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I really don't know Jesse,
The permissions issue keeps coming up, but to me it seems a non-issue as there is a CLI command to issue the appropriate permissions to a user. The directory link being separate is a painful but known issue, and my solution should work in most every-day ways, as long as the symlinks aren't dangling within the repository tree itself.
We could possibly limit the types of NTFS symbolic links that would actually be embedded in a git database to relative links (or is that done already?). I'm quite happy to have 'That type of NTFS symbolic link is not supported' as a valid solution to anything that is outside of simple symbolic links.
Currently the biggest thing holding symlinks back from being complete is lack of support in MSYS itself - which might be solved by using MSYS2. I have worked around this in the tests by overriding various commands with shell functions that implement operations on symlinks via cmd.exe. The only current exception to this is tar, which I can't do much about.
I've just rebased my symlink branch onto pt/tentative-1.8.4 and am chasing down test failures.
The tests like to make the symlinks before creating directories, or to create dangling symlinks, which doesn't help my cause - but am working through it.
//.