Environment: EGit 188.8.131.52506240215-r on Windows 7
I can commit with Git bash and the pre-commit hook is invoked, but when I try to commit in EGit, the pre-commit hook is not invoked.
GIT hooks are nothing but scripts which are to be executed by /bin/sh. Which you cannot do since you are running on Windows OS and you don't have sh.exe.
Add the cygwin_root/bin to your PATH
Make sure you install GIT during the cygwin installation(Since git hook scripts will execute git commands)
Hope this will help