Improve documentation of project structure to ease onboarding of new contributors

[JuliaS92]

Is your feature request related to a problem? Please describe.
From the point of view of a new module developer I have some feedback on the documentation of the whole tool. It is currenlty rather laborious to find your way around the file structure, dependencies within the code base and how the data is handled and stored.

Describe the solution you'd like
Introduce a page to the documentation with a visual representation of the architecture of the tool. This should include the base classes used for ui and backend, how the data flows including where it is stored, where the skeleton code for proteobench ends and module specific code starts (e.g. the quant scores are proteobench wide as far as I understand?).

Additional context
I am currenlty trying to plan the implementation of my proposed module and rerunning of results files if the code changes and a visual representation of the data flow would be very helpful for that.

[mlocardpaulet]

Here is something that I dug up from old discussions :)

ProteoBench C, using common notation.pdf