Merge branch 'improvement/JAL-4262_deprecation_warning_when_old_CLI_arguments_are_pro...

diff --cc src/jalview/bin/Commands.java
index cd72e60,d910819..e6c7b54
--- 1/src/jalview/bin/Commands.java
--- 2/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@@ -140,28 -139,11 +141,30 @@@ public class Command
        }
  
      }
 +
 +    // report errors
 +    StringBuilder sb = new StringBuilder();
 +    for (String error : errors)
 +    {
 +      sb.append("- " + error);
 +      sb.append("\n");
 +    }
 +    if (Platform.isHeadless())
 +    {
 +      Console.debug("All errors from command line argument commands:\n"
 +              + sb.toString());
 +    }
 +    else
 +    {
 +      // scrollable dialog box
 +
 +    }
 +
      if (argParser.getBoolean(Arg.QUIT))
      {
-       Jalview.exit("Exiting due to " + Arg.QUIT.argString(), 0);
+       Jalview.getInstance().exit(
+               "Exiting due to " + Arg.QUIT.argString() + " argument.",
+               ExitCode.OK);
        return true;
      }
      // carry on with jalview.bin.Jalview