@Yoav L--No "quick fix" for that. The save_matproj function saves matprojData.workingDir as "pwd"; even more complicated, each filename of the mfiles open in the editor is saved as a fully-qualified filename, so you'd have to deal with that issue, too.
One solution I can think of would be to add two additional input arguments: one would contain the portion of the absolute pathname that you want to ignore (e.g., '/home/kevin/myProjectsDir/'); the second would contain the string you'd want to replace that portion of the pathname with (e.g., '../../'). In the code, then, the substitution would change (for example) '/home/kevin/myProjectsDir/todaysProject/myNiceMfile.m' to '../../todaysProject/myNiceMfile.m'.
Another alternative would be to work on the level of the operating system. You could use symbolic links if you're running on a Unix/Mac system or the Microsoft equivalent, if such a thing exists in Windows.
Very useful submission!
I am trying to modify it a bit so it can handle relative paths, making it possible to switch projects on different computers from a shared folder (that might have a different absolute path). any suggestions for quick fixes?