One of the things you should acquaint yourself with if you enjoy using sqlite, is the without rowid feature. It reduced the many to many table's size by nearly 2.4 Gb in a 3 gb file that we have.
It also improved performance significantly, so uh, if you can use it, then you should :D
It is of note that this is only worthwhile in tables with a covering primary key, or a non integer primary key.
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