If you have a lot of mutations in your SQLite3 database the file size of the db file will increase a lot over time.
This can be annoying, so you’ll need to clean up old indices and other cruft that’s making your db heavy.
The solution is über-easy:
$ sqlite3 mystuff.db SQLite version 188.8.131.52 sqlite> VACUUM; sqlite> .quit
Note that you need to use capitals here. This will clean your db file and reduce its file size dramatically (depending on the amount of cruft you have, of course).