Did you consider SQLite for this?
Keeping each database outside of the filesystem also gives us the flexibility to let people access the same database across multiple repls in the future.
I have lots of love for SQLite; early prototypes of Database were backed by it!
I've been figuring out how to run backups recently and grabbing a copy of the file isn't enough - you need to be sure there are no transactions going on, so you need to use the SQLite backup API or run VACUUM INTO a separate copy, which then doubles the amount of disk space you need.