You do not need to actually load the Fiji source code into Eclipse (which is what the "Developing Fiji in Eclipse" article is about). Rather, you are trying to develop an external ImageJ plugin: the 3D RoiManager. I agree that it is convenient to create a Maven project for it, so that you can easily develop the project in Eclipse, pull in other dependencies, etc.
I suggest using this project as a starting point: https://github.com/imagej/minimal-ij1-plugin
For more information, see this page: http://fiji.sc/Maven