Cleanup dependent package if in root of repo

[mmcc007]

If a dependent package is found in the root of a repo during cloning, the '.git' directory should be removed in this package from the resulting cloned standalone app (otherwise it looks like a git submodule in the cloned standalone app).

Also, and not as important, since this parent package is a parent of the app being cloned (by definition), the sub-directory leading to the parent package should be deleted in the parent package in the resulting cloned standalone app.

Workaround is just to delete the .git directory and the related sub-directory manually from the related package in the resulting cloned standalone app.