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JGit uses the system property user.home, but this is different from where Git for Windows (aka msysgit) thinks it is. I.e. JGit will read the "global" configuration file from my directory in C:/Documents and Settings, but my $HOME in msys bash is on a network share. In cygwin it is in the same location as Java thinks it is. We have some logic to detect Win32 with cygwin vs not, but there is a problem. When eclipse is launched neither cygwin or msys git is not necessariliy in the PATH, even when they are used extensively by a user. Suggestions? See also Bug 333216, which struggles with how to find which git's installation to reference for the system wide git configuration file. The problem is not exactly the same, though.
Correction. My cygwin's HOME points to the same place as msys' HOME, but cygwin uses a UNC path instead.
There is an open bug at Sun relating to user.home http://bugs.sun.com/view_bug.do?bug_id=4787931 Not that I expect it to be fixed, but there are some suggestions that I think wil work for us.
http://egit.eclipse.org/r/2237
Merged Robin's change.
