> I'm not sure if there are CS programs out that start with a small project and then force the students to make massive changes to that project throughout the course of the year

I studied Software Engineering at Swinburne University in Melbourne Australia, and we did exactly that.

One subject was "Software Maintenance Project" where we took an existing code-base we didn't write (a front-end for laTex for our year, the CVS code base for the next year students) and continually made changes to it. Halfway through the course we had to deal with changing requirements. We were graded on the quality of our code and how well it fit the existing style etc., not how fast we did it.

We also did a full-year final year project with 16 of us where we created a BIG code base from scratch. We decided to use an iterative approach (our choice) and so over the year we ran 6 iterations continually building on what we'd already done.

We also did awesome courses like "Personal Software Process" to teach us discipline in how we personally approach writing code.

EDIT: Sometimes I post to HN "hire/resume" threads about my hire-ability and how I personally think I'm "better" than the average person who studied CS because of things like the above. Normally everyone disagrees and says as long as I can code, it doesn't matter that I studied Software Engineering and am a certified Engineer. It's for reasons like the above I still personally feel I'm stronger than the average CS grad.