The Run Control Reference guide contains the documentation as it is generated out of the header files using docxx. It is recommended reading to understand the internals of the run control.
The following convention has been adopted for the code documentation: Interfaces are described in the header files, from which we generate the html documentation. In addition we describe for every process unit, what it does at the main state transition functions (initialise, download, start_run, end_run).
The code documentation in the source code files is rather short, but concentrates on giving explanations on what is done exactly and why and gives a few hints or caveats. In all cases, one should first read the documentation from the header files before dwelving into the source code.