Andy,
When you have to import more than 1 Jquery plugin in the hxml file, it fails:
(with only 1 plugin it works)

-lib jQueryExtern
-cp src
-js bin/DataTables.js
-main Main
--macro js.jquery.Config.addPlugin('externs.DataTable')
--macro js.jquery.Config.addPlugin('externs.Semantic')

It throws this compile error:
src/externs/Semantic.hx:4: lines 4-30 : JQuery class is already built before inserting plugin. Most likely due to missing
compiler option: --macro js.jquery.Config.addPlugin('externs.Semantic')
The terminal process terminated with exit code: 1

Sample project:
https://github.com/mmauri/DataTablesSample/

Thanks for your help!