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".
english.stackexchange.com/users/1547/Marthaª
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.
english.stackexchange.com/users/547/Colin Fine
There's actually evidence for treating a case such as "check in/to SVN" as a kind of elliptical form of "check in into", when you consider the possible combinations when you turn the sentence round.
Compare the possibility of the following: Which repository did you check it into?
Which repository did you check it in into?
Into which repository did you check it in? with the impossibility of the following: *Into which repository did you check it?
*
To which repository did you check it in?
From this point of view, it seems a bit more logical to write "check (in) into", whether or not you include the second "in".
english.stackexchange.com/users/4941/Neil Coffey
I think both are definitely allowable.
You can treat the verb 'check in' separately from 'toSVN because there is a direct object possible, for example 'my code':
I checked in my code to SVN.
This shows that the 'in' and 'to' are separable.
You can use the preposition 'into' with 'check'.
SVN, and other abstract repositories, still have a semantic connotation of being a receptacle or having an interior.
Using the separability check: I checked my code into SVN.
This shows that SVN acts like it has an interior.
The verb 'to log in' acts similarly.
Which is preferred?
I find 'checked in to SVN' better than 'checked into SVN', because I tend to use 'checkin' more often.
Compare contrast with 'check out': I like 'check out my code' but 'check out of svn' (and despite appearances, 'out of' corresponds to 'into').
english.stackexchange.com/users/4972/Mitch
In the sense that your source can be said to reside inside of the repository, I would argue that "into" is the correct usage here.
Compare with the example at your linked site (the URL needs to be fixed, btw) with either turning something "in to " a person (but it's not going into the person), or putting something "into" something else.
english.stackexchange.com/users/8339/Ben Hocking
I would treat "check in" as a compound term, and so, check some code in to a repository, rather than checking code into a repository.
english.stackexchange.com/users/6067/Marcin
Possible Duplicate:  When should “into” be used rather than “in to,” and vice versa?     I was recently submitting ("checking in") some data to a database and composed an email to my team informing them of the submission. What's the proper grammar to use here:   The changes are checked into the database   or    The changes are checked in to the database   What's the rule of thumb for proper usage between the two? Is there even a difference?
"Checked into the database" versus "checked in to the database"
english.stackexchange.com
<grammar><word-choice>
english.stackexchange.com/questions/5219
english.stackexchange.com/users/2178/fbrereto
It is possible that both are acceptable or, at least, there is no agreement on the correct usage. However, some would argue that "in" is actually part of the idiom "checked in". The words "in" and "to" need to be written separately in this case. "Into" does not require to be a destination or place to be a physical place. It could be considered an elliptical form of "check in into". Treat "check in" as a compound term. 
It is possible that both are acceptable or, at least, there is no agreement on the correct usage. However, some would argue that "in" is actually part of the idiom "checked in".  I think both are definitely allowable, but in this case, definitely write it as separate words, because the "in" is actually part of the idiom "checked in".  
Both usages are allowed in this example. Some say to write it as separate words, because the "in" is actually part of the idiom "checked in".  However, in the sense that your source can be said to reside inside of the repository, some would argue that "into" is the correct usage here. It is possible that both are acceptable or, at least, there is no agreement on the correct usage.
The words "in" and "to" need to be written separately in this case. "Into" does not require to be a destination or place to be a physical place.  It could be considered an elliptical form of "check in into".  Treat "check in" as a compound term. 
 In this case, definitely write it as separate words, because the "in" is actually part of the idiom "checked in".   It seems a bit more logical to write "check (in) into", whether or not you include the second "in".  I think both are definitely allowable.   
It is possible that both are acceptable or, at least, there is no agreement on the correct usage.