As an RL aerospace engineer, one of the fundamental things we do is 'Change Control', which means that whenever the design of something is changed (the drawings), not only do we approve the changes amongst a peer group/approvers, we make sure we record the changes in such a way that we have recorded all previous designs as they are developed. The same principles work with software versioning. This got me thinking about how saved craft files work. Why not have an extra variable to the craft file called 'version' or 'issue' or something so that your "space-rover 1001", that needed more solar panels, can be revised keeping the initial version intact for later use. The save files could be done using the current format of .craft files and use a directory structure to save the versioning: i.e. 'space-rover 1001' would be saved in a folder called 'space-rover 1001' and the craft file be either saved in mutiple sub-folders (1,2,2.1,2.2 etc...) or have the issue appended to the filename. The big advantages to this are if you are developing a large and complex vessel and make a design error and then do lots of other work, then it can be rolled back without too much hassle. Other uses could be that you can roll back an existing design to use it for a different purpose (i.e. change a science ship to a fuel-tug, using the same staging) Just my thoughts on the matter... D.
