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: 
I use [rsync](http://samba.org/rsync/) which is a fast command line tool which only sends the changed parts of files. You can set it up to exclude .svn directories as outlined [here](http://blog.gungfu.de/archives/2005/09/25/using-rsync-together-with-subversion/): 

If you wish to continue doing this with fileZilla you can go to View->Filename Filters and select to ignore SVN and CVS directories. You can also only upload changed files with FileZilla however I find rsync far faster. As rsync is command line based you could easily hook it up with Eclipse as an external tool to enable 1 click transferring
I stumbled recently on the same issue running Ubuntu 9.
In FileZilla you can choose ignore filters which contain even presets to prevent copying .svn folders and windows .thumb files! You can find this in the **View** menu under **Filename filters...** Works like a charm!

Thumbs up for the FileZilla folks!