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/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]
+}