Merge branch 'JAL-957_jbake' into Release_2_8_Branch

diff --combined build.xml
index 70b7e29,369e8b9..6487a2d
--- 1/build.xml
--- 2/build.xml
+++ b/build.xml
@@@ -350,7 -350,6 +350,7 @@@
      <!--
                                <association mime-type="application-x/ext-file" extensions="fa"/>
          <association mime-type="application-x/ext-file" extensions="fasta"/>
 +        <association mime-type="application-x/ext-file" extensions="mfa"/>
          <association mime-type="application-x/ext-file" extensions="fastq"/>
          <association mime-type="application-x/ext-file" extensions="blc"/>
          <association mime-type="application-x/ext-file" extensions="msf"/>
@@@ -665,6 -664,8 +665,8 @@@
        </jar>
      </presetdef>
      <!-- create differently privileged artefacts -->
+     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
+     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}"/>
      <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
      <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
      <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
@@@ -685,6 -686,7 +687,7 @@@
      <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
  
        <fileset dir="${packageDir}/examples">
+         <exclude name="u_*.jar"/>
          <include name="*.jar" />
        </fileset>
      </signjar>