Add 'bd clean' command to remove temporary merge artifacts

This command cleans up temporary files created during git merges by reading
patterns directly from .beads/.gitignore (Merge artifacts section).

Files removed:
- 3-way merge snapshots (beads.base.jsonl, beads.left.jsonl, beads.right.jsonl)
- Merge metadata (*.meta.json)
- Git merge driver temp files (*.json[0-9], *.jsonl[0-9])

Files preserved:
- beads.jsonl (source of truth)
- beads.db (SQLite database)
- metadata.json, config.yaml
- All daemon files

Usage:
  bd clean           # Clean up temporary files
  bd clean --dry-run # Preview what would be deleted

Implementation:
- Reads patterns from .beads/.gitignore instead of hardcoding them
- No --force flag needed - just runs by default
- Only cleans truly temporary merge artifacts, never the database

Also:
- Restored beads.jsonl to 538 issues from commit 6cd3a32
- Set issue-prefix to "bd" in config.yaml

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

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

cmd/bd/clean.go

@@ -0,0 +1,161 @@
+package main
+
+import (
+	"bufio"
+	"fmt"
+	"os"
+	"path/filepath"
+	"strings"
+
+	"github.com/fatih/color"
+	"github.com/spf13/cobra"
+)
+
+var cleanCmd = &cobra.Command{
+	Use:   "clean",
+	Short: "Clean up temporary beads artifacts",
+	Long: `Delete temporary beads artifacts to clean up after git operations.
+
+This removes temporary files created during git merges and conflicts from the
+.beads directory.
+
+Files removed:
+- 3-way merge snapshots (beads.base.jsonl, beads.left.jsonl, beads.right.jsonl)
+- Merge metadata (*.meta.json)
+- Git merge driver temp files (*.json[0-9], *.jsonl[0-9])
+
+Files preserved:
+- beads.jsonl (source of truth)
+- beads.db (SQLite database)
+- metadata.json
+- config.yaml
+- All daemon files
+
+EXAMPLES:
+Clean up temporary files:
+  bd clean
+
+Preview what would be deleted:
+  bd clean --dry-run`,
+	Run: func(cmd *cobra.Command, args []string) {
+		dryRun, _ := cmd.Flags().GetBool("dry-run")
+
+		// Find beads directory
+		beadsDir := findBeadsDir()
+		if beadsDir == "" {
+			fmt.Fprintf(os.Stderr, "Error: .beads directory not found\n")
+			os.Exit(1)
+		}
+
+		// Read patterns from .beads/.gitignore (only merge artifacts section)
+		cleanPatterns, err := readMergeArtifactPatterns(beadsDir)
+		if err != nil {
+			fmt.Fprintf(os.Stderr, "Error reading .gitignore: %v\n", err)
+			os.Exit(1)
+		}
+
+		// Collect files to delete
+		var filesToDelete []string
+		for _, pattern := range cleanPatterns {
+			matches, err := filepath.Glob(filepath.Join(beadsDir, pattern))
+			if err != nil {
+				fmt.Fprintf(os.Stderr, "Warning: error matching pattern %s: %v\n", pattern, err)
+				continue
+			}
+			filesToDelete = append(filesToDelete, matches...)
+		}
+
+		if len(filesToDelete) == 0 {
+			fmt.Println("Nothing to clean - all artifacts already removed")
+			return
+		}
+
+		// Just run by default, no --force needed
+
+		if dryRun {
+			fmt.Println(color.YellowString("DRY RUN - no changes will be made"))
+		}
+		fmt.Printf("Found %d file(s) to clean:\n", len(filesToDelete))
+		for _, file := range filesToDelete {
+			relPath, err := filepath.Rel(beadsDir, file)
+			if err != nil {
+				relPath = file
+			}
+			fmt.Printf("  %s\n", relPath)
+		}
+
+		if dryRun {
+			return
+		}
+
+		// Actually delete the files
+		deletedCount := 0
+		errorCount := 0
+		for _, file := range filesToDelete {
+			if err := os.Remove(file); err != nil {
+				if !os.IsNotExist(err) {
+					relPath, _ := filepath.Rel(beadsDir, file)
+					fmt.Fprintf(os.Stderr, "Warning: failed to delete %s: %v\n", relPath, err)
+					errorCount++
+				}
+			} else {
+				deletedCount++
+			}
+		}
+
+		fmt.Printf("\nDeleted %d file(s)", deletedCount)
+		if errorCount > 0 {
+			fmt.Printf(" (%d error(s))", errorCount)
+		}
+		fmt.Println()
+	},
+}
+
+// readMergeArtifactPatterns reads the .beads/.gitignore file and extracts
+// patterns from the "Merge artifacts" section
+func readMergeArtifactPatterns(beadsDir string) ([]string, error) {
+	gitignorePath := filepath.Join(beadsDir, ".gitignore")
+	file, err := os.Open(gitignorePath)
+	if err != nil {
+		return nil, fmt.Errorf("failed to open .gitignore: %w", err)
+	}
+	defer file.Close()
+
+	var patterns []string
+	inMergeSection := false
+	scanner := bufio.NewScanner(file)
+
+	for scanner.Scan() {
+		line := strings.TrimSpace(scanner.Text())
+
+		// Look for the merge artifacts section
+		if strings.Contains(line, "Merge artifacts") {
+			inMergeSection = true
+			continue
+		}
+
+		// Stop at the next section (starts with #)
+		if inMergeSection && strings.HasPrefix(line, "#") {
+			break
+		}
+
+		// Collect patterns from merge section
+		if inMergeSection && line != "" && !strings.HasPrefix(line, "#") {
+			// Skip negation patterns (starting with !)
+			if !strings.HasPrefix(line, "!") {
+				patterns = append(patterns, line)
+			}
+		}
+	}
+
+	if err := scanner.Err(); err != nil {
+		return nil, fmt.Errorf("error reading .gitignore: %w", err)
+	}
+
+	return patterns, nil
+}
+
+func init() {
+	cleanCmd.Flags().Bool("dry-run", false, "Preview what would be deleted without making changes")
+	rootCmd.AddCommand(cleanCmd)
+}