Fix bd-afd: Auto-fix metadata.json jsonl_export mismatch

## Summary

When metadata.json gets deleted (git clean, merge conflict, rebase), the
version tracking code auto-recreates it using DefaultConfig() which hardcoded
jsonl_export to 'issues.jsonl'. But many repos (including beads itself) use
'beads.jsonl', causing a mismatch between config and actual JSONL file.

## Changes

1. **bd doctor --fix auto-detection** (cmd/bd/doctor/fix/database_config.go)
   - New DatabaseConfig() fix function that auto-detects actual JSONL file
   - Prefers beads.jsonl over issues.jsonl (canonical name)
   - Skips backup files and merge artifacts
   - Wired into doctor.go applyFixes()

2. **Version tracking auto-detection** (cmd/bd/version_tracking.go)
   - trackBdVersion() now scans for existing JSONL files before defaulting
   - Prevents mismatches when metadata.json gets recreated
   - Added findActualJSONLFile() helper function

3. **Canonical default name** (internal/configfile/configfile.go)
   - DefaultConfig() changed from issues.jsonl to beads.jsonl
   - Aligns with canonical naming convention

4. **FindJSONLPath preference** (internal/beads/beads.go)
   - Now prefers beads.jsonl over issues.jsonl when scanning
   - Default changed from issues.jsonl to beads.jsonl

5. **Test coverage**
   - Added comprehensive tests for DatabaseConfig fix
   - Updated configfile tests for new default
   - Verified backup file skipping logic

## Testing

- All existing tests pass
- New tests verify auto-fix behavior
- Integration tested with simulated mismatches

Closes: bd-afd

cmd/bd/doctor.go

@@ -198,6 +198,8 @@ func applyFixes(result doctorResult) {
 			err = fix.MergeDriver(result.Path)
 		case "Sync Branch Config":
 			err = fix.SyncBranchConfig(result.Path)
+		case "Database Config":
+			err = fix.DatabaseConfig(result.Path)
 		default:
 			fmt.Printf("  ⚠ No automatic fix available for %s\n", check.Name)
 			fmt.Printf("  Manual fix: %s\n", check.Fix)

cmd/bd/doctor/fix/database_config.go

@@ -0,0 +1,164 @@
+package fix
+
+import (
+	"fmt"
+	"os"
+	"path/filepath"
+	"strings"
+
+	"github.com/steveyegge/beads/internal/configfile"
+)
+
+// DatabaseConfig auto-detects and fixes metadata.json database/JSONL config mismatches.
+// This fixes the issue where metadata.json gets recreated with wrong JSONL filename.
+//
+// bd-afd: bd doctor --fix should auto-fix metadata.json jsonl_export mismatch
+func DatabaseConfig(path string) error {
+	if err := validateBeadsWorkspace(path); err != nil {
+		return err
+	}
+
+	beadsDir := filepath.Join(path, ".beads")
+
+	// Load existing config
+	cfg, err := configfile.Load(beadsDir)
+	if err != nil {
+		return fmt.Errorf("failed to load config: %w", err)
+	}
+	if cfg == nil {
+		// No config exists - nothing to fix
+		return fmt.Errorf("no metadata.json found")
+	}
+
+	fixed := false
+
+	// Check if configured JSONL exists
+	if cfg.JSONLExport != "" {
+		jsonlPath := cfg.JSONLPath(beadsDir)
+		if _, err := os.Stat(jsonlPath); os.IsNotExist(err) {
+			// Config points to non-existent file - try to find actual JSONL
+			actualJSONL := findActualJSONLFile(beadsDir)
+			if actualJSONL != "" {
+				fmt.Printf("  Updating jsonl_export: %s → %s\n", cfg.JSONLExport, actualJSONL)
+				cfg.JSONLExport = actualJSONL
+				fixed = true
+			}
+		}
+	}
+
+	// Check if configured database exists
+	if cfg.Database != "" {
+		dbPath := cfg.DatabasePath(beadsDir)
+		if _, err := os.Stat(dbPath); os.IsNotExist(err) {
+			// Config points to non-existent file - try to find actual database
+			actualDB := findActualDBFile(beadsDir)
+			if actualDB != "" {
+				fmt.Printf("  Updating database: %s → %s\n", cfg.Database, actualDB)
+				cfg.Database = actualDB
+				fixed = true
+			}
+		}
+	}
+
+	if !fixed {
+		return fmt.Errorf("no configuration mismatches detected")
+	}
+
+	// Save updated config
+	if err := cfg.Save(beadsDir); err != nil {
+		return fmt.Errorf("failed to save config: %w", err)
+	}
+
+	return nil
+}
+
+// findActualJSONLFile scans .beads/ for the actual JSONL file in use.
+// Prefers beads.jsonl over issues.jsonl, skips backups and merge artifacts.
+func findActualJSONLFile(beadsDir string) string {
+	entries, err := os.ReadDir(beadsDir)
+	if err != nil {
+		return ""
+	}
+
+	var candidates []string
+	for _, entry := range entries {
+		if entry.IsDir() {
+			continue
+		}
+		name := entry.Name()
+
+		// Must end with .jsonl
+		if !strings.HasSuffix(name, ".jsonl") {
+			continue
+		}
+
+		// Skip merge artifacts and backups
+		lowerName := strings.ToLower(name)
+		if strings.Contains(lowerName, "backup") ||
+			strings.Contains(lowerName, ".orig") ||
+			strings.Contains(lowerName, ".bak") ||
+			strings.Contains(lowerName, "~") ||
+			strings.HasPrefix(lowerName, "backup_") {
+			continue
+		}
+
+		candidates = append(candidates, name)
+	}
+
+	if len(candidates) == 0 {
+		return ""
+	}
+
+	// Prefer beads.jsonl over issues.jsonl (canonical name)
+	for _, name := range candidates {
+		if name == "beads.jsonl" {
+			return name
+		}
+	}
+
+	// Fall back to first candidate
+	return candidates[0]
+}
+
+// findActualDBFile scans .beads/ for the actual database file in use.
+// Prefers beads.db (canonical name), skips backups and vc.db.
+func findActualDBFile(beadsDir string) string {
+	entries, err := os.ReadDir(beadsDir)
+	if err != nil {
+		return ""
+	}
+
+	var candidates []string
+	for _, entry := range entries {
+		if entry.IsDir() {
+			continue
+		}
+		name := entry.Name()
+
+		// Must end with .db
+		if !strings.HasSuffix(name, ".db") {
+			continue
+		}
+
+		// Skip backups and vc.db
+		if strings.Contains(name, "backup") || name == "vc.db" {
+			continue
+		}
+
+		candidates = append(candidates, name)
+	}
+
+	if len(candidates) == 0 {
+		return ""
+	}
+
+	// Prefer beads.db (canonical name)
+	for _, name := range candidates {
+		if name == "beads.db" {
+			return name
+		}
+	}
+
+	// Fall back to first candidate
+	return candidates[0]
+}

cmd/bd/doctor/fix/database_config_test.go

@@ -0,0 +1,124 @@
+package fix
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+
+	"github.com/steveyegge/beads/internal/configfile"
+)
+
+// TestDatabaseConfigFix_JSONLMismatch tests that DatabaseConfig fixes JSONL mismatches.
+// bd-afd: Verify auto-fix for metadata.json jsonl_export mismatch
+func TestDatabaseConfigFix_JSONLMismatch(t *testing.T) {
+	// Create temporary directory
+	tmpDir := t.TempDir()
+	beadsDir := filepath.Join(tmpDir, ".beads")
+	if err := os.Mkdir(beadsDir, 0755); err != nil {
+		t.Fatalf("Failed to create .beads dir: %v", err)
+	}
+
+	// Create beads.jsonl file (actual JSONL)
+	jsonlPath := filepath.Join(beadsDir, "beads.jsonl")
+	if err := os.WriteFile(jsonlPath, []byte(`{"id":"test-123"}`), 0644); err != nil {
+		t.Fatalf("Failed to create beads.jsonl: %v", err)
+	}
+
+	// Create metadata.json with wrong JSONL filename (issues.jsonl)
+	cfg := &configfile.Config{
+		Database:    "beads.db",
+		JSONLExport: "issues.jsonl", // Wrong - should be beads.jsonl
+	}
+	if err := cfg.Save(beadsDir); err != nil {
+		t.Fatalf("Failed to save config: %v", err)
+	}
+
+	// Run the fix
+	if err := DatabaseConfig(tmpDir); err != nil {
+		t.Fatalf("DatabaseConfig failed: %v", err)
+	}
+
+	// Verify the config was updated
+	updatedCfg, err := configfile.Load(beadsDir)
+	if err != nil {
+		t.Fatalf("Failed to load updated config: %v", err)
+	}
+
+	if updatedCfg.JSONLExport != "beads.jsonl" {
+		t.Errorf("Expected JSONLExport to be 'beads.jsonl', got %q", updatedCfg.JSONLExport)
+	}
+}
+
+// TestDatabaseConfigFix_PrefersBeadsJSONL tests that DatabaseConfig prefers beads.jsonl over issues.jsonl.
+func TestDatabaseConfigFix_PrefersBeadsJSONL(t *testing.T) {
+	// Create temporary directory
+	tmpDir := t.TempDir()
+	beadsDir := filepath.Join(tmpDir, ".beads")
+	if err := os.Mkdir(beadsDir, 0755); err != nil {
+		t.Fatalf("Failed to create .beads dir: %v", err)
+	}
+
+	// Create both beads.jsonl and issues.jsonl
+	beadsJSONL := filepath.Join(beadsDir, "beads.jsonl")
+	if err := os.WriteFile(beadsJSONL, []byte(`{"id":"test-123"}`), 0644); err != nil {
+		t.Fatalf("Failed to create beads.jsonl: %v", err)
+	}
+
+	issuesJSONL := filepath.Join(beadsDir, "issues.jsonl")
+	if err := os.WriteFile(issuesJSONL, []byte(`{"id":"test-456"}`), 0644); err != nil {
+		t.Fatalf("Failed to create issues.jsonl: %v", err)
+	}
+
+	// Create metadata.json with wrong JSONL filename (old.jsonl)
+	cfg := &configfile.Config{
+		Database:    "beads.db",
+		JSONLExport: "old.jsonl", // Wrong - should prefer beads.jsonl
+	}
+	if err := cfg.Save(beadsDir); err != nil {
+		t.Fatalf("Failed to save config: %v", err)
+	}
+
+	// Run the fix
+	if err := DatabaseConfig(tmpDir); err != nil {
+		t.Fatalf("DatabaseConfig failed: %v", err)
+	}
+
+	// Verify the config was updated to beads.jsonl (not issues.jsonl)
+	updatedCfg, err := configfile.Load(beadsDir)
+	if err != nil {
+		t.Fatalf("Failed to load updated config: %v", err)
+	}
+
+	if updatedCfg.JSONLExport != "beads.jsonl" {
+		t.Errorf("Expected JSONLExport to be 'beads.jsonl', got %q", updatedCfg.JSONLExport)
+	}
+}
+
+// TestFindActualJSONLFile_SkipsBackups tests that backup files are skipped.
+func TestFindActualJSONLFile_SkipsBackups(t *testing.T) {
+	// Create temporary directory
+	tmpDir := t.TempDir()
+
+	// Create beads.jsonl and various backup files
+	files := []string{
+		"beads.jsonl",
+		"beads.jsonl.backup",
+		"backup_beads.jsonl",
+		"beads.jsonl.orig",
+		"beads.jsonl.bak",
+		"beads.jsonl~",
+	}
+
+	for _, name := range files {
+		path := filepath.Join(tmpDir, name)
+		if err := os.WriteFile(path, []byte(`{"id":"test"}`), 0644); err != nil {
+			t.Fatalf("Failed to create %s: %v", name, err)
+		}
+	}
+
+	// findActualJSONLFile should return beads.jsonl (not backups)
+	result := findActualJSONLFile(tmpDir)
+	if result != "beads.jsonl" {
+		t.Errorf("Expected 'beads.jsonl', got %q", result)
+	}
+}

cmd/bd/doctor/legacy.go

@@ -252,7 +252,7 @@ func CheckDatabaseConfig(repoPath string) DoctorCheck {
 		Status:  "warning",
 		Message: "Configuration mismatch detected",
 		Detail:  strings.Join(issues, "\n  "),
-		Fix: "Update configuration in .beads/metadata.json:\n" +
+		Fix: "Run 'bd doctor --fix' to auto-detect and fix mismatches, or manually:\n" +
 			"  1. Check which files are actually being used\n" +
 			"  2. Update metadata.json to match the actual filenames\n" +
 			"  3. Or rename the files to match the configuration",

cmd/bd/version_tracking.go

@@ -4,6 +4,7 @@ import (
 	"context"
 	"fmt"
 	"os"
+	"strings"
 
 	"github.com/steveyegge/beads/internal/beads"
 	"github.com/steveyegge/beads/internal/configfile"
@@ -34,6 +35,13 @@ func trackBdVersion() {
 		// No config file yet - create one with current version
 		cfg = configfile.DefaultConfig()
 		cfg.LastBdVersion = Version
+
+		// bd-afd: Auto-detect actual JSONL file instead of using hardcoded default
+		// This prevents mismatches when metadata.json gets deleted (git clean, merge conflict, etc.)
+		if actualJSONL := findActualJSONLFile(beadsDir); actualJSONL != "" {
+			cfg.JSONLExport = actualJSONL
+		}
+
 		_ = cfg.Save(beadsDir) // Best effort
 		return
 	}
@@ -175,6 +183,57 @@ func findSubstring(haystack, needle string) int {
 	return -1
 }
 
+// findActualJSONLFile scans .beads/ for the actual JSONL file in use.
+// Prefers beads.jsonl over issues.jsonl, skips backups and merge artifacts.
+// Returns empty string if no JSONL file is found.
+//
+// bd-afd: Auto-detect JSONL file to prevent metadata.json mismatches
+func findActualJSONLFile(beadsDir string) string {
+	entries, err := os.ReadDir(beadsDir)
+	if err != nil {
+		return ""
+	}
+
+	var candidates []string
+	for _, entry := range entries {
+		if entry.IsDir() {
+			continue
+		}
+		name := entry.Name()
+
+		// Must end with .jsonl
+		if !strings.HasSuffix(name, ".jsonl") {
+			continue
+		}
+
+		// Skip merge artifacts and backups
+		lowerName := strings.ToLower(name)
+		if strings.Contains(lowerName, "backup") ||
+			strings.Contains(lowerName, ".orig") ||
+			strings.Contains(lowerName, ".bak") ||
+			strings.Contains(lowerName, "~") ||
+			strings.HasPrefix(lowerName, "backup_") {
+			continue
+		}
+
+		candidates = append(candidates, name)
+	}
+
+	if len(candidates) == 0 {
+		return ""
+	}
+
+	// Prefer beads.jsonl over issues.jsonl (canonical name)
+	for _, name := range candidates {
+		if name == "beads.jsonl" {
+			return name
+		}
+	}
+
+	// Fall back to first candidate (including issues.jsonl if present)
+	return candidates[0]
+}
+
 // autoMigrateOnVersionBump automatically migrates the database when CLI version changes.
 // This function is best-effort - failures are silent to avoid disrupting commands.
 // Called from PersistentPreRun after daemon check but before opening DB for main operation.