classpath ordering

classpath ordering

- j11lib needs to be declared before j8lib for saaj and probably many
others.

- Jalview.java allows synchronization

- CommandLineOperations working; seems at least on Bob's machine process
with file writing termination does not equate with file.exists(); join
is returning too early? How can that be...

- Jalview2xmlTests back to correct answer and now working with
Jalview.setSynchronized(true);