Here is a thought for Evgeni.
When we save Chameleon we are really backing up two different aspects that can be at dissonance.
2) data - programs loading, configs
e.g If you do an OS or early image reinstall, you may end up with very different programs and want (1) but not (2). In other cases, you might want both.
Thus, the save should be split up into the components. As it is now it is hard to save the settings without also getting the program data that you often might not want.
(This is off the top of my head, so if I am wrong on this, correct away.)