The site plugin is configured by the contents of the src/site directory.
Each file in the source folders (apt, fml, xdoc) is processed by the site plugin and results in an html document being placed in the target/site directory.
Use caution: when using the Reporting Plugins, the Index generates a file named index.html for your project. If you create a page named index.apt (in the apt directory), index.fml (in the fml directory), index.xml (in the xdoc directory), then you will pre-empt the Index report from creating the default index.html.
An introduction to the site descriptor is available in the mini-guide to creating a site. If you want to know more (like the poweredBy element, for example), you can dive into the Velocity file used for the default site...