Fix config version update in migrate command

- Save updated config with current version (fixes GH #193)
- Update version field when loading existing config
- Database version now stays in sync with binary version

Amp-Thread-ID: https://ampcode.com/threads/T-dfacc972-f6c8-4bb3-8997-faa079b5d070
Co-authored-by: Amp <amp@ampcode.com>

.beads/config.json

@@ -1,5 +1,5 @@
 {
   "database": "beads.db",
-  "version": "0.21.0",
+  "version": "0.21.3",
   "jsonl_export": "beads.jsonl"
 }

cmd/bd/migrate.go

@@ -440,6 +440,16 @@ This command:
 			}
 		}
 		
+		// Save updated config with current version (fixes GH #193)
+		if !dryRun {
+			if err := cfg.Save(beadsDir); err != nil {
+				if !jsonOutput {
+					color.Yellow("Warning: failed to update config.json version: %v\n", err)
+				}
+				// Don't fail migration if config save fails
+			}
+		}
+		
 		// Final status
 		if jsonOutput {
 			outputJSON(map[string]interface{}{
@@ -667,6 +677,9 @@ func loadOrCreateConfig(beadsDir string) (*configfile.Config, error) {
 	// Create default if no config exists
 	if cfg == nil {
 		cfg = configfile.DefaultConfig(Version)
+	} else {
+		// Update version field in existing config (fixes GH #193)
+		cfg.Version = Version
 	}
 	
 	return cfg, nil