Not using things like go to definition and any fancy tools, just manually forcing myself to work through files to understand how things fit together and using basic tools like grep
I use "go to definition"/"find references" to go all around the code base and at the same time try to figure out how each files interact with each others.
Pharo(Smalltalk) IDE is one of the best IDE I've ever used. It even has a feature where you give input object and output object and it tells you what messages you need to send to get from input to output.