I use a combination of (1) breakpoint debugging, finding the connection between program start and various features (2) Doxygen to generate a dependency graph

I use a combination of (1) breakpoint debugging, finding the connection between program start and various features (2) Doxygen to generate a dependency graph (3) create json performance profiles, manually instrumenting functions, and navigate traces using Google Chrome about://tracing or similar tools. (4) trace and look at the data input and output, using a hex editor or over the network using wireshark