I'm curious about in what way your scratchbox setup is getting ***ed up? Is it the scratchbox installation itself? If so, what kind of actions causes this? I haven't had any such issues myself (note I'm on pre-fremantle scratchbox). As for applications or software I'm working on, I'm using GIT to keep track of versions, problems and roll-backs. I access the scratchbox user area from my host login (using the host GIT), I only use the scratchbox login to do the actual builds (and any apt-get commands). This way I can also clone the code I'm working on to somewhere else.