GitHub has an enterprise plan where you can run it behind your firewall.
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'with source code they could examine' you seemed to have skipped over?
Well, obviously it's not open source, but GH Enterprise is delivered as a running Ruby app, so you can take a look. Of course the TOS says you shouldn't read or reverse engineer or whatever.
But I know people fix bugs that GitHub won't fix in their enterprise product by patching the Ruby source after each new update.