Problem:
- Sync branch setup occurred before the config file was initialized
- Persistence only targeted the database, leading to loss on re-init
Solution:
- Reorder initialization to create the config file before sync setup
- Synchronize sync branch state to both config file and database
Impact:
- Settings are preserved across re-initialization and DB clears
- Better consistency between file and database state
Fixes: #927 (Bug 3)
362b07d74f