Resources within projects are to be placed inside the resources directory of the project. To obtain a reference to the specific file one can use Core.getConfiguration().getResourcesPath().
E.g.: I've placed mysettings.properites inside /resources. Then I can obtain a File using:
File myFile = new File(Core.getConfiguration().getResourcesPath() + File.separator + "mysettings.properties");
From there you can also create a FileInputStream and read its contents.
Thanks Arjen. I solved it with a jar added to the userlib. In my case these were external DTDs and not property files, so it made sense to do that way. I will remember this approach when I want to load a file.