This one had me stumbled for a while. JWSC was reporting compilation failures, but the final build status was a success. In addition when I examined the produced WAR file, it contained the very classes and packages that JWSC was claiming were missing.
My JWSC task was being used like this...
Since I was using module and jwsfileset and specifying srcdir attribute on the jwsfileset, I didn't think to set the same attribute on the jwsc task itself.
This resulted in output like this (sanitised for readability):
Once I set the srcdir attribute on the jwsc task, all of these processing errors went away. It seems a little redundant to have to specify the source directory in multiple places to me, but I guess there is little choice if you want clean build system output.