Organisation of source files in the repository

[mlange05]

This issue was originally raised by @pmarguinaud in GPU adaptation additions. It pertains to the "Guidelines and recommendations" section. The original in-line comment was:

 >>PM: I think we should also discuss how source files are organized in the git repository;                                                                                                                                        
 in particular, having an arpifs/module directory with all the modules does not make                                                                                                                                               
 sense.<<