Index: gradle/jalview/build.gradle
===================================================================
diff -u -N -r0bd9f2be3a7356b69a0b044e7becb5969ef80f70 -rad61eef93a851629358fd1005de3f0b10f560d71
--- gradle/jalview/build.gradle	(.../build.gradle)	(revision 0bd9f2be3a7356b69a0b044e7becb5969ef80f70)
+++ gradle/jalview/build.gradle	(.../build.gradle)	(revision ad61eef93a851629358fd1005de3f0b10f560d71)
@@ -14,9 +14,6 @@
 
     compileClasspath = files( java.outputDir )
     compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
-    //println("****** compileClasspath = "+compileClasspath.asPath)
-
-    //runtimeClasspath = compileClasspath
   }
 
 
@@ -75,11 +72,12 @@
   outputFile "$jalviewDir/$outputDir/$buildPropertiesFile"
   comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
   property "BUILD_DATE", getDate("dd MMMM yyyy")
-  property "VERSION", VERSION
+  property "VERSION", JALVIEW_VERSION
   property "INSTALLATION", INSTALLATION+" git-commit:"+getGitHash()+" ["+getGitBranch()+"]"
 }
 
-task prepare(type: Copy) {
+task prepareCopy(type: Copy) {
+  doLast {
     copy {
       from "$jalviewDir"
       include "$docDir/**/*.*"
@@ -92,10 +90,53 @@
       include "**/*.*"
       into "$jalviewDir/$outputDir"
     }
+  }
 }
 
+task syncDocs(type: Sync) {
+  String syncDir = "$jalviewDir/$outputDir/$docDir"
+  from fileTree("$jalviewDir/$docDir")
+  into "$jalviewDir/$outputDir/$docDir"
+
+}
+
+task syncHelp(type: Sync) {
+  String syncDir = "$jalviewDir/$outputDir/$helpDir"
+  from fileTree("$jalviewDir/$helpDir")
+  into syncDir
+}
+
+task syncLib(type: Sync) {
+  String syncDir = "$jalviewDir/$outputDir/$libDir"
+  from fileTree("$jalviewDir/$libDir")
+  into syncDir
+}
+
+task syncResources(type: Sync) {
+  from "$jalviewDir/$resourceDir"
+  include "**/*.*"
+  into "$jalviewDir/$outputDir"
+}
+
+task prepare {
+  dependsOn syncDocs
+  dependsOn syncHelp
+  dependsOn syncResources
+}
+
+task replaceVersionRel {
+  String helpFile = "$jalviewDir/$outputDir/$helpDir/help.jhm"
+  outputs.files(helpFile)
+  dependsOn syncHelp
+
+  doLast {
+    ant.replace(file: helpFile, token: '$$$$Version-Rel$$$$', value: JALVIEW_VERSION)
+  }
+}
+
 task buildIndices(type: JavaExec) {
   dependsOn prepare
+  dependsOn replaceVersionRel
   classpath = sourceSets.main.compileClasspath
   main = "com.sun.java.help.search.Indexer"
   workingDir = "$jalviewDir/$outputDir/$helpDir"
@@ -118,8 +159,10 @@
 }
 
 task cleanPackageDir(type: Delete) {
-  delete fileTree("$jalviewDir/$packageDir") {
-    include "*.jar"
+  doLast {
+    delete fileTree("$jalviewDir/$packageDir") {
+      include "*.jar"
+    }
   }
 }
 
@@ -152,15 +195,17 @@
 
 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
 task syncJars(type: Sync) {
-  from fileTree("$jalviewDir/$outputDir").include("**/*.jar").include("*.jar").files
+  from fileTree("$jalviewDir/$libDir").include("**/*.jar").include("*.jar").files
   into "$jalviewDir/$packageDir"
+  preserve {
+    include jar.archiveName
+  }
 }
 
 task makeDist {
   // order of "cleanPackageDir", "copyJars", "jar" important!
   jar.mustRunAfter cleanPackageDir
   syncJars.mustRunAfter cleanPackageDir
-  jar.mustRunAfter syncJars
   dependsOn cleanPackageDir
   dependsOn syncJars
   dependsOn jar
Index: gradle/jalview/gradle.properties
===================================================================
diff -u -N -r0bd9f2be3a7356b69a0b044e7becb5969ef80f70 -rad61eef93a851629358fd1005de3f0b10f560d71
--- gradle/jalview/gradle.properties	(.../gradle.properties)	(revision 0bd9f2be3a7356b69a0b044e7becb5969ef80f70)
+++ gradle/jalview/gradle.properties	(.../gradle.properties)	(revision ad61eef93a851629358fd1005de3f0b10f560d71)
@@ -2,7 +2,7 @@
 jalviewDir = ../..
 jreInstallsDir = /Users/bsoares/Java/installs
 
-VERSION = DEVELOPMENT
+JALVIEW_VERSION = DEVELOPMENT
 INSTALLATION = Source
 jalview_keystore = keys/.keystore
 jalview_keystore.pass = alignmentisfun