A patent is not a way to put some kind of copyright on your software. As far as I know, there is no reason to include that much code in "any" patent application.
To answer your question, you should not add new matter to the non-provisional if you already know that matter. If you add anything substantial, all claims relating to the new matter will have the new priority date. So if you add the main part of the description later, you could have filed later with almost the same effect.
Try getting a more abstract patent. If you need 3500 lines of code to describe what you are protecting, then taking your code and from there getting around your claims will be easier than reinventing what you wrote and getting around your claims from there. So basically, you would be hurting yourself with that application and it would have no value.
Oh and do you really think any examiner will read and understand 3500 lines of code? Getting that patent would not involve much fun.