Hey srdan and welcome to the fife community.
The generation of the swig wrappers is built into the SCons build system. The SCons build script can optionally only build the swig wrappers if you tell it to.
So if you don't want to rebuild all of FIFE and just want to generate the SWIG wrappers you would do this:
command line: scons fife-swig
On windows there is also a file update_swig_wrappers.bat which does exactly this.
However this command only generates python bindings as that is all FIFE officially supports.
If you want to attempt generating bindings in another language you will need to look here:https://github.com/fifengine/fifengine/blob/master/engine/SConscript#L253
Here is the code:
pythonext = env.PythonExtensions(target = [os.path.join('swigwrappers', 'python' ,'fife_wrap.cc'),
os.path.join('swigwrappers', 'python' ,'fife_wrap.h'),
os.path.join('python', 'fife', 'fife.py')],
source = os.path.join('swigwrappers', 'python' ,'fife.i'),
SWIGFLAGS=['-python','-c++','-w511', '-w473', '-w404'],
The important parts are the swig flags that are being passed and the files fife.i. You could try taking this code and changing -python to -java and maybe a couple other changes to see if you can get the correct swig call to generate java bindings.