Scientific software in C++ to be modified

I am a scientific researcher, and I have inherited a C++ software for some specialistic data analysis. The program performs the analysis itself fine (could be optimised, but this is not the point now). What I would ask you is to completely remove the GUI part and make the program usable by command line. Ideally, the input should be fetched from a web form and fed into the program (the web interface will be developed afterwards). I have the original source code, some examples, a scientific publication describing how it works (paper attached), and the static compiled executables. I will need a very well commented source which can be easily integrate with the web interface. Moreover, the program is currently written in Microsoft C++, and should be converted in Unix C++. Shall we discuss about it?