"Checked into the database" versus "checked in to the database" [duplicate]
In this case, definitely write it as separate words, because the "in" is actually part of the idiom "checked in".
I think that's probably as close as you're gonna get to a rule of thumb: write into as one word, unless it's actually functioning as two different words - for example, if the "in" is part of an expression such as "checked in".
No, "into" does not require that the destination be a physical place. One can be brought into poverty, a relationship, a realisation ...
So I would definitely check code into Subversion.