here is the tamplate of the cyanogenmod 11 with the new theme engine ... a big thanks to Esa Esa Laukkanen for share Great Freedom apk.

http://youtu.be/9SEDTtT93_0

The directory structure looks like this:

AndroidManifest.xml

src/

res/

assets/

boot-animation/

fonts/

icons/

res/ (note: same dir structure as res/ in trebuchet icon packs)

wallpapers/

ringtones/

notifications/

alarms/

overlays/

[target-pkg-name1]

res/

drawable/

drawable-hdpi/

...

layouts/

xml/

[target-pkg-name2]

res/

A theme APK is identified by meta-value data in AndroidManifest.xml. Here is an example:

<manifest xmlns:android="http://schemas.android.com/apk/res/android"
    package="com.botty.testcm11">

    <uses-feature android:name="org.cyanogenmod.theme" />
    <meta-data android:name="org.cyanogenmod.theme.name" android:value="My Test Theme"/>
    <meta-data android:name="org.cyanogenmod.theme.author" android:value="Botty Ivan" />

    <application android:allowBackup="true"
        android:label="@string/app_name"
        android:icon="@drawable/ic_launcher"
        android:theme="@style/AppTheme">

    </application>

</manifest>

Click here to see the full documentation.