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JGit has active bugs where symlinks are not supported correctly.
Another bug is that our current NGit cannot do change detect when symlinks are involved. When we do comparisons involving modification dates or file sizes, the ngit repository reports the values for the symlink but NGit uses the regular System.IO apis which end up reporting the values for the target of the symlink. As these differ, symlinks always show up as being different.
The patch was landed to ngit master and is now merged into monodevelop