Hi,
I don't normally use the supervisor so I am afraid can't be of help there. To answer your question regards which is which:
All cli.txt files are boundary conditions file. Note that this is different from the liquid boundaries file.
Geo is the geometry file which contains information about the mesh and bathymetry of your domain.
Absolutely invariably you need a geo and a boundary conditions file, steering file to run a computation.
A fortran file commonly named princi.f in tutorials is optional depending on what you need to do, i.e. simple constant straighforward computations can be done without it.
I am sure this is not all :) , so please come back with more questions and I will definitely help if I have the answers,
Good luck and welcome aboard
Zeinab