Is there any way to make this work, without changing the library to a single level file structure?
I use a third party AMD plugin in my syntax highlighter filter: https://github.com/sharpchi/moodle-filter_syntaxhighlighter
Basically, I copied the compiled js and put it in amd/src and amd/build
I also added the files to thirdpartylibs.xml so that Moodle wouldn't check them for linting errors.
Hope that helps