The base directory of the project is only really used to build the website, the manual and the installer for the project. There is little to no sense in making this the base directory in eclipse as there is no java here. What I recommend is setting up two seperate projects in eclipse: one for the editor directory which is the editor properly and one for the classpath-alterer. You may not need to bother adding the classpath-alterer project as it is a simple shell only used to detect the jvm architecture and to load the correct version of the SWT library.
Both projects have the standard maven file directory structure, i.e. Java source code is in src/main/java. In order to build you will need to add the appropriate swt.jar to the build path. The maven eclipse:eclipse goal may work to generate the appropriate .classpath and .project files.
Once you've got the project building in eclipse, you can run the editor by adding a run configuration with the main class as sce.swt.SceneryConfigEditor. From there on it you should be able to build and try out your code.