JAL-3224 JAL-3225 Some fixes in install4j template and build.gradle, and a correction...

diff --git a/build.gradle b/build.gradle
index 4cb626d..ed3ace3 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -64,12 +64,14 @@ ext {
   modules_runtimeClasspath = modules_compileClasspath
 }
 
+def JAVA_INTEGER_VERSION
 def additional_compiler_args = []
 // these are getdown.txt properties defined dependent on the JAVA_VERSION 
 def getdown_alt_java_min_version
 // this property is assigned below and expanded to multiple lines in the getdown task
 def getdown_alt_multi_java_location
 if (JAVA_VERSION.equals("1.8")) {
+  JAVA_INTEGER_VERSION = "8"
   libDir = j11libDir
   libDistDir = j8libDir
   compile_source_compatibility = 1.8
@@ -77,6 +79,7 @@ if (JAVA_VERSION.equals("1.8")) {
   getdown_alt_java_min_version = getdown_alt_java8_min_version
   getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location
 } else if (JAVA_VERSION.equals("11")) {
+  JAVA_INTEGER_VERSION = "11"
   libDir = j11libDir
   libDistDir = j11libDir
   compile_source_compatibility = 11
@@ -805,15 +808,15 @@ def install4jConfFile = "jalview-installers-java"+JAVA_VERSION+".install4j"
 install4jConf = "$install4jDir/$install4jConfFile"
   
 task copyInstall4jTemplate(type: Copy) {
-  macosJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/macos-jre"+JAVA_VERSION+"/java_vm"
+  macosJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/macos-jre"+JAVA_VERSION+"/jre"
   macosJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre"+JAVA_VERSION+".tar.gz"
-  windowsJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/windows-jre"+JAVA_VERSION+"/java_vm"
+  windowsJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/windows-jre"+JAVA_VERSION+"/jre"
   windowsJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre"+JAVA_VERSION+".tar.gz"
   from (install4jDir) {
     include install4jTemplate
     rename (install4jTemplate, install4jConfFile)
     filter(ReplaceTokens, beginToken: '', endToken: '', tokens: ['9999999999': JAVA_VERSION])
-    filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['JAVA_VERSION': JAVA_VERSION, 'VERSION': JALVIEW_VERSION, 'MACOS_JAVA_VM_DIR': macosJavaVMDir, 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz, 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir, 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz])
+    filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['JAVA_VERSION': JAVA_VERSION, 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION, 'VERSION': JALVIEW_VERSION, 'MACOS_JAVA_VM_DIR': macosJavaVMDir, 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz, 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir, 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz])
   }
   into install4jDir
   inputs.files("$install4jDir/$install4jTemplate")

diff --git a/j11lib/getdown-core-1.8.3-SNAPSHOT.jar b/j11lib/getdown-core-1.8.3-SNAPSHOT.jar
deleted file mode 100644 (file)
index e9b8c4a..0000000
Binary files a/j11lib/getdown-core-1.8.3-SNAPSHOT.jar and /dev/null differ

diff --git a/j8lib/getdown-core-1.8.3-SNAPSHOT.jar b/j8lib/getdown-core-1.8.3-SNAPSHOT.jar
deleted file mode 100644 (file)
index e9b8c4a..0000000
Binary files a/j8lib/getdown-core-1.8.3-SNAPSHOT.jar and /dev/null differ

diff --git a/lib/getdown-core-1.8.3-SNAPSHOT.jar b/lib/getdown-core-1.8.3-SNAPSHOT.jar
deleted file mode 100644 (file)
index e9b8c4a..0000000
Binary files a/lib/getdown-core-1.8.3-SNAPSHOT.jar and /dev/null differ

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index b5fa7fa..c66e63e 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -52,6 +52,11 @@ import java.net.MalformedURLException;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.net.URL;
+import java.security.AllPermission;
+import java.security.CodeSource;
+import java.security.PermissionCollection;
+import java.security.Permissions;
+import java.security.Policy;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Vector;
@@ -59,7 +64,6 @@ import java.util.Vector;
 import javax.swing.LookAndFeel;
 import javax.swing.UIManager;
 
-import com.sun.xml.ws.policy.Policy;
 import com.threerings.getdown.util.LaunchUtil;
 
 import groovy.lang.Binding;
@@ -94,8 +98,6 @@ public class Jalview
   static
   {
     // grab all the rights we can the JVM
-    Policy.createEmptyPolicy();
-    /*
     Policy.setPolicy(new Policy()
     {
       @Override
@@ -111,7 +113,6 @@ public class Jalview
       {
       }
     });
-    */
   }
 
   /**

diff --git a/utils/install4j/install4j_template.install4j b/utils/install4j/install4j_template.install4j
index 3366b72..0877e5c 100644 (file)
--- a/utils/install4j/install4j_template.install4j
+++ b/utils/install4j/install4j_template.install4j
@@ -34,10 +34,10 @@
       <mountPoint id="885" root="883" location="" mode="755" />
     </mountPoints>
     <entries>
-      <dirEntry mountPoint="454" file="../../getdown/files/$$JAVA_VERSION$$" overwriteMode="4" shared="false" fileMode="644" uninstallMode="0" overrideFileMode="false" overrideOverwriteMode="true" overrideUninstallMode="true" entryMode="direct" subDirectory="files" excludeSuffixes="" dirMode="755" overrideDirMode="false">
+      <dirEntry mountPoint="454" file="../../getdown/files/$$JAVA_VERSION$$" overwriteMode="4" shared="false" fileMode="644" uninstallMode="2" overrideFileMode="false" overrideOverwriteMode="true" overrideUninstallMode="true" entryMode="direct" subDirectory="files" excludeSuffixes="" dirMode="755" overrideDirMode="false">
         <exclude />
       </dirEntry>
-      <dirEntry mountPoint="736" file="../../getdown/website/$$JAVA_VERSION$$" overwriteMode="4" shared="false" fileMode="644" uninstallMode="0" overrideFileMode="false" overrideOverwriteMode="true" overrideUninstallMode="true" entryMode="direct" subDirectory="files" excludeSuffixes="" dirMode="755" overrideDirMode="false">
+      <dirEntry mountPoint="736" file="../../getdown/website/$$JAVA_VERSION$$" overwriteMode="4" shared="false" fileMode="644" uninstallMode="2" overrideFileMode="false" overrideOverwriteMode="true" overrideUninstallMode="true" entryMode="direct" subDirectory="files" excludeSuffixes="" dirMode="755" overrideDirMode="false">
         <exclude />
       </dirEntry>
       <dirEntry mountPoint="884" file="$$MACOS_JAVA_VM_DIR$$" overwriteMode="4" shared="false" fileMode="755" uninstallMode="0" overrideFileMode="true" overrideOverwriteMode="false" overrideUninstallMode="true" entryMode="subdir" subDirectory="jre" excludeSuffixes="" dirMode="755" overrideDirMode="false">
@@ -79,9 +79,9 @@
     </components>
   </files>
   <launchers>
-    <launcher name="Offline Jalview Launcher" id="737" customizedId="" external="false" excludeFromMenu="false" unixMode="755" unixAutoStart="true" menuName="${compiler:sys.shortName}-${compiler:sys.version}" icnsFile="../../resources/images/jalview_logos.icns" customMacBundleIdentifier="false" macBundleIdentifier="" swtApp="false" fileset="734" macBundleBinary="JavaApplicationStub" addMacEntitlements="false" macEntitlementsFile="" useCustomMacosExecutableName="true" customMacosExecutableName="${compiler:sys.shortName}" useJavaMinVersionOverride="false" javaMinVersionOverride="" useJavaMaxVersionOverride="false" javaMaxVersionOverride="" checkUpdater="false" updateExecutionMode="unattendedProgress" unattendedUpdateTitle="${i18n:updater.WindowTitle(&quot;${compiler:sys.fullName}&quot;)}">
-      <executable name="Jalview" type="1" iconSet="true" iconFile="../../resources/images/jalview_logos.ico" executableDir="." redirectStderr="true" stderrFile="error.log" stderrMode="overwrite" redirectStdout="true" stdoutFile="output.log" stdoutMode="overwrite" failOnStderrOutput="true" executableMode="1" changeWorkingDirectory="true" workingDirectory="." singleInstance="true" serviceStartType="2" serviceDependencies="" serviceDescription="" jreLocation="" executionLevel="asInvoker" checkConsoleParameter="true" globalSingleInstance="false" singleInstanceActivate="true" dpiAware="java9+">
-        <versionInfo include="false" fileVersion="" fileDescription="" legalCopyright="" internalName="" productName="" />
+    <launcher name="Offline Jalview Launcher" id="737" customizedId="" external="false" excludeFromMenu="false" unixMode="755" unixAutoStart="true" menuName="${compiler:sys.shortName}" icnsFile="../../resources/images/jalview_logos.icns" customMacBundleIdentifier="false" macBundleIdentifier="" swtApp="false" fileset="734" macBundleBinary="JavaApplicationStub" addMacEntitlements="false" macEntitlementsFile="" useCustomMacosExecutableName="true" customMacosExecutableName="${compiler:sys.shortName}" useJavaMinVersionOverride="false" javaMinVersionOverride="" useJavaMaxVersionOverride="false" javaMaxVersionOverride="" checkUpdater="false" updateExecutionMode="unattendedProgress" unattendedUpdateTitle="${i18n:updater.WindowTitle(&quot;${compiler:sys.fullName}&quot;)}">
+      <executable name="${compiler:sys.shortName}" type="1" iconSet="true" iconFile="../../resources/images/jalview_logos.ico" executableDir="." redirectStderr="true" stderrFile="error.log" stderrMode="overwrite" redirectStdout="true" stdoutFile="output.log" stdoutMode="overwrite" failOnStderrOutput="true" executableMode="1" changeWorkingDirectory="true" workingDirectory="." singleInstance="true" serviceStartType="2" serviceDependencies="" serviceDescription="" jreLocation="" executionLevel="asInvoker" checkConsoleParameter="true" globalSingleInstance="false" singleInstanceActivate="true" dpiAware="java9+">
+        <versionInfo include="true" fileVersion="" fileDescription="${compiler:sys.shortName}" legalCopyright="..." internalName="${compiler:sys.shortName}" productName="${compiler:sys.shortName}" />
       </executable>
       <splashScreen show="false" width="640" height="480" bitmapFile="../../resources/images/jalview_logo_background_fade-640x480.png" textOverlay="true">
         <text>
@@ -113,9 +113,9 @@
         <file path="../../resources/images/Jalview_Logo.png" />
       </iconImageFiles>
     </launcher>
-    <launcher name="Network Jalview Launcher" id="1402" customizedId="" external="false" excludeFromMenu="false" unixMode="755" unixAutoStart="true" menuName="${compiler:sys.shortName}-${compiler:sys.version}" icnsFile="../../resources/images/jalview_logos.icns" customMacBundleIdentifier="false" macBundleIdentifier="" swtApp="false" fileset="" macBundleBinary="JavaApplicationStub" addMacEntitlements="false" macEntitlementsFile="" useCustomMacosExecutableName="true" customMacosExecutableName="${compiler:sys.shortName}" useJavaMinVersionOverride="false" javaMinVersionOverride="" useJavaMaxVersionOverride="false" javaMaxVersionOverride="" checkUpdater="false" updateExecutionMode="unattendedProgress" unattendedUpdateTitle="${i18n:updater.WindowTitle(&quot;${compiler:sys.fullName}&quot;)}">
+    <launcher name="Network Jalview Launcher" id="1402" customizedId="" external="false" excludeFromMenu="false" unixMode="755" unixAutoStart="true" menuName="${compiler:sys.shortName}" icnsFile="../../resources/images/jalview_logos.icns" customMacBundleIdentifier="false" macBundleIdentifier="" swtApp="false" fileset="" macBundleBinary="JavaApplicationStub" addMacEntitlements="false" macEntitlementsFile="" useCustomMacosExecutableName="true" customMacosExecutableName="${compiler:sys.shortName}" useJavaMinVersionOverride="false" javaMinVersionOverride="" useJavaMaxVersionOverride="false" javaMaxVersionOverride="" checkUpdater="false" updateExecutionMode="unattendedProgress" unattendedUpdateTitle="${i18n:updater.WindowTitle(&quot;${compiler:sys.fullName}&quot;)}">
       <executable name="Jalview" type="1" iconSet="true" iconFile="../../resources/images/jalview_logos.ico" executableDir="." redirectStderr="true" stderrFile="error.log" stderrMode="overwrite" redirectStdout="true" stdoutFile="output.log" stdoutMode="overwrite" failOnStderrOutput="true" executableMode="1" changeWorkingDirectory="true" workingDirectory="." singleInstance="true" serviceStartType="2" serviceDependencies="" serviceDescription="" jreLocation="" executionLevel="asInvoker" checkConsoleParameter="true" globalSingleInstance="false" singleInstanceActivate="true" dpiAware="java9+">
-        <versionInfo include="false" fileVersion="" fileDescription="" legalCopyright="" internalName="" productName="" />
+        <versionInfo include="true" fileVersion="" fileDescription="${compiler:sys.shortName}" legalCopyright="..." internalName="${compiler:sys.shortName}" productName="${compiler:sys.shortName}" />
       </executable>
       <splashScreen show="false" width="640" height="480" bitmapFile="../../resources/images/jalview_logo_background_fade-640x480.png" textOverlay="true">
         <text>
@@ -963,6 +963,72 @@ return console.askYesNo(message, true);
                 </serializedBean>
                 <condition />
               </action>
+              <action name="" id="1525" customizedId="" beanClass="com.install4j.runtime.beans.actions.files.DeleteFileAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="">
+                <serializedBean>
+                  <java class="java.beans.XMLDecoder">
+                    <object class="com.install4j.runtime.beans.actions.files.DeleteFileAction">
+                      <void property="files">
+                        <array class="java.io.File" length="10">
+                          <void index="0">
+                            <object class="java.io.File">
+                              <string>jre</string>
+                            </object>
+                          </void>
+                          <void index="1">
+                            <object class="java.io.File">
+                              <string>.install4j</string>
+                            </object>
+                          </void>
+                          <void index="2">
+                            <object class="java.io.File">
+                              <string>dist</string>
+                            </object>
+                          </void>
+                          <void index="3">
+                            <object class="java.io.File">
+                              <string>resource</string>
+                            </object>
+                          </void>
+                          <void index="4">
+                            <object class="java.io.File">
+                              <string>getdown-launcher.jar</string>
+                            </object>
+                          </void>
+                          <void index="5">
+                            <object class="java.io.File">
+                              <string>getdown-launcher-old.jar</string>
+                            </object>
+                          </void>
+                          <void index="6">
+                            <object class="java.io.File">
+                              <string>getdown-launcher-new.jar</string>
+                            </object>
+                          </void>
+                          <void index="7">
+                            <object class="java.io.File">
+                              <string>digest.txt</string>
+                            </object>
+                          </void>
+                          <void index="8">
+                            <object class="java.io.File">
+                              <string>digest2.txt</string>
+                            </object>
+                          </void>
+                          <void index="9">
+                            <object class="java.io.File">
+                              <string>getdown.txt</string>
+                            </object>
+                          </void>
+                        </array>
+                      </void>
+                      <void property="recursive">
+                        <boolean>true</boolean>
+                      </void>
+                    </object>
+                  </java>
+                </serializedBean>
+                <condition />
+              </action>
               <action name="" id="660" customizedId="" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" enabled="true" commentSet="false" comment="" actionElevationType="none" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
@@ -1574,7 +1640,7 @@ return console.askYesNo(message, true);
         <content />
       </postUninstallScript>
     </linuxRPM>
-    <windows name="Offline Windows" id="743" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_${compiler:sys.version}" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="$$WINDOWS_JAVA_VM_TGZ$$" manualJREEntry="true" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="" contentFilesType="1" verifyIntegrity="true">
+    <windows name="Offline Windows" id="743" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="$$WINDOWS_JAVA_VM_TGZ$$" manualJREEntry="true" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="" contentFilesType="1" verifyIntegrity="true">
       <excludedComponents>
         <component id="1155" />
         <component id="1156" />
@@ -1596,7 +1662,7 @@ return console.askYesNo(message, true);
         <customAttributes />
       </autoUpdate>
     </windows>
-    <macosArchive name="Offline macOS Single Bundle Archive" id="878" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}-app_${compiler:sys.version}" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false" archiveType="dmg" volumeName="${compiler:sys.shortName} Installer" launcherId="737">
+    <macosArchive name="Offline macOS Single Bundle Archive" id="878" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}-app_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false" archiveType="dmg" volumeName="${compiler:sys.shortName} Installer" launcherId="737">
       <excludedComponents>
         <component id="1156" />
         <component id="1276" />
@@ -1617,10 +1683,10 @@ return console.askYesNo(message, true);
         <symlink name="&quot; &quot;" target="/Applications" />
         <file name=".background/jalview_dmg_background.png" file="./jalview_dmg_background.png" />
         <file name=".DS_Store" file="./DS_Store" />
-        <symlink name="Jalview.app/Contents/Resources/app/java_vm/Contents/MacOS/libjli.dylib" target="../Home/lib/jli/libjli.dylib" />
+        <symlink name="Jalview.app/Contents/Resources/app/jre/Contents/MacOS/libjli.dylib" target="../Home/lib/jli/libjli.dylib" />
       </topLevelFiles>
     </macosArchive>
-    <windows name="Network Windows" id="1272" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}_${compiler:sys.version}" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="$$WINDOWS_JAVA_VM_TGZ$$" manualJREEntry="true" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="" contentFilesType="1" verifyIntegrity="true">
+    <windows name="Network Windows" id="1272" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="$$WINDOWS_JAVA_VM_TGZ$$" manualJREEntry="true" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="" contentFilesType="1" verifyIntegrity="true">
       <excludedComponents>
         <component id="1031" />
         <component id="1155" />
@@ -1642,7 +1708,7 @@ return console.askYesNo(message, true);
         <customAttributes />
       </autoUpdate>
     </windows>
-    <macosArchive name="Network macOS Single Bundle Archive" id="1274" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}-app_${compiler:sys.version}" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="$$WINDOWS_JAVA_VM_TGZ$$" manualJREEntry="true" archiveType="dmg" volumeName="${compiler:sys.shortName} Installer" launcherId="1402">
+    <macosArchive name="Network macOS Single Bundle Archive" id="1274" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}-app_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false" archiveType="dmg" volumeName="${compiler:sys.shortName} Installer" launcherId="1402">
       <excludedComponents>
         <component id="1031" />
         <component id="1156" />
@@ -1663,7 +1729,7 @@ return console.askYesNo(message, true);
         <symlink name="&quot; &quot;" target="/Applications" />
         <file name=".background/jalview_dmg_background.png" file="./jalview_dmg_background.png" />
         <file name=".DS_Store" file="./DS_Store" />
-        <symlink name="Jalview.app/Contents/Resources/app/java_vm/Contents/MacOS/libjli.dylib" target="../Home/lib/jli/libjli.dylib" />
+        <symlink name="Jalview.app/Contents/Resources/app/jre/Contents/MacOS/libjli.dylib" target="../Home/lib/jli/libjli.dylib" />
       </topLevelFiles>
     </macosArchive>
   </mediaSets>