phpDocumentor: php documentor version 3 is not using configuration file

Expected Behavior

I have a configuration file that defines another target for the parser, another target for the transformer and a template. I expect that it still works or at least the documentation says how to configure this now and what needs to be changed for version 3.

Actual Behavior

It renders the default template to the default path which is useless for me.

Steps to Reproduce the Problem

1. Create a custom template
2. Create a configuration file
3. run phpDocumentor v3 with -c <path-to-config.xml>

Your environment

• Version used: 3.0.0-alpha.2
• Install method: downloaded .phar with public key
• php version 7.2.9
• Operating system: Manjaro (rolling release)
• Link to your project: https://github.com/tflori/orm

<?xml version="1.0" encoding="UTF-8" ?>
<phpdoc>
    <parser>
        <target>/tmp/phpdoc/orm</target>
    </parser>
    <transformer>
        <target>docs</target>
    </transformer>
    <transformations>
        <template name="docs/_reference"/>
    </transformations>
    <files>
        <directory>src</directory>
    </files>
</phpdoc>