I've setup the eclipse scout RT source in eclipse and all in compiling ok.
I would now like to be able to hack around at individual modules and deploy them to a runtime with my running Scout application. Is this possible? I think it maybe isn't because of the WAR packaging of all libraries?
If you have your Scout application and the Scout Runtime code in the same workspace, when you start your Scout application, Eclipse will use the compiled library (containing your modification). You will be able to debug (and to add additional System.out.println in the code to see what happens). This is exactly how I work, when I want to modify something in the Scout RT.
You can go one step further:
With Maven, you can build the runtime jars (mvn clean install in your clone of the repository). This will also build a p2 update site.
In your Eclipse containing your application, you can update the runtime libraries with the one you have built:
Help menu > Install new software: indicate this as update Site ("Work with" field):