// dslFile is a .dsl file (loading this resource works as expected)
	public static void generateCode(File dslFile) throws IOException {
		try {
			Injector injector = new MyDslStandaloneSetup().createInjectorAndDoEMFRegistration();
			
			XtextResourceSet resourceSet = injector.getInstance(XtextResourceSet.class);
			resourceSet.addLoadOption(XtextResource.OPTION_RESOLVE_ALL, Boolean.TRUE);
			
			File myDslRuntime = new File("MyDslRuntime.jar");
			// TODO: how to load resources from jar file???? a jar handler is not defined
			resourceSet.getResource(URI.createFileURI(myDslRuntime.getAbsolutePath()), true);
			
			
			File javaSourceFiles = new File("input-path/src");
			Arrays.stream(javaSourceFiles.listFiles()).filter(file -> file.isFile() && file.getName().endsWith(".java")).forEach(file -> {
				// TODO: how to load resources from java source file???? a .java handler is not defined
				resourceSet.getResource(URI.createFileURI(file.getAbsolutePath()), true);
			});
			
			XtextResource resource = (XtextResource) resourceSet.getResource(URI.createFileURI(source.getAbsolutePath()), true);
			
			// TODO: is there a better way to create a simple FSA?
			class FSA implements IFileSystemAccess {
				private File root;
				
				public FSA(File root) {
					this.root = root;
					this.root.mkdirs();
				}
				
				@Override
				public void generateFile(String fileName, CharSequence contents) {
					this.generateFile(fileName, null, contents);
				}

				@Override
				public void generateFile(String fileName, String outputConfigurationName, CharSequence contents) {
					File file = new File(root.getAbsolutePath() + File.separator + fileName);
					file.getParentFile().mkdirs();
					try {
						FileWriter fw = new FileWriter(file);
						fw.write(contents.toString());
						fw.close();
					} catch (Exception e) {
						throw new RuntimeException(e);
					}
				}

				@Override
				public void deleteFile(String fileName) {
					File file = new File(root.getAbsolutePath() + File.separator + fileName);
					if(file.exists()) {
						file.delete();
					}
				}
			}
			
			// this works but fails when it cannot find the types in the runtime/Java source resources
			MyDslGenerators generators = injector.getInstance(MyDslGenerators.class);
			generators.doGenerate(resource, new FSA(new File("output-path/src-gen/")));
		} catch (Exception e) {
			e.printStackTrace();
		}
	}

    private static void loadFiles(File directory, XtextResourceSet resourceSet) {
		Arrays.stream(directory.listFiles()).forEach(file -> {
			if(file.isDirectory()) {
				loadFiles(file, resourceSet);
			} else if (file.getName().endsWith(".dsl")){
				loadDSLFile(resourceSet, file);
			} else if (file.getName().endsWith(".java")){
				// TODO: how to load java source resources?
			} else if (file.getName().endsWith(".jar")){
				// TODO: how to load jar resources?
			} else {
				throw new IllegalArgumentException("Unhandled resource type");
			}
		});
	}

	private static void loadDSLFile(XtextResourceSet resourceSet, File file) {
		System.out.println("Loading: " + file.getAbsolutePath());
		resourceSet.getResource(URI.createFileURI(file.getAbsolutePath()), true);
	}

JavaIoFileSystemAccess fsa = injector.getInstance(JavaIoFileSystemAccess.class);
fsa.setOutputPath("output-path/src-gen/");

Cannot create a resource for 'file:...MyClass.class'; a registered resource factory is needed