codes taken from allatori documentations.

allatori.xml

<config>
    <input basedir="input-jars" single-jar="application.jar">
        <jar in="app.jar" out="app-obf.jar"/>
        <jar in="input/*.jar" out="output/*.jar"/>

        <dir in="in-dir" out="out-dir"/>
    </input>

    <classpath basedir="library-jars">
        <!-- Adding library.jar to the classpath -->
        <jar name="library.jar"/>
        <!-- Adding all jars in the lib directory to the classpath -->
        <jar name="lib/*.jar"/>
        <!-- Adding all jars in the lib2 directory and its subdirectories to the classpath -->
        <jar name="lib2/**/*.jar"/>
    </classpath>

    <keep-names>
        <class template="class SomeClass"/>
        <class template="class * instanceof java.io.Serializable"/>
        <class template="class com.package.*"/>
        <class access="protected+">
            <field access="protected+"/>
            <method access="protected+"/>
        </class>
        <class template="class com.company.abc.*">
            <field template="public int *"/>
            <method template="public get*(*)"/>
            <method template="public set*(*)"/>
        </class>
    </keep-names>

    <watermark key="secure-key-to-extract-watermark" value="Customer: John Smith"/>

    <expiry date="2017/01/01" string="EXPIRED!"/>

    <!-- Configuration properties, all properties are optional -->
    <!-- General properties, we recommend to use these two properties -->
    <property name="log-file" value="renaming-log.xml"/>
    <property name="random-seed" value="type anything here"/>

    <!-- String encryption -->
    <property name="string-encryption" value="enable"/>
    <property name="string-encryption-type" value="fast"/>
    <property name="string-encryption-version" value="v4"/>
    <property name="string-encryption-ignored-strings" value="patterns.txt"/>

    <!-- Control flow obfuscation -->
    <property name="control-flow-obfuscation" value="enable"/>
    <property name="extensive-flow-obfuscation" value="normal"/>

    <!-- Renaming -->
    <property name="default-package" value="com.package"/>
    <property name="force-default-package" value="enable"/>

    <property name="packages-naming" value="abc"/>
    <property name="classes-naming" value="compact"/>
    <property name="methods-naming" value="compact"/>
    <property name="fields-naming" value="compact"/>
    <property name="local-variables-naming" value="optimize"/>

    <property name="update-resource-names" value="enable"/>
    <property name="update-resource-contents" value="enable"/>

    <!-- Other -->
    <property name="line-numbers" value="obfuscate"/>
    <property name="generics" value="remove"/>
    <property name="inner-classes" value="remove"/>
    <property name="member-reorder" value="random"/>
    <property name="finalize" value="disable"/>
    <property name="version-marker" value="anyValidIdentifierName"/>
    <property name="synthetize-methods" value="all"/>
    <property name="synthetize-fields" value="all"/>
    <property name="remove-toString" value="enable"/>
    <property name="remove-calls" value="com.package.Logger.debug"/>
    <property name="output-jar-compression-level" value="9"/>

    <!-- Incremental obfuscation -->
    <property name="incremental-obfuscation" value="input-renaming-log.xml"/>
</config>