Where in the pom.xml do I configure the Javadoc Plugin?

Like all other site report plugins, the Javadoc Plugin goes in the <reporting/> section of your pom.xml.

Where do I put Javadoc resources like HTML files or images?

All javadoc resources like HTML files, images could be put in the ${basedir}/src/main/javadoc directory.

Here is the directory layout expected by Maven Javadoc Plugin:

yourproject |-- src |-- main |-- java |-- org |... `-- MyClass.java |-- javadoc |-- org |... `-- package.html
How to know exactly the Javadoc command line?

The Javadoc Plugin calls the Javadoc tool with argument files, i.e. files called 'options', 'packages' and 'argfile' (or 'files' with Jdk < 1.4): ${project.reporting.outputDirectory}/apidocs/javadoc.exe(or .sh) \ @options @packages | @argfile

These argument files are generated at runtime depending the Javadoc Plugin configuration and are deleted when the Javadoc Plugin ended.

To preserve them, just add <debug>true<debug> in your Javadoc Plugin configuration.