Usage of annotations not detected by javac analysis

[stuhood]

In some cases (depending on the RetentionPolicy), usage of annotations ends up in classfiles, and should be possible to detect in ClassToAPI and Analyze. Currently, annotations do not seem to be detected in any cases.

[SethTisue]

A more narrowly focused ticket in this area is #630; I'm working on a fix. It isn't clear to yet whether that fix might fully address this ticket, or merely constitute progress on it.