Merge branch 'Jalview-JS/JAL-3253-applet' of

https://source.jalview.org/git/jalview.git into
Jalview-JS/JAL-3253-applet

Conflicts:
	src/jalview/project/Jalview2XML.java

diff --cc src/jalview/project/Jalview2XML.java
index ab4a3eb,801632f..4ad61d9
--- 1/src/jalview/project/Jalview2XML.java
--- 2/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@@ -2859,9 -2856,7 +2859,11 @@@ public class Jalview2XM
          }
          String name = (jarentry == null ? null : jarentry.getName());
          if (name != null && name.endsWith(".xml")
 -                && name.indexOf(" Dataset for ") < 0 // BH 2019.05.21
 +        // The question here is what to do with the two
 +        // .xml files in the jvp file. They are identical?
 +        // && name.indexOf(" Dataset for ") < 0 // BH 2019.05.21
++        // we need to talk about how to avoid the full duplication of
++        // reading these.
          )
          {
            JAXBContext jc = JAXBContext