Question: Im looking to see if there are any pre-existing projects that do this.

Generally, I need something that will load in a c++ file and parse it and then based on a set of rules in script, transform it, say to add headers, reformat, or remove coding quirks for example, turning const int parameters in functions to int parameters, etc Or perhaps something that would generate a dom of some sorts based on the c++ file fed in that could be manipulated and written out again.

Are there any such projects/products out there free or commercial?

Answer: 
You can use the export function of subversion, this will allow you to export all files under version control, but also all files NOT under control. Both methods will skip the .svn folders.

You didn't mention your client, but Tortoise has the 'export unversioned files too' option.

See [here](http://svnbook.red-bean.com/en/1.0/re10.html) for commandline syntax
You can use an ftp client if it's support filters (exclude .svn folders, i.e FlashFXP).

Currently I'm using Nusphere PhpEd IDE's built in feature called "Smart upload", so it only updates changed files (with modified time changed).