Update code to work with apigen

Important parts for apigen:
* Use the `@package` tag at the head of each page
* Add `{@link <class>:<function>}` for hyperlinking within documentation
* For the nonstandard `@argument` tag, add HTML formatting where necessary to ensure good display
    * This includes wrapping the variable name in the semantic `<var>` tag, for which the default apigen CSS files provides a distinctive appearance.
    * Apigen supports markdown (i.e., surrounding code with backticks (`` ` ``) will cause the code to show in monotype)
* With a few exceptions, apigen supports [all phpdocumentor tags](http://www.phpdoc.org/docs/latest/internals/tags.html)
* The actual apigen code is in the [apidocs repository](https://github.com/tubepress/apidocs)