Remove %GIT_DIR% before calling git.exe

This fixes diff nested submodule failure

Signed-off-by: Sup Yut Sum <ch3cooli@gmail.com>
Fix FF rebase failure (regression of 59b422d3dae39b681fd82a6e4bd356a016eed7c3)

Signed-off-by: Sup Yut Sum <ch3cooli@gmail.com>