Javadocs are not including all the Atlassian classes

The Javadocs for the JIRA source is a significant resource for plugin developers. As more source code gets move to packages outside com.atlassian.jira, those packages have to be added to the list of directories that Javadoc should use.

For instance
http://docs.atlassian.com/jira/4.3.4/com/atlassian/jira/portal/ProjectValuesGenerator.html#getValues(java.util.Map)
has the information: "getValues in interface com.atlassian.configurable.ValuesGenerator"

The text "com.atlassian.configurable.ValuesGenerator" is a link to that interface in 4.2 but in 4.3 and later it is not.
Javadoc now allows you to build the documents in separate builds and have the links added in later builds.