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At some point you're probably going to say, “Hey, I understand what's going on, and I want to build my new game, Laser Cats, based on RTSimpleApp.” (or RT3DApp, etc)
Proton uses hundreds of files and it's a complete chore to attempt to create Windows, iOS, webOS, BBX, OSX, and Android projects/scripts from scratch.
So let me introduce you to my secret little friend I've used for the last ten years or so…
First, grab [http://www.codeproject.com/KB/cpp/vsrename.aspx|vsrename (Visual Studio Project Renamer)] - what it does is intelligently search and replace in file names and inside text file (it can figure out what is a text file or not) in an entire directory tree. Don't let the Visual Studio in the name fool you, it doesn't really care what files it works on.
Grab vsrename.exe and throw it somewhere in your path to get ready.
For this example, we'll assume you want to clone RTSimpleApp into your new app, LaserCats
Now, at this point you can open windows/lasercats.sln and build the game for windows and it should work. (Don't forget to rebuild your resources with media/build_media.bat )
But - one fault of vsrename is it doesn't change directories, and android does have a directory named the app name.. so you'll have to rename android/src/com/rtsoft/barebones to android/src/com/mycompany/lasercats.
There are probably other things you'll end up having to hand tweak as you build for each platform, feel free to add them here.
And there go, more or less ready to go. Keep in mind you can't move this project directory anywhere, you need to keep it in the same directory as proton's shared directory, as most of the scripts and tools use relative paths to minimize setup.
It IS possible to do directory checkout of your own svn located inside of your svn proton checkout btw - it's what I do for client projects, works like charm.