Great! You won't believe me but I discovered the --recursive flag only a few weeks ago. :-) Before, I was always running
git submodule init
git submodule update
Anyway, I've added it into README.rst, so it shows on the github main page. Hopefully that's visible enough. If you think there are even better places to mention this, just give a shout.
Oh, in case you plan to work on pyffi -...
Have you tried to do a recursive clone (doing so will get you all submodules automatically)?
git clone --recursive git://pyffi.git.sourceforge.net/gitroot/pyffi/pyffi
or (faster, github's connection is usually better)
git clone --recursive git://github.com/amorilia/pyffi.git
Just tested this, and both worked here, including the xml files.
Thanks for reporting. The import of your uploaded nif is fixed with this patch:
http://github.com/amorilia/blender_nif_scripts/commit/b1b408bc589e1db44fd3275be428391780d37c01
You can test the update using the installers here:
http://niftools.sourceforge.net/forum/viewtopic.php?f=13&t=2531&p=18445
If you would still find distorted imports, just keep reporting them.