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What's the best way to manage such a thing!? Is their any type of hierarchy or structure the code should follow? Such as, how should the code be split-up, a seperate folder for each section of the engine (Audio, Network, etc.). When developing an engine, what is the best way to keep track of all the header files, and .cpp's, I hear CVS or SVN is good, is this true? Finally, what is the best way to release an engine (Freeware) to the public? Thankyyyyyy!
I can't help you about the code organization, but I can clear up a misconception.
CVS and SVN are source control systems. They help you keep track of the changes done over time to your source base, they allow you to go back to old versions of the source, they allow you to make cheap snapshots of the source, they help collaboration of several people. They do not help you organize your code.
But wouldn't that be a good thing? Code will change over the course of development, and an easy way to update will be good. I only want to use CVS or SVN because I want a backup of all my files, since I occasionally delete stuff in my folders and stuff. So would it make a good backup source?
Yes, using SVN is a very good idea. (Of course, you should regularly backup your repositories.)
I'm just saying that it doesn't help you organize your code into good blocks.