To load a resource from your deployed bundle, you can do the following (the resource to load needs to be included in your build.properties binary build setup):
Bundle bundle = YourBundleActivator.getDefault().getBundle();
IPath path = new Path("rules/setup.txt");
URL setupUrl = FileLocator.find(bundle, path, Collections.EMPTY_MAP);
File setupFile = new File(FileLocator.toFileURL(setupUrl).toURI());
Note that this is different from getting something from the workspace, as when your bundle is running, finding something in the workspace will refer to the runtime workspace, not the development workspace. If you do want something from the runtime workspace, you can access it like this:
IWorkspaceRoot root = ResourcesPlugin.getWorkspace().getRoot();
IResource resourceInRuntimeWorkspace = root.findMember("rules/setup.txt");
File file = new File(resourceInRuntimeWorkspace.getLocationURI());