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 --combined build.xml
index 0e13756,2673e9b..bf84feb
--- 1/build.xml
--- 2/build.xml
+++ b/build.xml
@@@ -412,9 -412,13 +412,13 @@@
                                <include name="*.jar"/>
                        </fileset>
                </delete>
-               <jar destfile="${packageDir}/${outputJar}">
+               <jar destfile="${packageDir}/${outputJar}" index="true">
                        <manifest>
                                <attribute name="Main-Class" value="jalview.bin.Jalview" />
+         <attribute name="Permissions" value="all-permissions" />
+         <!--<attribute name="Trusted-Lib" value="true" /> -->
+         <attribute name="Application-Name" value="Jalview Desktop"/>
+         <attribute name="Codebase" value="*"/>
                        </manifest>
                        <fileset dir="${outputDir}/">
                                <exclude name="cache*/**" />
@@@ -460,11 -464,13 +464,15 @@@
        <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
                <copy file="${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/**" />
@@@ -473,7 -479,6 +481,7 @@@
                                <include name=".build_properties" />
                                <include name="images/idwidth.gif" />
                                <include name="images/link.gif" />
 +                              <include name="lang/**" />
                        </fileset>
                </jar>
        </target>
@@@ -582,7 -587,14 +590,14 @@@
                      <include name="**/*"/>
                        </fileset>
          </copy>
-                       
+           <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
+           <jar update="true" index="true" jarfile="${packageDir}/examples/$(jmolJar}"/>
+     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+ 
+       <fileset dir="${packageDir}/examples">
+         <include name="*.jar" />
+       </fileset>
+     </signjar>
        </target>
        <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
         <javadoc destdir="${javadocDir}">

diff --combined utils/InstallAnywhere/Jalview.iap_xml
index 0416611,25a990c..e34e520
--- 1/utils/InstallAnywhere/Jalview.iap_xml
--- 2/utils/InstallAnywhere/Jalview.iap_xml
+++ b/utils/InstallAnywhere/Jalview.iap_xml
@@@ -1,8 -1,8 +1,8 @@@
  <?xml version="1.0" encoding="UTF-8"?>
  <!-- This script was automatically generated using InstallAnywhere 2013 Professional, Build 4538
       STATUS: Fully Functional LICENSED Edition
-      DATE:   Mon Oct 21 14:27:40 BST 2013 -->
- <InstallAnywhere_Deployment_Project increments="5104">
+      DATE:   Fri Nov 01 13:57:32 GMT 2013 -->
+ <InstallAnywhere_Deployment_Project increments="5103">
        <!-- ** DO NOT EDIT ** Essential authorization and configuration data ** DO NOT EDIT ** -->
        <essentialScriptInfo>
                <versionID major="15" minor="0" revision="0"/>
@@@ -10,7 -10,7 +10,7 @@@
                <scriptID>12,42,11,85,78,76,73,67,69,78,83,69,68</scriptID>
                <buildID>3,13,71,76,105,110,117,120,44,32,50,46,54,46,51,50,45,50,55,57,46,50,50,46,49,46,101,108,54,46,120,56,54,95,54,52,44,32,97,109,100,54,52,59,32,74,97,118,97,32,49,46,55,46,48,95,50,53,44,32,79,114,97,99,108,101,32,67,111,114,112,111,114,97,116,105,111,110,44,32,104,116,116,112,58,47,47,106,97,118,97,46,111,114,97,99,108,101,46,99,111,109,47,59,32,101,110,44,32,85,110,107,110,111,119,110,59,32,73,83,79,45,56,56,53,57,45,49</buildID>
                <!-- The authorizationID may change between project saves and builds.  This does not effect the integrity of the project, nor do changes in this value represent changes in the actual InstallAnywhere project. -->
-               <authorizationID>1,0,0,64,-35,60,16,-128,80,127,118,101,93,105,116,96,121,48,48,49,56,52,67,98,113,112,112,37,82,101,96,63,55,-11,2,11,7,83,27,1,1,0,0</authorizationID>
+               <authorizationID>1,0,0,64,29,-4,96,96,80,127,118,101,93,105,116,96,121,48,48,49,56,52,67,98,113,112,112,37,82,101,96,63,55,-11,2,0,1,84,19,2,1,0,0</authorizationID>
        </essentialScriptInfo>
        <installationObjects uniqueObjects="217">
                <object class="com.zerog.ia.installer.Installer" objectID="fe7d63eda660">
@@@ -1268,7 -1268,7 +1268,7 @@@ and any path to a file to save to the f
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
 -                                                              <string><![CDATA[min-jaba-client-2.0.jar]]></string>
 +                                                              <string><![CDATA[min-jabaws-client-2.1.0.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@@ -1286,7 -1286,7 +1286,7 @@@
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
 -                                                              <string><![CDATA[min-jaba-client-2.0.jar]]></string>
 +                                                              <string><![CDATA[min-jabaws-client-2.1.0.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
                                                                <long>133065</long>
@@@ -4037,7 -4037,7 +4037,7 @@@ Press "Done" to quit the installer.]]><
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="credentialInformation">
-                                                               <object class="com.flexera.ia.vapp.datastructures.VMWareCredentialInformationImpl" objectID="eeb45609a007">
+                                                               <object class="com.flexera.ia.vapp.datastructures.VMWareCredentialInformationImpl" objectID="27759feba050">
                                                                        <property name="hostName">
                                                                                <string><![CDATA[]]></string>
                                                                        </property>
@@@ -4231,7 -4231,7 +4231,7 @@@
                                        </method>
                                        <method name="put">
                                                <string><![CDATA[com.zerog.ia.project.save.last.date]]></string>
-                                               <string><![CDATA[21 October 2013 14:27:40 o'clock BST]]></string>
+                                               <string><![CDATA[01 November 2013 13:57:31 o'clock GMT]]></string>
                                        </method>
                                        <method name="put">
                                                <string><![CDATA[com.zerog.ia.build.options.optimization.platform.cdrom]]></string>
@@@ -6822,7 -6822,7 +6822,7 @@@ and any path to a file to read from tha
                                                                                                <boolean>false</boolean>
                                                                                        </property>
                                                                                        <property name="totalSize">
-                                                                                               <long>13096</long>
+                                                                                               <long>1</long>
                                                                                        </property>
                                                                                        <property name="macBinary">
                                                                                                <boolean>false</boolean>
@@@ -7340,7 -7340,6 +7340,6 @@@
                        </visualChildren>
                        <installChildren>
                                <object refID="fe7d6493a66a"/>
-                               <object refID="ee9b98899f7a"/>
                        </installChildren>
                </object>
        </installationObjects>