Cross-compile Jalview to Javascript

Umbrella issue for work on using Bob Hanson's 'transpiler' to build and maintain a Javascript Jalview from Java source code.
To include, but not limited to:
- any required Java code changes
- solution for 'yielding' threads
- JalviewJS / JSmol / VarnaJS bridge
- build script (for IDE - Eclipse)
- build script (for continuous integration / release - Bamboo)
- scriptable tests
- web site integration example(s)
- developer documentation (coding and debugging guide, build process, update procedure...)
- user documentation (site deployment guide)