The annotation processing API makes use of classes in the javax.lang.model(.*)
packages. These model language constructs and said models must be generated during compilation. Since a compiler is intended to ignore comments and documentation, there doesn't seem to be anything in those packages, nor did I expect there to be, that gives you access to comments/doc.
I'm not certain how the javadoc facility performs its work, maybe that can be of help.
Kapep's answer looks interesting, but do mind that it uses stuff from a com.sun.*
package, which is implementation-specific. Unless you're absolutely sure that the resources offered to your annotatation processor environment are implemented using those classes and you can safely downcast from the interfaces, it's best not to use that. It'd be a brittle solution at best.
EDIT: as an aside, I'm also using custom annotations + processor to generate metadata in XML format for wiring, validation etc. And I also need descriptions. So what I do is keep the JavaDoc for programming purposes and details that might be interesting to someone directly using the class in code, while having some description key in the annotation (or a default based on class name/other annotation values if none is given) that can be used to obtain a description from some resource file. The description is intended for the "end user" and focuses on high-level stuff, not code specifics. It has the added benefit of facilitating internationalization. I'm not certain this would be of any use to you, but there's my two cents.