Quentin,
I don't know if this will help you or not, but we install everything
in core in the SYSTEM domain, which requires these steps:
cd base
./configure --with-installation-domain=SYSTEM
make GNUSTEP_INSTALLATION_DOMAIN=SYSTEM install
cd ../gui
make GNUSTEP_INSTALLATION_DOMAIN=SYSTEM install
cd ../back
make GNUSTEP_INSTALLATION_DOMAIN=SYSTEM install
The ./configure step is only needed in base. If you have previously
installed things, you may need to do a 'make
GNUSTEP_INSTALLATION_DOMAIN=SYSTEM distclean' in each directory first.