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"
 }