Adding an implementation dependency on biojava libraries from maven central causes Jalview's Desktop to remain invisible when launched from a getdown launched Jalview

If you include the biojava libraries in the jalview-app/build.gradle file with

  implementation("org.biojava:biojava-core:4.1.0")
  implementation("org.biojava:biojava-ontology:4.1.0")

and build the getdown appdir, or installers with

  ./gradlew :jalview-launchers:getdownAppdirBuild
or
  ./gradlew :jalview-installers:installerFiles

and run (
  cd ./jalview-launcher/build/getdown/appdir/default/11
  java11 -jar ./getdown-launcher.jar . jalview
) or install Jalview from that, when you launch that Jalview, the Jalview Desktop does not appear. If you have the Jalview Console set to appear, it DOES appear.

If you use the same setup to build a shadowJar, it works fine.

The reason for this is not known or investigated (simply diagnosed as being the two biojava jars, although possibly it is one in particular).