[Tainnor]

In the case of Java at least, what helps is that the IDE can decompile the code or, which is often even more helpful, download the source code and allow you to step through it while debugging, at least if a source JAR was published (which is pretty often the case).

In the case of non-compiled languages, of course you don't even need this step since all your libs exist in source form already, so it was pretty simple for me to step through Ruby library code with a simple debugger and no fancy IDE.

I have a habit of sometimes debugging even horribly abstract framework (e.g. Spring) code when I don't understand what it's doing. That's maybe not the most efficient method, but it does usually make me understand why thing X is not working the way I expected it to work.