The problem as it turned out was to do with classes generated by wsimport. My bad, I should have paid more attention. Lets see the error message first though.
This is a part of the JWSC output, but it shows the error.
Update: The original fix suggested to delete all of the package-info.java files. Instead, I started excluding them in my build system, I think this is a cleaner approach. So my jwsfileset looks like this now...
Below is the original approach I used.
So the fix is to find and delete all of the package-info.java files in your source directory. JWSC seems to expect these, but they don't get processed somehow. No issue, there is nothing useful in these files so they are quite safe to delete.
After I deleted all of these in my project, the issue went away.