One issue is that the impl of FSArray changed the return type for getting an element from FeatureStructure to TOP.
This breaks binary backwards compatibility. (Binary meaning that code compiled with v2 should run using v3 without recompiling). So, I'm planning to change the return type back to FeatureStructure. The other concerns complex use cases involving running within 1 class loader, multiple UIMA pipelines, having similar type systems, using 1 set of JCas class definitions. This is related to https://issues.apache.org/jira/browse/UIMA-5698. The general use cases can have more variety than the current implementation supports. I'm still figuring this out but will soon put in a Jira to cover this. -Marshall