The standard way of compiling núcleo is to have it in one directory and to compile it in a separate one, which allows to compile for different platforms from the same source tree. You should also be able to compile it in the source tree, if you insist.
Assuming that the source code is in an existing directory ~/src/nucleo/ and you want to compile it in an existing directory ~/dst/, simply do the following:
cd ~/src/nucleo/
./build-utils/bootstrap # if the 'configure' script is not present already
cd ~/dst/
mkdir nucleo ; cd nucleo
~/src/nucleo/configure
make
su # if needed
make install
The trick with configure is that you might need to set appropriate values for CPPFLAGS, CXXFLAGS, LDFLAGS, LIBS or CXX. Try things like env CXX=CC ~/src/nucleo/configure.
Everything is installed in /usr/local by default. This can be changed by passing the --prefix=other_directory to configure. Try configure --help=recursive to get a list of all the other options supported.
Feel free to contact me (roussel@lri.fr) if you have any trouble. Just have a look at the config.log file first...