Merge branch 'merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch' into...

diff --cc build.gradle
index 2c7f138,2060073..682b5c2
--- 1/build.gradle
--- 2/build.gradle
+++ b/build.gradle
@@@ -1243,7 -1364,7 +1364,7 @@@ task getdownWebsite() 
      // getdown-launcher.jar should not be in main application class path so the main application can move it when updated.  Listed as a resource so it gets updated.
      //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
      getdownTextString += "resource = ${getdown_launcher_new}\n"
--    getdownTextString += "class = ${mainClass}\n"
++    getdownTextString += "class = ${main_class}\n"
  
      def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
      getdown_txt.write(getdownTextString)

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

diff --cc src/jalview/gui/AlignFrame.java
index f484508,e4aa736..4582f4d
--- 1/src/jalview/gui/AlignFrame.java
--- 2/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -137,8 -138,8 +138,9 @@@ import jalview.schemes.ColourSchemeI
  import jalview.schemes.ColourSchemes;
  import jalview.schemes.ResidueColourScheme;
  import jalview.schemes.TCoffeeColourScheme;
 +import jalview.util.HttpUtils;
  import jalview.util.MessageManager;
+ import jalview.util.Platform;
  import jalview.viewmodel.AlignmentViewport;
  import jalview.viewmodel.ViewportRanges;
  import jalview.ws.DBRefFetcher;