I have even tried putting the jar in the basex\lib folder.
This should work – as long as you start BaseX with the start scripts.
I think we’ll need a little, ideally self-contained example of your wrapper class and XQuery code to guess what may go wrong.
I have been able to install my wrapper class and run it successfully, but when I include the 3rd party jar, I get "Module not initialized" for the classes in the 3rd party jar because they are in another package. I have tried packaging everything into one jar, but that did not help. I have added a main class to the manifest of the 3rd party jar and it loaded fine but I cannot include the namespace in my xquery. My example is similar to the FOP.jar example on the file server, however I do not see query ussage example of this example. I have not yet tried the expath-pkg.xml route.