The simulation code itself is under the MEMPHYS_vis/MEMPHYS directory.
Here you will find the classes describing the detector construction (MEMPHYS/DetectorConstruction[.h,.cc]), the event action (MEMPHYS/EventAction[.h,.cc]), stepping action, primary generator, etc...
From this, MEMPHYS_vis initialises the simulation in the 'Geant4 traditional way of doing' in the MEMPHYS_vis/main class constructor. Someone familiar with Geant4 examples should not be lost here. (All the insh commands known by the program are declared also here).
Today the geometry is compiled, then to modify it, you have to change the code in MEMPHYS_vis/MEMPHYS and rebuild the application. But good part of the MEMPHYS classes have 'messengers' (Geant4 commands), and then a lot of customization could be done through them (in particular with the insh 'g4_apply_command' command) without having to rebuild the application.
Note that during the simulation initialisation, the files job_options.mac and init.g4m containing Geant4 commands are, if found, executed. They are searched in the user document directory and then in the internal resource directory of the application.