For build information and dependencies have a look in Build.md.
User manual and developer documentation can be found in the DOC folder, for how to make the files, refer to Build.md.
Shared code is located in COMMON, the relativistic code is under NEO-2-PAR and the multispecies version under NEO-2-QL. Also there are folders for cmake-/octave-/python-/shell-scripts.
Contains all code that is shared, or at least not specific for one code. Contains also other files that are shared, e.g. ProjectConfig.cmake.in and cmake_version.f90.in.