I agree with most of the comments about Matlab not being terribly supportive of modern software source code structuring but I don't believe it's too difficult to impose some of your own structure with a little discipline.
Organise your source files into a hierarchy of directories, as you would the source files for any program written in another programming language. You don't need to stick to a hierarchy, choose your own structure if you wish. Use the setpath command (or whatever the heck it is called) to tell Matlab where to look for your m files when you are working.
Acquaint yourself with the Matlab profiler tool which can give you call graphs (not terribly graphically, more like gprof's call graphs) which is some help in deciphering spaghetti code.
Of course, all our m files are in the repository and we serve them out of that. We keep a private toolbox on one of our networked drives and all users can call the 'released' code in that toolbox directly.
