diff --git a/.beads/config.yaml b/.beads/config.yaml
index dabc20c1..dc1e19ed 100644
--- a/.beads/config.yaml
+++ b/.beads/config.yaml
@@ -6,7 +6,7 @@
 # Issue prefix for this repository (used by bd init)
 # If not set, bd init will auto-detect from directory name
 # Example: issue-prefix: "myproject" creates issues like "myproject-1", "myproject-2", etc.
-# issue-prefix: ""
+issue-prefix: "bd"
 
 # Use no-db mode: load from JSONL, no SQLite, write back after each command
 # When true, bd will use .beads/issues.jsonl as the source of truth
diff --git a/cmd/bd/clean.go b/cmd/bd/clean.go
new file mode 100644
index 00000000..f7bfc18b
--- /dev/null
+++ b/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)
+}
diff --git a/cmd/bd/merge.go b/cmd/bd/merge.go
index 7db900f9..ddc0415d 100644
--- a/cmd/bd/merge.go
+++ b/cmd/bd/merge.go
@@ -3,6 +3,9 @@ package main
 import (
 	"fmt"
 	"os"
+	"os/exec"
+	"path/filepath"
+	"strings"
 
 	"github.com/spf13/cobra"
 	"github.com/steveyegge/beads/internal/merge"
@@ -45,10 +48,15 @@ Vendored into bd with permission.`,
 		leftPath := args[2]
 		rightPath := args[3]
 
+		// Ensure cleanup runs after merge completes
+		defer func() {
+			cleanupMergeArtifacts(outputPath, debugMerge)
+		}()
+
 		err := merge.Merge3Way(outputPath, basePath, leftPath, rightPath, debugMerge)
 		if err != nil {
 			// Check if error is due to conflicts
-			if err.Error() == fmt.Sprintf("merge completed with %d conflicts", 1) || 
+			if err.Error() == fmt.Sprintf("merge completed with %d conflicts", 1) ||
 			   err.Error() == fmt.Sprintf("merge completed with %d conflicts", 2) ||
 			   err.Error()[:len("merge completed with")] == "merge completed with" {
 				// Conflicts present - exit with 1 (standard for merge drivers)
@@ -63,6 +71,61 @@ Vendored into bd with permission.`,
 	},
 }
 
+func cleanupMergeArtifacts(outputPath string, debug bool) {
+	// Determine the .beads directory from the output path
+	// outputPath is typically .beads/beads.jsonl
+	beadsDir := filepath.Dir(outputPath)
+
+	if debug {
+		fmt.Fprintf(os.Stderr, "=== CLEANUP ===\n")
+		fmt.Fprintf(os.Stderr, "Cleaning up artifacts in: %s\n", beadsDir)
+	}
+
+	// 1. Find and remove any files with "backup" in the name
+	entries, err := os.ReadDir(beadsDir)
+	if err != nil {
+		if debug {
+			fmt.Fprintf(os.Stderr, "Warning: failed to read directory for cleanup: %v\n", err)
+		}
+		return
+	}
+
+	for _, entry := range entries {
+		if entry.IsDir() {
+			continue
+		}
+		if strings.Contains(strings.ToLower(entry.Name()), "backup") {
+			fullPath := filepath.Join(beadsDir, entry.Name())
+
+			// Try to git rm if tracked
+			gitRmCmd := exec.Command("git", "rm", "-f", "--quiet", fullPath)
+			gitRmCmd.Dir = filepath.Dir(beadsDir)
+			_ = gitRmCmd.Run() // Ignore errors, file may not be tracked
+
+			// Also remove from filesystem if git rm didn't work
+			if err := os.Remove(fullPath); err == nil {
+				if debug {
+					fmt.Fprintf(os.Stderr, "Removed backup file: %s\n", entry.Name())
+				}
+			}
+		}
+	}
+
+	// 2. Run git clean -f in .beads/ directory to remove untracked files
+	cleanCmd := exec.Command("git", "clean", "-f")
+	cleanCmd.Dir = beadsDir
+	if debug {
+		cleanCmd.Stderr = os.Stderr
+		cleanCmd.Stdout = os.Stderr
+		fmt.Fprintf(os.Stderr, "Running: git clean -f in %s\n", beadsDir)
+	}
+	_ = cleanCmd.Run() // Ignore errors, git clean may fail in some contexts
+
+	if debug {
+		fmt.Fprintf(os.Stderr, "Cleanup complete\n\n")
+	}
+}
+
 func init() {
 	mergeCmd.Flags().BoolVar(&debugMerge, "debug", false, "Enable debug output to stderr")
 	rootCmd.AddCommand(mergeCmd)