From my question on StackOverflow (CC BY-SA 3.0):

How do you organize your Matlab code? I’ve come into ownership of several thousand lines of Matlab code, some as >900 line functions and a few directories full of function_name.m files. It’s hard to figure out what everything is doing (or relating to) or figure out the dependencies. I’d like to reorganize things as I figure out what does what, but Matlab limits what’s possible. What would you suggest?