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

internal/beads/beads.go

@@ -222,7 +222,7 @@ func FindBeadsDir() string {
 
 // FindJSONLPath returns the expected JSONL file path for the given database path.
 // It searches for existing *.jsonl files in the database directory and returns
-// the first one found, or defaults to "beads.jsonl".
+// the first one found, preferring beads.jsonl over issues.jsonl (bd-afd).
 //
 // This function does not create directories or files - it only discovers paths.
 // Use this when you need to know where bd stores its JSONL export.
@@ -238,12 +238,18 @@ func FindJSONLPath(dbPath string) string {
 	pattern := filepath.Join(dbDir, "*.jsonl")
 	matches, err := filepath.Glob(pattern)
 	if err == nil && len(matches) > 0 {
-		// Return the first .jsonl file found
+		// bd-afd: Prefer beads.jsonl over issues.jsonl (canonical name)
+		for _, match := range matches {
+			if filepath.Base(match) == "beads.jsonl" {
+				return match
+			}
+		}
+		// Return the first .jsonl file found if beads.jsonl not present
 		return matches[0]
 	}
 
-	// Default to issues.jsonl
-	return filepath.Join(dbDir, "issues.jsonl")
+	// bd-afd: Default to beads.jsonl (was issues.jsonl)
+	return filepath.Join(dbDir, "beads.jsonl")
 }
 
 // DatabaseInfo contains information about a discovered beads database

internal/configfile/configfile.go

@@ -18,7 +18,7 @@ type Config struct {
 func DefaultConfig() *Config {
 	return &Config{
 		Database:    "beads.db",
-		JSONLExport: "issues.jsonl",
+		JSONLExport: "beads.jsonl", // Default to canonical name (was issues.jsonl)
 	}
 }
 

internal/configfile/configfile_test.go

@@ -13,8 +13,9 @@ func TestDefaultConfig(t *testing.T) {
 		t.Errorf("Database = %q, want beads.db", cfg.Database)
 	}
 
-	if cfg.JSONLExport != "issues.jsonl" {
-		t.Errorf("JSONLExport = %q, want issues.jsonl", cfg.JSONLExport)
+	// bd-afd: Default changed from issues.jsonl to beads.jsonl (canonical name)
+	if cfg.JSONLExport != "beads.jsonl" {
+		t.Errorf("JSONLExport = %q, want beads.jsonl", cfg.JSONLExport)
 	}
 }