
		if isRunning, _ := isDaemonRunning(pidFile); isRunning {
			if os.Getenv("BD_DEBUG") != "" {
				fmt.Fprintf(os.Stderr, "Debug: force killing old daemon\n")
			}
			_ = process.Kill()
			forcedKill = true
		}
	}

	// Clean up stale socket and PID file after force kill or if not running
	if forcedKill || !isDaemonRunningQuiet(pidFile) {
		_ = os.Remove(socketPath)
		_ = os.Remove(pidFile)
	}

	// Start new daemon with current binary version
	exe, err := os.Executable()
	if err != nil {
		if os.Getenv("BD_DEBUG") != "" {
			fmt.Fprintf(os.Stderr, "Debug: failed to get executable path: %v\n", err)
		}
		return false
	}

	args := []string{"daemon"}
	cmd := exec.Command(exe, args...)
	cmd.Env = append(os.Environ(), "BD_DAEMON_FOREGROUND=1")

	// Set working directory to database directory so daemon finds correct DB
	if dbPath != "" {
		cmd.Dir = filepath.Dir(dbPath)
	}

	configureDaemonProcess(cmd)

	devNull, err := os.OpenFile(os.DevNull, os.O_RDWR, 0)
	if err == nil {
		cmd.Stdin = devNull
		cmd.Stdout = devNull
		cmd.Stderr = devNull
		defer devNull.Close()
	}

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

	// Reap the process to avoid zombies
	go func() { _ = cmd.Wait() }()

	// Wait for daemon to be ready using shared helper
	if waitForSocketReadiness(socketPath, 5*time.Second) {
		if os.Getenv("BD_DEBUG") != "" {
			fmt.Fprintf(os.Stderr, "Debug: new daemon started successfully\n")
		}
		return true
	}

	if os.Getenv("BD_DEBUG") != "" {
		fmt.Fprintf(os.Stderr, "Debug: new daemon failed to become ready\n")
	}
	return false
}

// isDaemonRunningQuiet checks if daemon is running without output
func isDaemonRunningQuiet(pidFile string) bool {
	isRunning, _ := isDaemonRunning(pidFile)
	return isRunning
}

// 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 func() { _ = 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 func() { _ = 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
//
//nolint:unparam // timeout is configurable even though current callers use 5s
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
	sandboxMode  bool
)

func init() {
	// Initialize viper configuration
	if err := config.Initialize(); err != nil {
		fmt.Fprintf(os.Stderr, "Warning: failed to initialize config: %v\n", err)
	}

	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")
	rootCmd.PersistentFlags().BoolVar(&sandboxMode, "sandbox", false, "Sandbox mode: disables daemon and auto-sync (equivalent to --no-daemon --no-auto-flush --no-auto-import)")
}

// 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
		// Get title from flag or positional argument
		titleFlag, _ := cmd.Flags().GetString("title")
		var title string

		if len(args) > 0 && titleFlag != "" {
			// Both provided - check if they match
			if args[0] != titleFlag {
				fmt.Fprintf(os.Stderr, "Error: cannot specify different titles as both positional argument and --title flag\n")
				fmt.Fprintf(os.Stderr, "  Positional: %q\n", args[0])
				fmt.Fprintf(os.Stderr, "  --title:    %q\n", titleFlag)
				os.Exit(1)
			}
			title = args[0] // They're the same, use either
		} else if len(args) > 0 {
			title = args[0]
		} else if titleFlag != "" {
			title = titleFlag
		} else {
			fmt.Fprintf(os.Stderr, "Error: title required (or use --file to create from markdown)\n")
			os.Exit(1)
		}
		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().String("title", "", "Issue title (alternative to positional argument)")
	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 := ""
					switch issue.CompactionLevel {
					case 1:
						tierEmoji = " 🗜️"
						statusSuffix = " (compacted L1)"
					case 2:
						tierEmoji = " 📦"
						statusSuffix = " (compacted L2)"
					}

					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 := ""
			switch issue.CompactionLevel {
			case 1:
				tierEmoji = " 🗜️"
				statusSuffix = " (compacted L1)"
			case 2:
				tierEmoji = " 📦"
				statusSuffix = " (compacted L2)"
			}

			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("description") {
			description, _ := cmd.Flags().GetString("description")
			updates["description"] = description
		}
		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 description, ok := updates["description"].(string); ok {
					updateArgs.Description = &description
				}
				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().StringP("description", "d", "", "Issue description")
	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)
	}
}