I often have many files open at the same time and it is very convenient to be able to switch between sets of files. matproj works well.
However, some days ago matproj caused me some trouble. This is what happened.
Background: I've used R2012a until recently. Matlab was first updated to R2012b, which I didn't use because of ribbon-phobia. Now, Matlab is updated to R2013a, which I use because some bugs are fixed.
Incident: Without too much thinking, I loaded an old "project" with matproj and I was instantly in trouble. The path to the R2013a installation was replaced by the path to R2012a. For me that was no big problem once I realized what had happened.
Proposal: Modify matproj so that it does not affect the path to Matlab proper.