Very useful tool!
However, in the latest version 20 Jun 2010, the maximum allowed m-file-name for class files (scripts and functions are ok) is 40 characters! For longer file names, fdep will produce an obscure error message:
In an assignment A(:) = B, the number of elements in A and B must be the same.
It took me some time to figure this out... Unfortunately I have no solution other than to use shorter class names at the moment. This does not seem to be related to depfun.