No, you cannot have two Git repositories exist in the same directory.
One reason for this is that each Git repo has a .git
subdirectory inside. If there are two repos in one directory, their .git
subdirectories will collide.
Another reason is that it's unclear what should happen if both repos contain a file at the same relative location.
You can have Git repos inside of other Git repos (see git help submodule
), but that's not quite what you're looking for.
You should probably look for an alternate solution for the higher-level problem to "compile the code properly." But if you're really stuck and out of easier ideas, you could consider making a directory of symbolic links which point to the required files in the two separate Git repos. That directory of links could even be checked in, either as a third repo or within one of the existing two.