Funnily enough the proliferation of those scripting languages has made it easier to get a picture of what's going on if you do get rooted by the consequences of running a flakey C app. In the old days the md5 binary would be broken and you were pretty much screwed if the other guy was good. But these days you can hammer out manual md5 algorithms and do other stuff using perl, python, and anything else at your disposal - things that are deployed by default on contemporary unix distributions. Better still, if you've got a book on unix systems calls you can absolutely fly through troubleshooting techniques that weren't practical before. (Sure the bad guys could just delete your VMs, but then that is a clear sign that the system has had it - and that signal is useful in and of itself - one of the difficult things in a situation like that is making a call on how far gone your system is so you can set short-term priorities in the lead up to rebuilding everything)
