Add cygwin support to init-repository.

Git submodule works only with cygwin on Windows. MSys Git has
problems with long paths. So matchesOS needs to identify
cygwin environment as Windows to get the right submodules.

Change-Id: Ie7acfaa4d1ef3d891710a39651049c4e5a9f3570
Reviewed-by: Andras Becsi <andras.becsi@digia.com>