build.gradle

// The following is in addition to the build.gradle for a normal application, not a library
 
afterEvaluate { project ->
    android.applicationVariants.each { variant ->
        File outputFile = new File(variant.mergeAssets.outputDir, "dexter.dex")
        def dexterExternalLibraries = task "dexter${variant.name}ExternalLibraries" {
            dependsOn variant.mergeAssets
            inputs.files configurations.provided
            outputs.file outputFile
            doLast {
                def builder = getPlugins().findPlugin('android').getAndroidBuilder(variant.mergeAssets.variant)
                builder.convertByteCode([], configurations.provided, null, outputFile.absolutePath, variant.dex.dexOptions, true)
            }
        }
        variant.processResources.dependsOn.add(dexterExternalLibraries)
        variant.javaCompile.classpath += configurations.provided
    }
}
 
configurations {
    provided
}
 
dependencies {
    provided 'group:module:version'
}

Dexter.java

public class Dexter {
 
    private static String optimizedDirectory = "optimized";
    private static String workDirectory = "working";
 
    public static void loadFromAssets(Context context, String fileName) throws Exception {
 
        File optimized = new File(optimizedDirectory);
        optimized = context.getDir(optimized.toString(), Context.MODE_PRIVATE);
        optimized = new File(optimized, fileName);
        optimized.mkdir();
 
        File work = context.getDir(workDirectory, Context.MODE_PRIVATE);
        work = new File(work, fileName);
 
        InputStream inputDex = context.getAssets().open(fileName);
        FileOutputStream outputDex = new FileOutputStream(work);
        byte[] buf = new byte[0x1000];
        while (true) {
            int r = inputDex.read(buf);
            if (r == -1)
                break;
            outputDex.write(buf, 0, r);
        }
        outputDex.close();
        inputDex.close();
 
        ClassLoader localClassLoader = Dexter.class.getClassLoader();
        BaseDexClassLoader classLoader = new DexClassLoader(work.getAbsolutePath(), optimized.getAbsolutePath(), null, localClassLoader);
 
        if(localClassLoader instanceof BaseDexClassLoader) {
            Object existing = getDexClassLoaderElements((BaseDexClassLoader) localClassLoader);
            Object incoming = getDexClassLoaderElements(classLoader);
            Object joined = joinArrays(incoming, existing);
            setDexClassLoaderElements((BaseDexClassLoader) localClassLoader, joined);
        } else {
            throw new UnsupportedOperationException("Class loader not supported");
        }
    }
 
    private static void setDexClassLoaderElements(BaseDexClassLoader classLoader, Object elements) throws Exception {
        Class<BaseDexClassLoader> dexClassLoaderClass = BaseDexClassLoader.class;
        Field pathListField = dexClassLoaderClass.getDeclaredField("pathList");
        pathListField.setAccessible(true);
        Object pathList = pathListField.get(classLoader);
        Field dexElementsField = pathList.getClass().getDeclaredField("dexElements");
        dexElementsField.setAccessible(true);
        dexElementsField.set(pathList, elements);
    }
 
    private static Object getDexClassLoaderElements(BaseDexClassLoader classLoader) throws Exception {
        Class<BaseDexClassLoader> dexClassLoaderClass = BaseDexClassLoader.class;
        Field pathListField = dexClassLoaderClass.getDeclaredField("pathList");
        pathListField.setAccessible(true);
        Object pathList = pathListField.get(classLoader);
        Field dexElementsField = pathList.getClass().getDeclaredField("dexElements");
        dexElementsField.setAccessible(true);
        Object dexElements = dexElementsField.get(pathList);
        return dexElements;
    }
 
    private static Object joinArrays(Object o1, Object o2) {
        Class<?> o1Type = o1.getClass().getComponentType();
        Class<?> o2Type = o2.getClass().getComponentType();
 
        if(o1Type != o2Type)
            throw new IllegalArgumentException();
 
        int o1Size = Array.getLength(o1);
        int o2Size = Array.getLength(o2);
        Object array = Array.newInstance(o1Type, o1Size + o2Size);
 
        int offset = 0, i;
        for(i = 0; i < o1Size; i++, offset++)
            Array.set(array, offset, Array.get(o1, i));
        for(i = 0; i < o2Size; i++, offset++)
            Array.set(array, offset, Array.get(o2, i));
 
        return array;
    }
}

MainActivity.java

public class MainActivity extends Activity {
 
    private static String[] DEX_FILES = {"dexter.dex"};
 
    @Override
    protected void onCreate(Bundle savedInstanceState) {
        super.onCreate(savedInstanceState);
 
        try {
            for (String dex : DEX_FILES)
                Dexter.loadFromAssets(this, dex);
        } catch (Exception e) {
            throw new RuntimeException("Unable to load DEX files", e);
        }
 
        try {
            startActivity(new Intent(MainActivity.this, getClassLoader().loadClass("the real activity")));
        } catch (ClassNotFoundException e) {
            throw new RuntimeException("Unable to start application", e);
        }
    }
}

Same here...