git repositories checkout into main tree

GetComponents should only use 'repos' for git clones if it has to, i.e., if the thorn/arrangement is deeper within the repository. If the repository only contains one thorn, and that thorn is what should be checked out, then we should check it out directly into its arrangement. Also, if we are going to have arrangement-repos in the future, these should also be checked out directly into the main tree. We need to figure out how to teach this to GetComponents, while still telling Cactus about all the contained thorns it should build.

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