Merge branch 'JAL-1286' into Release_2_8_1_Branch

slightly dirty merge - JAL-1400 patches have been brought in too
Conflicts:
	build.xml

diff --cc build.xml
index 0e13756,2673e9b..bf84feb
--- 1/build.xml
--- 2/build.xml
+++ b/build.xml
@@@ -460,11 -464,13 +464,15 @@@
        <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
                <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
                <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 +              <copy todir="${outputDir}/lang">
 +                      <fileset dir="${resourceDir}/lang"><include name="**.*"/></fileset></copy>
-               <jar destfile="in.jar">
+               <jar destfile="in.jar" index="true">
                        <manifest>
                                <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
+                               <attribute name="Permissions" value="sandbox" /> 
+         <!--<attribute name="Trusted-Lib" value="true" /> -->
+                               <attribute name="Application-Name" value="JalviewLite Applet"/>
+                               <attribute name="Codebase" value="www.jalview.org"/>
                        </manifest>
                        <fileset dir="${outputDir}">
                                <include name="com/**" />

diff --cc utils/InstallAnywhere/Jalview.iap_xml
Simple merge