1. I use KDevelop for an IDE. It integrates nicely with CMake projects.
2. You can run the simulation in debug mode and step through it. Basically, the engineering model controls the basic simulation strategy, calling all the other components to piece together a complete simulation.
There are also the diagrams in the API documentation, but those are cumbersome and way to detailed to be of any real use if you ask me.
For example, http://www.oofem.org/resources/doc/oofe … tatic.html
The inheritance diagrams are easy to grasp, but the collaboration diagram is not really useful at all. (In fact, I wonder if it's due to us not hiding the protected/private variables, so the collaboration diagram goes overboard)
The old programmers manual is quite dated, so I can't really recommend that one.
3. Newer MinGW or visual studio should both be able to do it, but I don't know for sure what Borek used.