Nice implementation and it's nice that it has the same output as "dir". My only grep is that it can be somewhat slow when you're recursing through really dense file structures. This could be my file system or the fact the implementation is pure MATLAB, which is nicely portable, but it would be nice to parse sections out to an option mex file for extra speed.
I'm having difficulty seeing what advantage this gives me over calling depfun and then deleting the files in matlabroot from the result. depfun is already recursive, and it looks like you disable this feature then replace it with your own code to traverse the dependency tree. I'm wondering if I've missed something and whether there is some non-apparent advantage?
This is a fabulous tool. One "feature request" I would love to see is a favorites list. The recent list is great, but since it tracks every folder visited, it can fill up fast with the intermediate folders needed to navigate to your new destination. Given that I frequently need to shift between widely separated directories on network shares and local drives, having a favorites that I could just use to hop to at least the approximate location would be great!