Have bare repositories in the tarballs
The tarballs for the dependencies (CTK, MITK etc) should store only the bare git repositories without the working copy. (The source files should not be there.)
In this way the files would be created by a git checkout after extracting the tarball. This solves the line ending problem on windows. Currently, on windows a git status shows that all files have been changed, because they have incorrect line endings, since they were checked out and targz-ed under Linux.
The size of the tarballs would also be smaller without the working copy.