PHPDocumentor

Download the PHAR from their website. This is the easiest method to start with and works perfectly.

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php ~/phpDocumentor.phar -d . -t docs

I found an excellent configuration file that you just need to place and it will make life easier.

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<?xml version="1.0" encoding="UTF-8" ?>

<phpdoc>

    <title>App Plugins Documentations</title>

    <parser>

        <target>reference/docs</target>

    </parser>

    <transformer>

        <target>reference/docs</target>

    </transformer>

    <files>

        <directory>.</directory> <!-- Scan and parse all the php files except those found in the paths below -->

        <ignore>assets/*</ignore>

        <ignore>includes/gm-virtual-pages/*</ignore>

        <ignore>includes/app_virtual_pages/*</ignore>

        <ignore>includes/third-party/*</ignore>

        <ignore>vendor/*</ignore>

        <ignore>reference/docs/*</ignore>

        <ignore>storage/*</ignore>

        <ignore>views/*</ignore>

        <ignore>index.php</ignore> <!-- Ignore all the index.php files -->

    </files>

</phpdoc>

Ignoring vendor directory should be the first step to start with.