It's been years the problem exists because there isn't a portable way for eclipse or java to detect symlinks.
Now symlinks are very, very useful so regardless of the non portable reason, would it be possible from an eclipse plugin to fix this and not have Egit consider symlinks and everything under it to be new files?
We plan to implement in JGit using Java 7 (though there is no concrete timeline yet, contributions welcome), see [1], there is also a draft for a JNI based native implementation [2].
[1] https://bugs.eclipse.org/bugs/show_bug.cgi?id=354367 [2] https://git.eclipse.org/r/#/c/2125/
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