I have git installed within cygwin and have set the windows path set to include the cygwin bin directory so I can use git within netbeans through cygwin. The issue I'm having with the git plugin is that when I checkout a project through cygwin and create the project in netbeans, it always seems to say that everything in my project has been changed. Maybe this is due to my own stupidity and I just need to check them out through netbeans. But it would seem as though it shouldn't come out with everything needing to be changed.