>>> Problem fixed. You can download a complete jalview .jar file from their github, that
is platform independent and has everything in a single file. The only thing you lose 
with that is the automated updates.

Jalview 2.11.1.0 is here, rather than in $BIRCH/java
 because the current version of Jalview has problems
working with Java 9, and doesn't yet work with Java 11.
If you don't have Java 8 on your system, the installer
will install a complete JRE for Java 8 in the Jalview
directory. Jalview simply won't run if you don't have Java 8.
This ends up taking up a LOT of disk space,
but there's no other way to distribute a working Jalview.
Thus, we need to have a MacOSX version of Jalview, and a
linux-x86_64 version, because the jre needs to have .dynlib
files for OSX, and .so files for linux.

This is described in the Jalview FAQ. They also say that 
work on Java 11 compatability is in progress, but that
will have to wait for a future version.