fix: read operations no longer modify database file (GH#804)

Add SQLite read-only mode for commands that only query data (list, ready,
show, stats, blocked, count, search, graph, duplicates, comments, export).

Changes:
- Add NewReadOnly() and NewReadOnlyWithTimeout() to sqlite package
  - Opens with mode=ro to prevent any file writes
  - Skips WAL pragma, schema init, and migrations
  - Skips WAL checkpoint on Close()
- Update main.go to detect read-only commands and use appropriate opener
- Skip auto-migrate, FlushManager, and auto-import for read-only commands
- Add tests verifying file mtime is unchanged after read operations

This fixes the issue where file watchers (like beads-ui) would go into
infinite loops because bd list/show/ready modified the database file.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

cmd/bd/main.go

@@ -82,6 +82,30 @@ var (
 	quietFlag      bool // Suppress non-essential output
 )
 
+// readOnlyCommands lists commands that only read from the database.
+// These commands open SQLite in read-only mode to avoid modifying the
+// database file (which breaks file watchers). See GH#804.
+var readOnlyCommands = map[string]bool{
+	"list":       true,
+	"ready":      true,
+	"show":       true,
+	"stats":      true,
+	"blocked":    true,
+	"count":      true,
+	"search":     true,
+	"graph":      true,
+	"duplicates": true,
+	"comments":   true, // list comments (not add)
+	"export":     true, // export only reads
+}
+
+// isReadOnlyCommand returns true if the command only reads from the database.
+// This is used to open SQLite in read-only mode, preventing file modifications
+// that would trigger file watchers. See GH#804.
+func isReadOnlyCommand(cmdName string) bool {
+	return readOnlyCommands[cmdName]
+}
+
 func init() {
 	// Initialize viper configuration
 	if err := config.Initialize(); err != nil {
@@ -656,14 +680,33 @@ var rootCmd = &cobra.Command{
 			debug.Logf("using direct mode (reason: %s)", daemonStatus.FallbackReason)
 		}
 
+		// Check if this is a read-only command (GH#804)
+		// Read-only commands open SQLite in read-only mode to avoid modifying
+		// the database file (which breaks file watchers).
+		useReadOnly := isReadOnlyCommand(cmd.Name())
+
 		// Auto-migrate database on version bump
+		// Skip for read-only commands - they can't write anyway
 		// Do this AFTER daemon check but BEFORE opening database for main operation
 		// This ensures: 1) no daemon has DB open, 2) we don't open DB twice
-		autoMigrateOnVersionBump(dbPath)
+		if !useReadOnly {
+			autoMigrateOnVersionBump(dbPath)
+		}
 
 		// Fall back to direct storage access
 		var err error
-		store, err = sqlite.NewWithTimeout(rootCtx, dbPath, lockTimeout)
+		if useReadOnly {
+			// Read-only mode: prevents file modifications (GH#804)
+			store, err = sqlite.NewReadOnlyWithTimeout(rootCtx, dbPath, lockTimeout)
+			if err != nil {
+				// If read-only fails (e.g., DB doesn't exist), fall back to read-write
+				// This handles the case where user runs "bd list" before "bd init"
+				debug.Logf("read-only open failed, falling back to read-write: %v", err)
+				store, err = sqlite.NewWithTimeout(rootCtx, dbPath, lockTimeout)
+			}
+		} else {
+			store, err = sqlite.NewWithTimeout(rootCtx, dbPath, lockTimeout)
+		}
 		if err != nil {
 			// Check for fresh clone scenario
 			beadsDir := filepath.Dir(dbPath)
@@ -682,10 +725,11 @@ var rootCmd = &cobra.Command{
 		// Initialize flush manager (fixes race condition in auto-flush)
 		// Skip FlushManager creation in sandbox mode - no background goroutines needed
 		// (improves Windows exit behavior and container scenarios)
+		// Skip for read-only commands - they don't write anything (GH#804)
 		// For in-process test scenarios where commands run multiple times,
 		// we create a new manager each time. Shutdown() is idempotent so
 		// PostRun can safely shutdown whichever manager is active.
-		if !sandboxMode {
+		if !sandboxMode && !useReadOnly {
 			flushManager = NewFlushManager(autoFlushEnabled, getDebounceDuration())
 		}
 
@@ -703,7 +747,8 @@ var rootCmd = &cobra.Command{
 		// Skip for import command itself to avoid recursion
 		// Skip for delete command to prevent resurrection of deleted issues
 		// Skip if sync --dry-run to avoid modifying DB in dry-run mode
-		if cmd.Name() != "import" && cmd.Name() != "delete" && autoImportEnabled {
+		// Skip for read-only commands - they can't write anyway (GH#804)
+		if cmd.Name() != "import" && cmd.Name() != "delete" && autoImportEnabled && !useReadOnly {
 			// Check if this is sync command with --dry-run flag
 			if cmd.Name() == "sync" {
 				if dryRun, _ := cmd.Flags().GetBool("dry-run"); dryRun {