X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=bbba335960469aff27c7cfbc466c77927409f352;hb=68afc8e1b0a462cc4e876e37f23a66adb20518d1;hp=b7f21620d9e825fbe1f8199a8d75a0a784ec29ef;hpb=ce0d0a188dc7362f95bb966dc4634d58aee8eb28;p=jalview.git

diff --git a/build.gradle b/build.gradle
index b7f2162..bbba335 100644
--- a/build.gradle
+++ b/build.gradle
@@ -22,17 +22,21 @@ plugins {
 // local build environment properties
 def localProps = "${jalviewDir}/local.properties"
 if (file(localProps).exists()) {
-  def p = new Properties()
-  def localPropsFIS = new FileInputStream(localProps)
-  p.load(localPropsFIS)
-  localPropsFIS.close()
-  p.each {
-    key, val -> 
-      def over = getProperty(key) != null
-      setProperty(key, val)
-      if (over) {
-        println("Overriding property '${key}' with local.properties value '${val}'")
-      }
+  try {
+    def p = new Properties()
+    def localPropsFIS = new FileInputStream(localProps)
+    p.load(localPropsFIS)
+    localPropsFIS.close()
+    p.each {
+      key, val -> 
+        def over = getProperty(key) != null
+        setProperty(key, val)
+        if (over) {
+          println("Overriding property '${key}' with local.properties value '${val}'")
+        }
+    }
+  } catch (Exception e) {
+    System.out.println("Exception reading local.properties")
   }
 }
 
@@ -74,7 +78,7 @@ ext {
   getdownDir = ""
   reportRsyncCmd = false
   buildDist = true
-  buildProperties = buildPropertiesFile
+  buildProperties = build_properties_file
   getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}"
   switch (CHANNEL) {
 
@@ -84,7 +88,7 @@ ext {
     getdown_channel_name = "${bamboo_planKey}/${JAVA_VERSION}"
     getdown_app_base = "${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}"
     getdown_app_dir = getdown_app_dir_alt
-    buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
+    buildProperties = "${jalviewDir}/${classesDir}/${build_properties_file}"
     break
 
     case "RELEASE":
@@ -92,7 +96,7 @@ ext {
     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
     getdown_app_base = "${getdown_channel_base}/${getdownDir}"
     getdown_app_dir = getdown_app_dir_release
-    buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
+    buildProperties = "${jalviewDir}/${classesDir}/${build_properties_file}"
     reportRsyncCommand = true
     break
 
@@ -106,7 +110,7 @@ ext {
       exit
     } else {
       packageDir = "${ARCHIVEDIR}/${packageDir}"
-      buildProperties = "${ARCHIVEDIR}/${classesDir}/${buildPropertiesFile}"
+      buildProperties = "${ARCHIVEDIR}/${classesDir}/${build_properties_file}"
       buildDist = false
     }
     reportRsyncCommand = true
@@ -122,7 +126,7 @@ ext {
       exit
     } else {
       packageDir = "${ARCHIVEDIR}/${packageDir}"
-      buildProperties = "${ARCHIVEDIR}/${classesDir}/${buildPropertiesFile}"
+      buildProperties = "${ARCHIVEDIR}/${classesDir}/${build_properties_file}"
       buildDist = false
     }
     reportRsyncCommand = true
@@ -134,7 +138,7 @@ ext {
     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
     getdown_app_base = "${getdown_channel_base}/${getdownDir}"
     getdown_app_dir = getdown_app_dir_alt
-    buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
+    buildProperties = "${jalviewDir}/${classesDir}/${build_properties_file}"
     reportRsyncCommand = true
     break
 
@@ -143,7 +147,7 @@ ext {
     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
     getdown_app_base = "${getdown_channel_base}/${getdownDir}"
     getdown_app_dir = getdown_app_dir_alt
-    buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
+    buildProperties = "${jalviewDir}/${classesDir}/${build_properties_file}"
     reportRsyncCommand = true
     break
 
@@ -152,14 +156,14 @@ ext {
     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
     getdown_app_base = "${getdown_channel_base}/${getdownDir}"
     getdown_app_dir = getdown_app_dir_alt
-    buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
+    buildProperties = "${jalviewDir}/${classesDir}/${build_properties_file}"
     reportRsyncCommand = true
     break
 
     case "LOCAL":
     getdown_app_base = file(getdownWebsiteDir).toURI().toString()
     getdown_app_dir = getdown_app_dir_alt
-    buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
+    buildProperties = "${jalviewDir}/${classesDir}/${build_properties_file}"
     getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}"
     break
 
@@ -242,6 +246,7 @@ if (JAVA_VERSION.equals("1.8")) {
   throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
 }
 
+
 sourceSets {
 
   main {
@@ -306,6 +311,7 @@ sourceSets {
   }
 }
 
+
 // clover bits
 dependencies {
   if (use_clover) {
@@ -314,11 +320,13 @@ dependencies {
   }
 }
 
+
 configurations {
   cloverRuntime
   cloverRuntime.extendsFrom cloverCompile
 }
 
+
 eclipse {
   project {
     name = eclipse_project_name
@@ -391,12 +399,13 @@ eclipse {
         }
 
         //fileTree(dir: "$jalviewDir/$utilsDir", include: ["test*/*.jar"]).each {
-        sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.each {
+        sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
           //no longer want to add outputDir as eclipse is using its own output dir in bin/main
           if (it.isDirectory() || ! it.exists()) {
             // don't add dirs to classpath
-            return false // groovy "break" in .each closure
+            return false // groovy "continue" in .any closure
           }
+
           def itPath = it.toString()
           if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
             itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
@@ -441,9 +450,13 @@ eclipse {
     }
 
   } // jdt
+  
+  synchronizationTasks "eclipseSynchronizationTask"
+  autoBuildTasks "eclipseAutoBuildTask"
 
 }
 
+
 task cloverInstr() {
   // only instrument source, we build test classes as normal
   inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
@@ -483,7 +496,6 @@ task cloverReport {
     com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
   }
 }
-
 // end clover bits
 
 
@@ -498,6 +510,7 @@ compileJava {
 
 }
 
+
 compileTestJava {
   if (use_clover) {
     dependsOn compileCloverJava
@@ -525,12 +538,14 @@ compileCloverJava {
   classpath += configurations.cloverRuntime
 }
 
+
 clean {
   doFirst {
     delete sourceSets.main.java.outputDir
   }
 }
 
+
 cleanTest {
   doFirst {
     delete sourceSets.test.java.outputDir
@@ -538,12 +553,14 @@ cleanTest {
   }
 }
 
+
 // format is a string like date.format("dd MMMM yyyy")
 def getDate(format) {
   def date = new Date()
   return date.format(format)
 }
 
+
 task setGitVals {
   def hashStdOut = new ByteArrayOutputStream()
   exec {
@@ -565,11 +582,12 @@ task setGitVals {
   outputs.upToDateWhen { false }
 }
 
+
 task createBuildProperties(type: WriteProperties) {
   dependsOn setGitVals
   inputs.dir("${jalviewDir}/${sourceDir}")
-  inputs.dir("${classes}")
   inputs.dir("${jalviewDir}/${resourceDir}")
+  file(buildProperties).getParentFile().mkdirs()
   outputFile (buildProperties)
   // taking time specific comment out to allow better incremental builds
   comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
@@ -580,6 +598,7 @@ task createBuildProperties(type: WriteProperties) {
   outputs.file(outputFile)
 }
 
+
 def buildingHTML = "${jalviewDir}/${docDir}/building.html"
 task cleanBuildingHTML(type: Delete) {
   doFirst {
@@ -587,6 +606,7 @@ task cleanBuildingHTML(type: Delete) {
   }
 }
 
+
 task convertBuildingMD(type: Exec) {
   dependsOn cleanBuildingHTML
   def buildingMD = "${jalviewDir}/${docDir}/building.md"
@@ -621,12 +641,14 @@ task convertBuildingMD(type: Exec) {
   outputs.file(buildingHTML)
 }
 
+
 clean {
   doFirst {
     delete buildingHTML
   }
 }
 
+
 task syncDocs(type: Sync) {
   dependsOn convertBuildingMD
   def syncDir = "${classes}/${docDir}"
@@ -635,16 +657,16 @@ task syncDocs(type: Sync) {
 
 }
 
-def helpFile = "${classes}/${helpDir}/help.jhm"
 
+def helpFile = "${classes}/${helpDir}/help.jhm"
 task copyHelp(type: Copy) {
   def inputDir = "${jalviewDir}/${helpParentDir}/${helpDir}"
   def outputDir = "${classes}/${helpDir}"
   from(inputDir) {
     exclude '**/*.gif'
-      exclude '**/*.jpg'
-      exclude '**/*.png'
-      filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")])
+    exclude '**/*.jpg'
+    exclude '**/*.png'
+    filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")])
   }
   from(inputDir) {
     include '**/*.gif'
@@ -658,12 +680,14 @@ task copyHelp(type: Copy) {
   outputs.dir(outputDir)
 }
 
+
 task syncLib(type: Sync) {
   def syncDir = "${classes}/${libDistDir}"
   from fileTree("${jalviewDir}/${libDistDir}")
   into syncDir
 }
 
+
 task syncResources(type: Sync) {
   from "${jalviewDir}/${resourceDir}"
   include "**/*.*"
@@ -673,6 +697,7 @@ task syncResources(type: Sync) {
   }
 }
 
+
 task prepare {
   dependsOn syncResources
   dependsOn syncDocs
@@ -706,6 +731,7 @@ test {
 
 }
 
+
 task buildIndices(type: JavaExec) {
   dependsOn copyHelp
   classpath = sourceSets.main.compileClasspath
@@ -725,6 +751,7 @@ task buildIndices(type: JavaExec) {
   outputs.file("${workingDir}/JavaHelpSearch/TMAP")
 }
 
+
 task compileLinkCheck(type: JavaCompile) {
   options.fork = true
   classpath = files("${jalviewDir}/${utilsDir}")
@@ -737,21 +764,28 @@ task compileLinkCheck(type: JavaCompile) {
   outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class")
 }
 
-def helplinkscheckertouchfile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.touch")
+
 task linkCheck(type: JavaExec) {
   dependsOn prepare, compileLinkCheck
+
+  def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out")
   classpath = files("${jalviewDir}/${utilsDir}")
   main = "HelpLinksChecker"
   workingDir = jalviewDir
   def help = "${classes}/${helpDir}"
   args = [ "${classes}/${helpDir}", "-nointernet" ]
 
-  doLast {
-    helplinkscheckertouchfile.createNewFile()
-  }
+  def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
+  def errFOS = outFOS
+  standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+    outFOS,
+    standardOutput)
+  errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+    outFOS,
+    errorOutput)
 
   inputs.dir("${classes}/${helpDir}")
-  outputs.file(helplinkscheckertouchfile)
+  outputs.file(helpLinksCheckerOutFile)
 }
 
 // import the pubhtmlhelp target
@@ -791,11 +825,13 @@ jar {
   outputs.file("${jalviewDir}/${packageDir}/${archiveName}")
 }
 
+
 task copyJars(type: Copy) {
   from fileTree(dir: "${classes}", include: "**/*.jar").files
   into "${jalviewDir}/${packageDir}"
 }
 
+
 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
 task syncJars(type: Sync) {
   from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
@@ -805,6 +841,7 @@ task syncJars(type: Sync) {
   }
 }
 
+
 task makeDist {
   group = "build"
   description = "Put all required libraries in dist"
@@ -817,6 +854,7 @@ task makeDist {
   outputs.dir("${jalviewDir}/${packageDir}")
 }
 
+
 task cleanDist {
   dependsOn cleanPackageDir
   dependsOn cleanTest
@@ -840,6 +878,7 @@ shadowJar {
   minimize()
 }
 
+
 task getdownWebsite() {
   group = "distribution"
   description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
@@ -860,7 +899,7 @@ task getdownWebsite() {
 
     copy {
       from buildProperties
-      rename(buildPropertiesFile, getdown_build_properties)
+      rename(build_properties_file, getdown_build_properties)
       into project.ext.getdownAppDir
     }
     getdownWebsiteResourceFilenames += "${getdown_app_dir}/${getdown_build_properties}"
@@ -1020,6 +1059,7 @@ task getdownWebsite() {
   outputs.dir(project.ext.getdownFilesDir)
 }
 
+
 task getdownDigest(type: JavaExec) {
   group = "distribution"
   description = "Digest the getdown website folder"
@@ -1033,6 +1073,7 @@ task getdownDigest(type: JavaExec) {
   outputs.file("${project.ext.getdownWebsiteDir}/digest2.txt")
 }
 
+
 task getdown() {
   group = "distribution"
   description = "Create the minimal and full getdown app folder for installers and website and create digest file"
@@ -1055,6 +1096,7 @@ task getdown() {
   }
 }
 
+
 clean {
   doFirst {
     delete project.ext.getdownWebsiteDir
@@ -1062,6 +1104,7 @@ clean {
   }
 }
 
+
 install4j {
   def install4jHomeDir = "/opt/install4j"
   def hostname = "hostname".execute().text.trim()
@@ -1082,6 +1125,7 @@ install4j {
   }
 }
 
+
 def install4jConf
 def macosJavaVMDir
 def macosJavaVMTgz
@@ -1150,6 +1194,7 @@ task copyInstall4jTemplate(type: Copy) {
   }
 }
 
+
 task installers(type: com.install4j.gradle.Install4jTask) {
   group = "distribution"
   description = "Create the install4j installers"
@@ -1175,12 +1220,14 @@ task installers(type: com.install4j.gradle.Install4jTask) {
   outputs.dir("${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}")
 }
 
+
 clean {
   doFirst {
     delete install4jConf
   }
 }
 
+
 task sourceDist (type: Tar) {
   
   def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
@@ -1251,6 +1298,7 @@ task sourceDist (type: Tar) {
 //  }
 }
 
+
 task helppages  {
   dependsOn copyHelp
   dependsOn pubhtmlhelp
@@ -1259,20 +1307,24 @@ task helppages  {
   outputs.dir("${helpOutputDir}")
 }
 
+
 def jalviewjsBuildDir
 def jalviewjsSiteDir
-def jalviewjsTransferSiteDir
+def jalviewjsTransferSiteJsDir
+def jalviewjsTransferSiteLibDir
+def jalviewjsTransferSiteSwingJsDir
+def jalviewjsTransferSiteCoreDir
 task jalviewjsSitePath {
   def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
   jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs"
-  if (jalviewjs_site_dir.startsWith('/')) {
-    jalviewjsSiteDir = jalviewjs_site_dir
-  } else {
-    jalviewjsSiteDir = "${jalviewjsBuildDir}/${jalviewjs_site_dir}"
-  }
-  jalviewjsTransferSiteDir = "${jalviewjsBuildDir}/tmp/site"
+  jalviewjsSiteDir = "${jalviewjsBuildDir}/${jalviewjs_site_dir}"
+  jalviewjsTransferSiteJsDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js"
+  jalviewjsTransferSiteLibDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib"
+  jalviewjsTransferSiteSwingJsDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs"
+  jalviewjsTransferSiteCoreDir = "${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core"
 }
 
+
 def eclipseWorkspace
 task jalviewjsSetEclipseWorkspace {
   def propKey = "jalviewjs_eclipse_workspace"
@@ -1283,12 +1335,13 @@ task jalviewjsSetEclipseWorkspace {
       propVal = System.getProperty("user.home") + propVal.substring(1)
     }
   }
-  def propsFileName = "${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
+  def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
+  def propsFile = file(propsFileName)
   def eclipseWsDir = propVal
   def props = new Properties()
 
-  if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && file(propsFileName).exists()) {
-    def ins = new FileInputStream("${jalviewDirAbsolutePath}/${propsFileName}")
+  if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
+    def ins = new FileInputStream(propsFileName)
     props.load(ins)
     ins.close()
     if (props.getProperty(propKey, null) != null) {
@@ -1296,30 +1349,33 @@ task jalviewjsSetEclipseWorkspace {
     }
   }
 
+  def writeProps = false
   if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
     def tempDir = File.createTempDir()
     eclipseWsDir = tempDir.getAbsolutePath()
-    props.setProperty(propKey, eclipseWsDir)
-    def propsFile = file(propsFileName)
-    propsFile.parentFile.mkdirs()
-    propsFile.createNewFile() // doesn't affect existing file
-    def outs = new FileOutputStream(propsFile, false)
-    props.store(outs, null)
-    outs.close()
+    writeProps = true
   }
-
   eclipseWorkspace = file(eclipseWsDir)
 
   doFirst {
+    if (writeProps) {
+      props.setProperty(propKey, eclipseWsDir)
+      propsFile.parentFile.mkdirs()
+      def bytes = new ByteArrayOutputStream()
+      props.store(bytes, null)
+      def propertiesString = bytes.toString()
+      propsFile.text = propertiesString
+    }
+
     println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
   }
-  inputs.property(propKey, eclipseWsDir)
+
+  //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
   outputs.file(propsFileName)
+  outputs.upToDateWhen { eclipseWorkspace.exists() }
 }
 
 
-def eclipseDropinsDir
-def utilsDropinsDir
 def eclipseBinary
 def eclipseVersion
 def eclipseDebug = false
@@ -1333,26 +1389,23 @@ task jalviewjsEclipsePaths {
   }
   if (OperatingSystem.current().isMacOsX()) {
     eclipseRoot += "/Eclipse.app"
-    eclipseDropinsDir = "${eclipseRoot}/Contents/Eclipse/dropins"
     eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
     eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
   } else if (OperatingSystem.current().isWindows()) { // check these paths!!
     if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
-      eclipseRoot += "/eclipse"
+      eclipseRoot += "/eclipse.exe"
     }
-    eclipseDropinsDir = "${eclipseRoot}/dropins"
     eclipseBinary = "${eclipseRoot}/eclipse"
     eclipseProduct = "${eclipseRoot}/.eclipseproduct"
   } else { // linux or unix
     if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
       eclipseRoot += "/eclipse"
     }
-    eclipseDropinsDir = "${eclipseRoot}/dropins"
     eclipseBinary = "${eclipseRoot}/eclipse"
     eclipseProduct = "${eclipseRoot}/.eclipseproduct"
   }
 
-  eclipseVersion = "4.12" // default
+  eclipseVersion = "4.13" // default
   def assumedVersion = true
   if (file(eclipseProduct).exists()) {
     def fis = new FileInputStream(eclipseProduct)
@@ -1362,74 +1415,38 @@ task jalviewjsEclipsePaths {
     fis.close()
     assumedVersion = false
   }
-  /*
-  String[] v = eclipseVersion.split("\\.")
-  def v0 = Integer.valueOf(v[0])
-  def v1 = Integer.valueOf(v[1])
-  if (v0 < 4 || ( v0 == 4 && v1 < 13 )) {
-    eclipseVersionSuffix = "_4.12"
-  } else {
-    eclipseVersionSuffix = "_4.13"
-  }
-  utilsDropinsDir = "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}${eclipseVersionSuffix}"
-  */
-
-  utilsDropinsDir = "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}"
+  
   def propKey = "eclipse_debug"
   eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
 
   doFirst {
     if (!assumedVersion) {
-      println("ECLIPSE_VERSION=${eclipseVersion}")
+      println("ECLIPSE VERSION=${eclipseVersion}")
     }
   }
 }
 
+
 task eclipseSetup {
   dependsOn eclipseProject
   dependsOn eclipseClasspath
   dependsOn eclipseJdt
 }
 
-/* using the Copy task below
-task OLDjalviewjsEclipseCopyDropins {
-  dependsOn jalviewjsEclipsePaths
-  dependsOn jalviewjsCleanEclipse
-  def inputFiles = fileTree(dir: utilsDropinsDir, include: "*.jar")
-  inputFiles += file(jalviewjs_j2s_plugin)
-  def outputDir = eclipseDropinsDir
-
-  inputs.files inputFiles
-  inputFiles.each { file ->
-    outputs.file("${outputDir}/${file.name}")
-  }
-
-  doLast {
-    inputFiles.each { file ->
-      copy {
-        from file
-        into outputDir
-      }
-    }
-  }
-}
-*/
 
 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
 task jalviewjsEclipseCopyDropins(type: Copy) {
   dependsOn jalviewjsEclipsePaths
 
-  from utilsDropinsDir
-  into eclipseDropinsDir
+  def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
+  inputFiles += file("${jalviewDir}/${jalviewjs_j2s_plugin}")
+  def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
 
-  doLast {
-    copy {
-      from jalviewjs_j2s_plugin
-      into eclipseDropinsDir
-    }
-  }
+  from inputFiles
+  into outputDir
 }
 
+
 // this eclipse -clean doesn't actually work
 task jalviewjsCleanEclipse(type: Exec) {
   dependsOn eclipseSetup
@@ -1448,36 +1465,61 @@ y
 """
   def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
   standardInput = inputByteStream
-
-  doFirst {
-    println("CLEAN ECLIPSE_DEBUG=${eclipseDebug}")
-  }
 }
+
 /* not really working yet
 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
 */
 
-task jalviewjsUnzipFiles {
+
+task jalviewjsTransferUnzipSwingJs {
+  dependsOn jalviewjsSitePath
+
+  def file_zip = "${jalviewDir}/${jalviewjs_swingjs_zip}"
+
+  doLast {
+    copy {
+      from zipTree(file_zip)
+      into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+    }
+  }
+
+  inputs.file file_zip
+  outputs.dir "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+}
+
+
+task jalviewjsTransferUnzipLib {
   dependsOn jalviewjsSitePath
 
   def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
-  zipFiles += "${jalviewDir}/${jalviewjs_swingjs_zip}"
 
   doLast {
     zipFiles.each { file_zip -> 
       copy {
         from zipTree(file_zip)
-        into "${jalviewDir}/${jalviewjsSiteDir}"
+        into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
       }
     }
   }
 
   inputs.files zipFiles
-  outputs.dir "${jalviewDir}/${jalviewjsSiteDir}"
+  outputs.dir "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+}
+
+
+task jalviewjsTransferUnzipAllLibs {
+  dependsOn jalviewjsTransferUnzipSwingJs
+  dependsOn jalviewjsTransferUnzipLib
 }
 
+
 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
+  group "JalviewJS"
+  description "Create the .j2s file from the j2s.* properties"
+
   dependsOn jalviewjsSitePath
+
   outputFile ("${jalviewDir}/${jalviewjs_j2s_settings}")
   def j2s_props = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
   def siteDirProperty = "j2s.site.directory"
@@ -1486,27 +1528,51 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) {
     if (val != null) {
       if (prop == siteDirProperty) {
         if (!(val.startsWith('/') || val.startsWith("file://") )) {
-          val = "${jalviewjsTransferSiteDir}/${val}"
+          val = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${val}"
         }
         setSiteDir = true
       }
       property(prop,val)
     }
     if (!setSiteDir) { // default site location, don't override specifically set property
-      property(siteDirProperty,jalviewjsTransferSiteDir)
+      property(siteDirProperty,"${jalviewDir}/${jalviewjsTransferSiteJsDir}")
     }
   }
   inputs.properties(j2s_props)
   outputs.file(outputFile)
 }
 
+
 task jalviewjsEclipseSetup {
   dependsOn jalviewjsEclipseCopyDropins
   dependsOn jalviewjsSetEclipseWorkspace
   dependsOn jalviewjsCreateJ2sSettings
 }
 
-task jalviewjsCopyResources (type: Sync) {
+
+task jalviewjsSyncAllLibs (type: Sync) {
+  dependsOn jalviewjsSitePath
+  dependsOn jalviewjsTransferUnzipAllLibs
+  def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
+  inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
+  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+
+  from inputFiles
+  into outputDir
+  def outputFiles = []
+  rename { filename ->
+    outputFiles += "${outputDir}/${filename}"
+    null
+  }
+  preserve {
+    include "**"
+  }
+  outputs.files outputFiles
+  inputs.files inputFiles
+}
+
+
+task jalviewjsSyncResources (type: Sync) {
   dependsOn jalviewjsSitePath
   def inputFiles = fileTree(dir: "${jalviewDir}/${resourceDir}")
   def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
@@ -1525,7 +1591,8 @@ task jalviewjsCopyResources (type: Sync) {
   inputs.files inputFiles
 }
 
-task jalviewjsCopySiteResources (type: Sync) {
+
+task jalviewjsSyncSiteResources (type: Sync) {
   dependsOn jalviewjsSitePath
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
   def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
@@ -1544,134 +1611,230 @@ task jalviewjsCopySiteResources (type: Sync) {
   inputs.files inputFiles
 }
 
+
+task jalviewjsSyncBuildProperties (type: Sync) {
+  dependsOn jalviewjsSitePath
+  dependsOn createBuildProperties
+  def inputFiles = [file(buildProperties)]
+  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+
+  from inputFiles
+  into outputDir
+  def outputFiles = []
+  rename { filename ->
+    outputFiles += "${outputDir}/${filename}"
+    null
+  }
+  preserve {
+    include "**"
+  }
+  outputs.files outputFiles
+  inputs.files inputFiles
+}
+
+
 task jalviewjsProjectImport(type: Exec) {
   dependsOn eclipseSetup
   dependsOn jalviewjsEclipsePaths
   dependsOn jalviewjsEclipseSetup
 
-  def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
+  doFirst {
+    // do not run a headless import when we claim to be in Eclipse
+    if (ECLIPSE_IDE_DEVELOPER.equals("true")) {
+      throw new StopExecutionException("Not running headless import whilst ECLIPSE_IDE_DEVELOPER is '"+ECLIPSE_IDE_DEVELOPER+"'")
+    }
+  }
+
+  //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
+  def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
   executable(eclipseBinary)
   args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
   if (eclipseDebug) {
     args += "-debug"
   }
-  // can we use args += ["--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=utils/jalviewjs/eclipse/dropins"] here? (instead of copying plugins to eclipse dropins dir)
-
-  doFirst {
-    println("IMPORT ECLIPSE_DEBUG=${eclipseDebug}")
-  }
+  args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
 
   inputs.file("${jalviewDir}/.project")
-  outputs.dir(projdir)
-  outputs.upToDateWhen { file(projdir).exists() }
+  outputs.upToDateWhen { 
+    file(projdir).exists()
+  }
 }
 
+
 task jalviewjsTranspile(type: Exec) {
   dependsOn jalviewjsEclipseSetup 
   dependsOn jalviewjsProjectImport
   dependsOn jalviewjsEclipsePaths
 
+  doFirst {
+    // do not run a headless transpile when we claim to be in Eclipse
+    if (ECLIPSE_IDE_DEVELOPER.equals("true")) {
+      throw new StopExecutionException("Not running headless transpile whilst ECLIPSE_IDE_DEVELOPER is '"+ECLIPSE_IDE_DEVELOPER+"'")
+    }
+  }
+
   executable(eclipseBinary)
   args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
   if (eclipseDebug) {
     args += "-debug"
   }
-  // can we use args += ["--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=swingjs"] here? (instead of copying plugins to eclipse dropins dir)
+  args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
 
   def stdout
   def stderr
-  stdout = new ByteArrayOutputStream()
-  stderr = new ByteArrayOutputStream()
+  doFirst {
+    stdout = new ByteArrayOutputStream()
+    stderr = new ByteArrayOutputStream()
 
-  def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}"
-  def logOutFile = file(logOutFileName)
-  logOutFile.createNewFile()
-  logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
+    def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
+    def logOutFile = file(logOutFileName)
+    logOutFile.createNewFile()
+    logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
 BINARY: ${eclipseBinary}
 VERSION: ${eclipseVersion}
 WORKSPACE: ${eclipseWorkspace}
 DEBUG: ${eclipseDebug}
 ----
 """
-  def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
-  //def logErrFileName = "${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}"
-  //def logErrFile = file(logFileName)
-  //logErrFile.createNewFile()
-  //def logErrFOS = new FileErrputStream(logErrFile, false)
-  // combine stdout and stderr
-  def logErrFOS = logOutFOS
-
-  if (jalviewjs_j2s_to_console.equals("true")) {
-    standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
-      new org.apache.tools.ant.util.TeeOutputStream(
-        logOutFOS,
-        stdout),
-      standardOutput)
+    def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
+    //def logErrFileName = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}"
+    //def logErrFile = file(logFileName)
+    //logErrFile.createNewFile()
+    //def logErrFOS = new FileErrputStream(logErrFile, false)
+    // combine stdout and stderr
+    def logErrFOS = logOutFOS
+
+    if (jalviewjs_j2s_to_console.equals("true")) {
+      standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+        new org.apache.tools.ant.util.TeeOutputStream(
+          logOutFOS,
+          stdout),
+        standardOutput)
       errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
         new org.apache.tools.ant.util.TeeOutputStream(
           logErrFOS,
           stderr),
         errorOutput)
-  } else {
-    standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
-      logOutFOS,
-      stdout)
+    } else {
+      standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+        logOutFOS,
+        stdout)
       errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
         logErrFOS,
         stderr)
+    }
   }
 
   doLast {
     if (stdout.toString().contains("Error processing ")) {
       // j2s did not complete transpile
-      throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}'")
+      //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+      throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
     }
   }
 
-  doFirst {
-    println("TRANSPILE ECLIPSE_DEBUG=${eclipseDebug}")
+  inputs.dir("${jalviewDir}/${sourceDir}")
+  outputs.dir("${jalviewDir}/${jalviewjsTransferSiteJsDir}")
+  outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
+}
+
+
+task jalviewjsNoTranspileSyncCore (type: Sync) {
+  dependsOn jalviewjsSitePath
+  dependsOn "jalviewjsNoTranspileBuildAllCores"
+  def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
+  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+
+  from inputFiles
+  into outputDir
+  def outputFiles = []
+  rename { filename ->
+    outputFiles += "${outputDir}/${filename}"
+    null
   }
+  preserve {
+    include "**"
+  }
+  outputs.files outputFiles
+  inputs.files inputFiles
+}
 
-  inputs.dir("${jalviewDir}/${sourceDir}")
-  outputs.dir("${jalviewDir}/${eclipse_bin_dir}/main")
-  outputs.dir("${jalviewDir}/${jalviewjsTransferSiteDir}")
-  outputs.upToDateWhen { file("${jalviewDir}/${jalviewjsTransferSiteDir}${jalviewjs_server_resource}").exists() }
 
+task jalviewjsSyncCore (type: Sync) {
+  dependsOn jalviewjsTranspile
+  dependsOn jalviewjsNoTranspileSyncCore
+  dependsOn "jalviewjsBuildAllCores"
 }
 
-task jalviewjsCopyTransferSite(type: Copy) {
+
+// this Copy version of TransferSiteJs will delete anything else in the target dir
+task jalviewjsCopyTransferSiteJs(type: Copy) {
   dependsOn jalviewjsTranspile
-  from "${jalviewDir}/${jalviewjsTransferSiteDir}"
+  from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
   into "${jalviewDir}/${jalviewjsSiteDir}"
 }
 
-jalviewjsUnzipFiles.mustRunAfter jalviewjsCopyTransferSite
-jalviewjsCopyResources.mustRunAfter jalviewjsCopyTransferSite
-jalviewjsCopySiteResources.mustRunAfter jalviewjsCopyTransferSite
+
+// this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
+task jalviewjsNoTranspileSyncTransferSiteJs(type: Sync) {
+  from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+  include "**/*.*"
+  into "${jalviewDir}/${jalviewjsSiteDir}"
+  preserve {
+    include "**"
+  }
+}
+
+jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
+
+jalviewjsSyncAllLibs.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs
+jalviewjsSyncResources.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs
+jalviewjsSyncSiteResources.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs
+jalviewjsSyncBuildProperties.mustRunAfter jalviewjsNoTranspileSyncTransferSiteJs
+
+
+task jalviewjsNoTranspilePrepareSite {
+  dependsOn jalviewjsSyncAllLibs
+  dependsOn jalviewjsSyncResources
+  dependsOn jalviewjsSyncSiteResources
+  dependsOn jalviewjsSyncBuildProperties
+  dependsOn jalviewjsNoTranspileSyncCore
+}
+
 
 task jalviewjsPrepareSite {
   group "JalviewJS"
   description "Prepares the website folder including unzipping files and copying resources"
-  dependsOn jalviewjsSitePath
-  dependsOn jalviewjsUnzipFiles
-  dependsOn jalviewjsCopyResources
-  dependsOn jalviewjsCopySiteResources
+  dependsOn jalviewjsSyncAllLibs
+  dependsOn jalviewjsSyncResources
+  dependsOn jalviewjsSyncSiteResources
+  dependsOn jalviewjsSyncBuildProperties
+  dependsOn jalviewjsSyncCore
 }
 
+
 task jalviewjsBuildSite {
   group "JalviewJS"
   description "Builds the whole website including transpiled code"
-  dependsOn jalviewjsCopyTransferSite
+  dependsOn jalviewjsCopyTransferSiteJs
   dependsOn jalviewjsPrepareSite
 }
 
+
 task cleanJalviewjsSite {
   doFirst {
-    delete jalviewjsTransferSiteDir
-    delete jalviewjsSiteDir
+    delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+    delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+    delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
+    delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+    delete "${jalviewDir}/${jalviewjsSiteDir}"
   }
 }
 
+
 task jalviewjsSiteTar(type: Tar) {
   group "JalviewJS"
   description "Creates a tar.gz file for the website"
@@ -1685,17 +1848,19 @@ task jalviewjsSiteTar(type: Tar) {
 
   compression Compression.GZIP
 
-  from jalviewjsSiteDir
+  from "${jalviewDir}/${jalviewjsSiteDir}"
   into jalviewjs_site_dir // this is inside the tar file
 
-  inputs.dir(jalviewjsSiteDir)
+  inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
 }
 
+
 task jalviewjsServer {
   group "JalviewJS"
-  description "Starts a webserver on localhost to test the website"
+  def filename = "jalviewjsTest.html"
+  description "Starts a webserver on localhost to test the website. See ${filename} to access local site on most recently used port."
   dependsOn jalviewjsSitePath
-  def htmlFile = "${jalviewDirAbsolutePath}/jalviewjsTest.html"
+  def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
   doLast {
 
     SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
@@ -1729,6 +1894,7 @@ task jalviewjsServer {
   outputs.upToDateWhen({false})
 }
 
+
 task cleanJalviewjsAll {
   group "JalviewJS"
   description "Delete all configuration and build artifacts to do with JalviewJS build"
@@ -1736,15 +1902,18 @@ task cleanJalviewjsAll {
   dependsOn jalviewjsEclipsePaths
   
   doFirst {
-    delete jalviewjsBuildDir
+    delete "${jalviewDir}/${jalviewjsBuildDir}"
     delete "${jalviewDir}/${eclipse_bin_dir}"
     if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
       delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
     }
     delete "${jalviewDir}/${jalviewjs_j2s_settings}"
   }
+
+  outputs.upToDateWhen( { false } )
 }
 
+
 task jalviewjs {
   group "JalviewJS"
   description "Build the site"
@@ -1752,33 +1921,270 @@ task jalviewjs {
 }
 
 
-task jalviewjsIDECopyTransferSite(type: Copy) {
-  from jalviewjsTransferSiteDir
-  into jalviewjsSiteDir
+
+task jalviewjsIDE_CopyTransferSiteJs(type: Copy) {
+  from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+  into "${jalviewDir}/${jalviewjsSiteDir}"
 }
 
-task jalviewjsIDEj2s {
-  group "JalviewJS in Eclipse"
+
+task jalviewjsIDE_j2sFile {
+  group "00 JalviewJS in Eclipse"
   description "Creates the .j2s file"
   dependsOn jalviewjsCreateJ2sSettings
 }
 
-task jalviewjsIDEBuildSite {
-  group "JalviewJS in Eclipse"
-  description "Copies the Eclipse transpiled site and unzips supporting zipfiles"
-  dependsOn jalviewjsIDECopyTransferSite
-  dependsOn jalviewjsPrepareSite
+
+task jalviewjsIDE_AssembleSite {
+  group "00 JalviewJS in Eclipse"
+  description "Assembles the Eclipse transpiled site and unzips supporting zipfiles"
+  dependsOn jalviewjsIDE_CopyTransferSiteJs
+  dependsOn jalviewjsNoTranspilePrepareSite
 }
 
-task jalviewjsIDESiteClean {
-  group "JalviewJS in Eclipse"
+
+task jalviewjsIDE_SiteClean {
+  group "00 JalviewJS in Eclipse"
   description "Deletes the Eclipse transpiled site"
   dependsOn cleanJalviewjsSite
 }
 
-task jalviewjsIDEServer {
-  group "JalviewJS in Eclipse"
+
+task jalviewjsIDE_Server {
+  group "00 JalviewJS in Eclipse"
   description "Starts a webserver on localhost to test the website"
   dependsOn jalviewjsServer
 }
 
+
+// buildship runs this at import
+task eclipseSynchronizationTask {
+  dependsOn eclipseSetup
+  dependsOn jalviewjsIDE_j2sFile
+}
+
+
+// buildship runs this at build time
+task eclipseAutoBuildTask {
+  dependsOn jalviewjsNoTranspileSyncTransferSiteJs
+  dependsOn jalviewjsNoTranspilePrepareSite
+}
+
+
+
+
+
+
+
+
+// closure
+
+def jalviewjsCallCore(FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
+
+  def stdout = new ByteArrayOutputStream()
+  def stderr = new ByteArrayOutputStream()
+
+  def coreFile = file(jsfile)
+  def msg = ""
+  msg = "Generating ${jsfile}"
+  println(msg)
+  logOutFile.createNewFile()
+  logOutFile.append(msg+"\n")
+
+  def coreTop = file(prefixFile)
+  def coreBottom = file(suffixFile)
+  coreFile.getParentFile().mkdirs()
+  coreFile.createNewFile()
+  coreFile.write( coreTop.text )
+  list.each {
+    f ->
+    if (f.exists()) {
+      def t = f.text
+      t.replaceAll("Clazz\\.","Clazz_")
+      t.replaceAll("Class__","Clazz._")
+      coreFile.append( t )
+    } else {
+      msg = "...file '"+f.getPath()+"' does not exist, skipping"
+      println(msg)
+      logOutFile.append(msg+"\n")
+    }
+  }
+  coreFile.append( coreBottom.text )
+
+  msg = "Generating ${zjsfile}"
+  println(msg)
+  logOutFile.append(msg+"\n")
+  def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
+  def logErrFOS = logOutFOS
+
+  javaexec {
+    classpath = files(["${jalviewDir}/tools/closure_compiler.jar"])
+    args = [ "--js", jsfile, "--js_output_file", zjsfile ]
+
+    msg = "\nRunning '"+commandLine.join(' ')+"'\n"
+    println(msg)
+    logOutFile.append(msg+"\n")
+
+    if (logOutConsole) {
+      standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+        new org.apache.tools.ant.util.TeeOutputStream(
+          logOutFOS,
+          stdout),
+        standardOutput)
+        errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+          new org.apache.tools.ant.util.TeeOutputStream(
+            logErrFOS,
+            stderr),
+          errorOutput)
+    } else {
+      standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+        logOutFOS,
+        stdout)
+        errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+          logErrFOS,
+          stderr)
+    }
+  }
+  msg = "--"
+  println(msg)
+  logOutFile.append(msg+"\n")
+}
+
+
+task jalviewjsNoTranspileBuildAllCores {
+  dependsOn jalviewjsSitePath
+  dependsOn jalviewjsTransferUnzipSwingJs
+
+  def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
+  def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
+  def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
+  def prefixFile = "${jsDir}/core/coretop2.js"
+  def suffixFile = "${jsDir}/core/corebottom2.js"
+
+  inputs.file prefixFile
+  inputs.file suffixFile
+
+  def classlistFiles = []
+  // add the classlists found int the jalviewjs_classlists_dir
+  fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
+    file ->
+    def name = file.getName() - ".txt"
+    classlistFiles += [
+      'file': file,
+      'name': name
+    ]
+  }
+
+  // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
+  classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
+  classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': "_jalview" ]
+
+  def classlists = []
+
+  classlistFiles.each {
+    hash ->
+
+    def file = hash['file']
+    if (! file.exists()) {
+      println("...classlist file '"+file.getPath()+"' does not exist, skipping")
+      return false // this is a "continue" in groovy .each closure
+    }
+    def name = hash['name']
+    if (name == null) {
+      name = file.getName() - ".txt"
+    }
+
+    def filelist = []
+    file.eachLine {
+      line ->
+        filelist += line
+    }
+    def list = fileTree(dir: j2sDir, includes: filelist)
+
+    def jsfile = "${outputDir}/core${name}.js"
+    def zjsfile = "${outputDir}/core${name}.z.js"
+
+    classlists += [
+    'jsfile': jsfile,
+    'zjsfile': zjsfile,
+    'list': list
+    ]
+
+    inputs.file(file)
+    inputs.files(list)
+    outputs.file(jsfile)
+    outputs.file(zjsfile)
+  }
+  
+  // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
+  def stevesoftClasslist = [
+    'jsfile': "${outputDir}/core_stevesoft.js",
+    'zjsfile': "${outputDir}/core_stevesoft.z.js",
+    'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js")
+  ]
+  classlists += stevesoftClasslist
+  inputs.files(stevesoftClasslist['list'])
+  outputs.file(stevesoftClasslist['jsfile'])
+  outputs.file(stevesoftClasslist['zjsfile'])
+
+  doFirst {
+    def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
+    logOutFile.getParentFile().mkdirs()
+    logOutFile.createNewFile()
+    logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsNoTranspileBuildAllCores\n----\n")
+
+    classlists.each {
+      jalviewjsCallCore(it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
+    }
+  }
+
+}
+
+
+jalviewjsNoTranspileBuildAllCores.mustRunAfter jalviewjsTranspile
+
+
+task jalviewjsBuildAllCores {
+  group "JalviewJS"
+  description "Build the core js lib closures listed in the classlists dir"
+  dependsOn jalviewjsTranspile
+  dependsOn jalviewjsNoTranspileBuildAllCores
+}
+
+
+task jalviewjsIDE_BuildAllCores {
+  group "00 JalviewJS in Eclipse"
+  description "Build the core js lib closures listed in the classlists dir"
+  dependsOn jalviewjsNoTranspileBuildAllCores
+}
+
+
+task jalviewjsPublishCoreTemplate(type: Sync) {
+  dependsOn jalviewjsSitePath
+  dependsOn jalviewjsBuildAllCores
+
+// clean this up
+  def inputFile = file("${jalviewDir}/${j2s_template_html}")
+  def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+
+// clean this up
+  def jalviewTemplateName = "JalviewJS"
+  def jalviewCoreName = "_jalview"
+
+  from inputFile
+  into outputDir
+  def outputFiles = []
+  rename { filename ->
+    outputFiles += "${outputDir}/${filename}"
+    if (filename.equals(inputFile.getName())) {
+      return "${jalviewTemplateName}_${jalviewCoreName}.html"
+    }
+    return null
+  }
+  filter(ReplaceTokens, beginToken: '', endToken: '', tokens: ['NONE': jalviewCoreName])
+  preserve {
+    include "**"
+  }
+  outputs.files outputFiles
+  inputs.files inputFile
+}