Not great, somebody else used my program and they got root on my server...
> I have no idea how anyone could keep the callgraph of even a minimal gui application in their head
Practice.Lots and lots of practice.
Write it down. Do things the hard way. Build the diagrams by hand and make sure you know what's going on. Trace programs. Pull out the debugger! Pull out the profiler!
If you do those things, you too will gain that skill. Obviously you can't do this for a giant program but it is all about the resolution of your call graph anyways.
If you are junior, this is the most important time to put in that work. You will get far more from it than you lose. If you're further along, well the second best time to plant a tree is today.