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

 Conflicts:
	src/jalview/bin/Jalview.java

diff --cc resources/lang/Messages.properties
Simple merge

diff --cc resources/lang/Messages_es.properties
Simple merge

diff --cc src/jalview/bin/Cache.java
Simple merge

diff --cc src/jalview/bin/Jalview.java
index 0ec9889,e259cc2..a988a09
--- 1/src/jalview/bin/Jalview.java
--- 2/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@@ -324,13 -299,23 +325,25 @@@ public class Jalvie
      // report Jalview version
      Cache.loadBuildProperties(true);
  
+     // old ArgsParser
      ArgsParser aparser = new ArgsParser(args);
 +
      boolean headless = false;
  
+     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);
+     }
+ 
      String usrPropsFile = aparser.getValue("props");
 -    Cache.loadProperties(usrPropsFile); // must do this before
 +    Cache.loadProperties(usrPropsFile); // must do this
 +                                        // before
      if (usrPropsFile != null)
      {
        System.out.println(

diff --cc src/jalview/gui/AlignFrame.java
Simple merge

diff --cc src/jalview/gui/AlignViewport.java
Simple merge

diff --cc src/jalview/gui/StructureChooser.java
Simple merge

diff --cc src/jalview/io/FileLoader.java
Simple merge