In my experience, it's important to architect early an not be afraid of tearing everything down and rewriting it (most of it can be reused). The structure of a

In my experience, it's important to architect early an not be afraid of tearing everything down and rewriting it (most of it can be reused). The structure of a program gets really bad when you continue to pile more and more code on a bad architecture. Refactor early, refactor often - get to the point where you are comfortable with modifying large chunks. Of course that means you have enough test frameworks at every level. Matlab as a language itself is more of a laboratory language, convenient for playing with math and quickly prototyping things. As a language that can scale to dozens of thousands of lines, it is poorly suited. You definitely need a senior programmer in your team, else it will soon turn into a nightmare.