The current version of Jalview requires Java 8. The platform-independent Java jar for 
Jalview is in $BIRCH/java/Jalview, but we have to have a system-specific JRE
for each platform, so the jalview script uses this JRE.

We should be able to eliminate this directory when Jalview becomes fully
Java 11 compliant.

Mesquite.3.70 freezes on some systems with system Java commands
Therefore we also use this jre with Mesquite.