autogen.sh: run git commands in the (potentially) git dir

If the build dir is outside of the git dir, the order matters :)

Signed-off-by: Eric Engestrom <eric.engestrom@imgtec.com>
Reviewed-by: Chad Versace <chadversary@chromium.org>
Reviewed-by: Emil Velikov <emil.velikov@collabora.com>