Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects

 Conflicts:
	src/jalview/bin/Jalview.java

diff --cc src/jalview/bin/Jalview.java
index a988a09,71c6cf0..99ae815
--- 1/src/jalview/bin/Jalview.java
--- 2/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@@ -448,6 -465,19 +465,18 @@@ public class Jalvie
      System.setProperty("http.agent",
              "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
  
+     try
+     {
+       Console.initLogger();
+     } catch (
+ 
+     NoClassDefFoundError error)
+     {
+       error.printStackTrace();
+       System.out.println("\nEssential logging libraries not found."
+               + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
+       System.exit(0);
+     }
 -
      desktop = null;
  
      setLookAndFeel();

diff --cc src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
Simple merge