Michael, I was looking over PearAnalysisEngineWrapper.java and I think there's something missing.
When you create your CAS you aren't telling it the ClassLoader for the PEAR. So if JCAS were used and the JCas classes were in the PEAR, I think you would get class not found exceptions. Have you tried a JCAS annotator with this? The way to tell the CAS about the ClassLoader is to pass the ResourceManager (the same one you passed to produceAnalysisEngine) to the CasCreationUtils.createCas call. It's an optional argument you can add in addition to the arguments you're already passing. -Adam
