Merge branch 'JAL-957_jbake' into Release_2_8_Branch

diff --combined build.xml
index 6487a2d,83425ce..ad1b781
--- 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"/>
@@@ -687,8 -686,14 +687,14 @@@
      <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
  
        <fileset dir="${packageDir}/examples">
-         <exclude name="u_*.jar"/>
-         <include name="*.jar" />
+         <include name="${jalviewLiteJar}" />
+         <include name="${jmolJar}" />
+         <include name="to_${jalviewLiteJar}" />
+         <include name="to_${jmolJar}" />
+         <include name="tl_${jalviewLiteJar}" />
+         <include name="tl_${jmolJar}" />
+         <include name="ap_${jalviewLiteJar}" />
+         <include name="ap_${jmolJar}" />
        </fileset>
      </signjar>
    </target>