Merge branch 'core' into astronomy

Conflicts:
	src/main/install4j/taverna-commandline.install4j
diff --git a/src/main/install4j/taverna-commandline.install4j b/src/main/install4j/taverna-commandline.install4j
index ae6915d..febb117 100644
--- a/src/main/install4j/taverna-commandline.install4j
+++ b/src/main/install4j/taverna-commandline.install4j
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>

-<install4j version="5.1.8" transformSequenceNumber="4">

+<install4j version="5.1.11" transformSequenceNumber="4">

   <directoryPresets config="../../../target/taverna-workbench-dist/taverna.sh" />

   <application name="${compiler:product-name}" distributionSourceDir="" applicationId="2111-8232-4743-5748" mediaDir="../../../target/media" mediaFilePattern="${compiler:sys.shortName}-${compiler:sys.version}-${compiler:sys.platform}" compression="6" lzmaCompression="false" pack200Compression="false" excludeSignedFromPacking="true" commonExternalFiles="false" createMd5Sums="true" shrinkRuntime="false" shortName="taverna-commandline-${compiler:edition}" publisher="myGrid" publisherWeb="http://www.taverna.org.uk/" version="2.5-SNAPSHOT" allPathsRelative="true" backupOnSave="false" autoSave="true" convertDotsToUnderscores="false" macSignature="????" installerName="" javaMinVersion="1.7" javaMaxVersion="" allowBetaVM="false" jdkMode="runtimeJre" jdkName="">

     <languages skipLanguageSelection="false" languageSelectionInPrincipalLanguage="false">

@@ -14,11 +14,11 @@
     <variables>

       <variable name="maxMemory" value="1g" description="" category="" />

       <variable name="maxPermGenSpace" value="400m" description="" category="" />

-      <variable name="srcDir" value="../../../target/dist" description="Source directory for the distribution, as output by Maven in workbench-distro, e.g. &#xA;../../../target/taverna-workbench-dist" category="" />

+      <variable name="srcDir" value="../../../target/dist" description="Source directory for the distribution, as output by Maven, e.g. &#xA;../../../target/taverna-commandline-dist" category="" />

       <variable name="edition" value="snapshot" description="" category="" />

     </variables>

     <mergedProjects />

-    <codeSigning macEnabled="true" macPkcs12File="/tmp/code-signing.pfx" windowsEnabled="true" windowsKeySource="pkcs12" windowsPvkFile="" windowsSpcFile="" windowsPkcs12File="/tmp/code-signing.pfx" />    

+    <codeSigning macEnabled="false" macPkcs12File="/tmp/code-signing.pfx" windowsEnabled="false" windowsKeySource="pkcs12" windowsPvkFile="" windowsSpcFile="" windowsPkcs12File="/tmp/code-signing.pfx" />

   </application>

   <files keepModificationTimes="false" missingFilesStrategy="error" globalExcludeSuffixes="" defaultOverwriteMode="3" defaultUninstallMode="0" launcherOverwriteMode="3" defaultFileMode="644" defaultDirMode="755">

     <filesets>

@@ -41,11 +41,8 @@
       <mountPoint id="105" root="102" location="" mode="755" />

     </mountPoints>

     <entries>

-      <dirEntry mountPoint="22" file="${compiler:srcDir}" overwriteMode="4" shared="false" fileMode="644" uninstallMode="0" overrideFileMode="false" overrideOverwriteMode="false" overrideUninstallMode="false" entryMode="direct" subDirectory="taverna-workbench-dist" excludeSuffixes="*.sha1,*.md5" dirMode="755" overrideDirMode="false">

-        <exclude>

-          <entry location="executeworkflow.bat" fileType="regular" />

-          <entry location="executeworkflow.sh" fileType="regular" />

-        </exclude>

+      <dirEntry mountPoint="22" file="${compiler:srcDir}" overwriteMode="4" shared="false" fileMode="644" uninstallMode="0" overrideFileMode="false" overrideOverwriteMode="false" overrideUninstallMode="false" entryMode="direct" subDirectory="" excludeSuffixes="*.sha1,*.md5" dirMode="755" overrideDirMode="false">

+        <exclude />

       </dirEntry>

       <fileEntry mountPoint="95" file="${compiler:srcDir}/executeworkflow.bat" overwriteMode="4" shared="false" fileMode="644" uninstallMode="0" overrideFileMode="false" overrideOverwriteMode="false" overrideUninstallMode="false" />

       <fileEntry mountPoint="99" file="${compiler:srcDir}/executeworkflow.sh" overwriteMode="4" shared="false" fileMode="755" uninstallMode="0" overrideFileMode="true" overrideOverwriteMode="false" overrideUninstallMode="false" />

@@ -496,13 +493,12 @@
         <content />

       </postUninstallScript>

     </linuxDeb>

-    <linuxRPM name="Linux RPM x64" id="84" customizedId="linux_x86_64" mediaFileName="${compiler:sys.shortName}-${compiler:sys.version}-${compiler:sys.platform}_x86_64" installDir="/opt/taverna-workbench" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" includedJRE="./openjdk-1.7.0-u40-unofficial-linux-amd64-image" manualJREEntry="true" os="linux" arch="i386">

+    <linuxRPM name="Linux RPM x64" id="84" customizedId="linux_x86_64" mediaFileName="${compiler:sys.shortName}-${compiler:sys.version}-${compiler:sys.platform}_x86_64" installDir="/opt/${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" includedJRE="./openjdk-1.7.0-u40-unofficial-linux-amd64-image" manualJREEntry="true" os="linux" arch="i386">

       <excludedLaunchers />

       <excludedBeans />

       <overriddenPrincipalLanguage id="en" customLocalizationFile="" />

       <exclude>

         <entry location=".i4j_fileset_93" fileType="regular" />

-        <entry location=".i4j_external_98/bin/linux-x86" fileType="regular" />

         <entry location=".i4j_fileset_101" fileType="regular" />

       </exclude>

       <variables>

@@ -515,10 +511,10 @@
       <preInstallScript mode="1" file="">

         <content />

       </preInstallScript>

-      <postInstallScript mode="3" file="">

-        <content>ln -sf /opt/taverna-workbench/taverna.desktop /usr/share/applications/taverna-workbench.desktop</content>

+      <postInstallScript mode="1" file="">

+        <content />

       </postInstallScript>

-      <preUninstallScript mode="3" file="">

+      <preUninstallScript mode="1" file="">

         <content>rm -f /usr/share/applications/taverna-workbench.desktop</content>

       </preUninstallScript>

       <postUninstallScript mode="1" file="">