X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=build.gradle;h=4f9798cc05f9739e4e5f9b01587a9ad5d0068697;hp=365168937eb04cd0d8c7669d95155a1fd2042709;hb=ac63b721ce80f32a04a6d0eeff29192bad50972e;hpb=1814154a223744655b17f1be40a0afff4adb41f2

diff --git a/build.gradle b/build.gradle
index 3651689..4f9798c 100644
--- a/build.gradle
+++ b/build.gradle
@@ -12,6 +12,7 @@ import java.security.MessageDigest
 import groovy.transform.ExternalizeMethods
 import groovy.util.XmlParser
 import groovy.xml.XmlUtil
+import groovy.json.JsonBuilder
 import com.vladsch.flexmark.util.ast.Node
 import com.vladsch.flexmark.html.HtmlRenderer
 import com.vladsch.flexmark.parser.Parser
@@ -22,6 +23,11 @@ import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension
 import com.vladsch.flexmark.ext.autolink.AutolinkExtension
 import com.vladsch.flexmark.ext.anchorlink.AnchorLinkExtension
 import com.vladsch.flexmark.ext.toc.TocExtension
+import com.google.common.hash.HashCode
+import com.google.common.hash.Hashing
+import com.google.common.io.Files
+import org.jsoup.Jsoup
+import org.jsoup.nodes.Element
 
 buildscript {
   repositories {
@@ -30,6 +36,7 @@ buildscript {
   }
   dependencies {
     classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
+    classpath "org.jsoup:jsoup:1.14.3"
   }
 }
 
@@ -40,9 +47,9 @@ plugins {
   id 'eclipse'
   id "com.diffplug.gradle.spotless" version "3.28.0"
   id 'com.github.johnrengelman.shadow' version '4.0.3'
-  id 'com.install4j.gradle' version '8.0.4'
-  id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with  gradle task1 [task2 ...] taskTree
-  id 'com.palantir.git-version' version '0.12.3'
+  id 'com.install4j.gradle' version '9.0.6'
+  id 'com.dorongold.task-tree' version '2.1.0' // only needed to display task dependency tree with  gradle task1 [task2 ...] taskTree
+  id 'com.palantir.git-version' version '0.13.0' apply false
 }
 
 repositories {
@@ -52,29 +59,19 @@ repositories {
 }
 
 
+
 // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
 def string(Object o) {
   return o == null ? "" : o.toString()
 }
 
-
-ext {
-  jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
-  jalviewDirRelativePath = jalviewDir
-
-  // local build environment properties
-  // can be "projectDir/local.properties"
-  def localProps = "${projectDir}/local.properties"
-  def propsFile = null;
-  if (file(localProps).exists()) {
-    propsFile = localProps
-  }
-  // or "../projectDir_local.properties"
-  def dirLocalProps = projectDir.getParent() + "/" + projectDir.getName() + "_local.properties"
-  if (file(dirLocalProps).exists()) {
-    propsFile = dirLocalProps
+def overrideProperties(String propsFileName, boolean output = false) {
+  if (propsFileName == null) {
+    return
   }
-  if (propsFile != null) {
+  def propsFile = file(propsFileName)
+  if (propsFile != null && propsFile.exists()) {
+    println("Using properties from file '${propsFileName}'")
     try {
       def p = new Properties()
       def localPropsFIS = new FileInputStream(propsFile)
@@ -82,24 +79,51 @@ ext {
       localPropsFIS.close()
       p.each {
         key, val -> 
-          def oldval = findProperty(key)
-          setProperty(key, val)
-          if (oldval != null) {
-            println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
+          def oldval
+          if (project.hasProperty(key)) {
+            oldval = project.findProperty(key)
+            project.setProperty(key, val)
+            if (output) {
+              println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
+            }
           } else {
-            println("Setting unknown property '${key}' with ${file(propsFile).getName()}s value '${val}'")
+            ext.setProperty(key, val)
+            if (output) {
+              println("Setting ext property '${key}' with ${file(propsFile).getName()}s value '${val}'")
+            }
           }
       }
     } catch (Exception e) {
-      System.out.println("Exception reading local.properties")
+      println("Exception reading local.properties")
+      e.printStackTrace()
     }
   }
+}
+
+ext {
+  jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+  jalviewDirRelativePath = jalviewDir
+  date = new Date()
+
+  getdownChannelName = CHANNEL.toLowerCase()
+  // default to "default". Currently only has different cosmetics for "develop", "release", "default"
+  propertiesChannelName = ["develop", "release", "test-release", "jalviewjs", "jalviewjs-release" ].contains(getdownChannelName) ? getdownChannelName : "default"
+  // Import channel_properties
+  channelDir = string("${jalviewDir}/${channel_properties_dir}/${propertiesChannelName}")
+  channelGradleProperties = string("${channelDir}/channel_gradle.properties")
+  channelPropsFile = string("${channelDir}/${resource_dir}/${channel_props}")
+  overrideProperties(channelGradleProperties, false)
+  // local build environment properties
+  // can be "projectDir/local.properties"
+  overrideProperties("${projectDir}/local.properties", true)
+  // or "../projectDir_local.properties"
+  overrideProperties(projectDir.getParent() + "/" + projectDir.getName() + "_local.properties", true)
 
   ////  
   // Import releaseProps from the RELEASE file
   // or a file specified via JALVIEW_RELEASE_FILE if defined
   // Expect jalview.version and target release branch in jalview.release        
-  def releaseProps = new Properties();
+  releaseProps = new Properties();
   def releasePropFile = findProperty("JALVIEW_RELEASE_FILE");
   def defaultReleasePropFile = "${jalviewDirAbsolutePath}/RELEASE";
   try {
@@ -114,6 +138,7 @@ ext {
   if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
     JALVIEW_VERSION = releaseProps.get("jalview.version")
   }
+  println("JALVIEW_VERSION is set to '${JALVIEW_VERSION}'")
   
   // this property set when running Eclipse headlessly
   j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
@@ -147,6 +172,9 @@ ext {
   }
   */
 
+  // datestamp
+  buildDate = new Date().format("yyyyMMdd")
+
   // essentials
   bareSourceDir = string(source_dir)
   sourceDir = string("${jalviewDir}/${bareSourceDir}")
@@ -167,29 +195,43 @@ ext {
   //cloverTestClassesDir = cloverClassesDir
   cloverDb = string("${cloverBuildDir}/clover.db")
 
-  resourceClassesDir = useClover ? cloverClassesDir : classesDir
-
   testSourceDir = useClover ? cloverTestInstrDir : testDir
   testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
 
-  getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
+  getdownChannelDir = string("${getdown_website_dir}/${propertiesChannelName}")
+  getdownAppBaseDir = string("${jalviewDir}/${getdownChannelDir}/${JAVA_VERSION}")
+  getdownArchiveDir = string("${jalviewDir}/${getdown_archive_dir}")
+  getdownFullArchiveDir = null
+  getdownTextLines = []
+  getdownLaunchJvl = null
+  getdownVersionLaunchJvl = null
   buildDist = true
+  buildProperties = null
 
   // the following values might be overridden by the CHANNEL switch
-  getdownChannelName = CHANNEL.toLowerCase()
   getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
   getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
+  getdownArchiveAppBase = getdown_archive_base
   getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
   getdownAppDistDir = getdown_app_dir_alt
-  buildProperties = string("${resourceDir}/${build_properties_file}")
+  getdownImagesDir = string("${jalviewDir}/${getdown_images_dir}")
+  getdownSetAppBaseProperty = false // whether to pass the appbase and appdistdir to the application
   reportRsyncCommand = false
   jvlChannelName = CHANNEL.toLowerCase()
   install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
-  install4jDSStore = "DS_Store-NON-RELEASE"
-  install4jDMGBackgroundImage = "jalview_dmg_background-NON-RELEASE.png"
+  install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
+  install4jDMGBackgroundImage = "${install4j_images_dir}/${install4j_dmg_background}"
   install4jInstallerName = "${jalview_name} Non-Release Installer"
-  install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase()
+  install4jExecutableName = install4j_executable_name
   install4jExtraScheme = "jalviewx"
+  install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
+  install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
+  install4jPngIconFile = string("${install4j_images_dir}/${install4j_png_icon_file}")
+  install4jBackground = string("${install4j_images_dir}/${install4j_background}")
+  install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
+  install4jCheckSums = true
+
+  applicationName = "${jalview_name}"
   switch (CHANNEL) {
 
     case "BUILD":
@@ -205,12 +247,11 @@ ext {
     install4jExtraScheme = "jalviewb"
     break
 
-    case "RELEASE":
+    case [ "RELEASE", "JALVIEWJS-RELEASE" ]:
     getdownAppDistDir = getdown_app_dir_release
+    getdownSetAppBaseProperty = true
     reportRsyncCommand = true
     install4jSuffix = ""
-    install4jDSStore = "DS_Store"
-    install4jDMGBackgroundImage = "jalview_dmg_background.png"
     install4jInstallerName = "${jalview_name} Installer"
     break
 
@@ -232,7 +273,7 @@ ext {
     case "ARCHIVELOCAL":
     getdownChannelName = string("archive/${JALVIEW_VERSION}")
     getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
-    getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+    getdownAppBase = file(getdownAppBaseDir).toURI().toString()
     if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
       throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
     } else {
@@ -248,19 +289,18 @@ ext {
 
     case "DEVELOP":
     reportRsyncCommand = true
-    
+    getdownSetAppBaseProperty = true
     // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
-    JALVIEW_VERSION=JALVIEW_VERSION+"-develop"
+    JALVIEW_VERSION=JALVIEW_VERSION+"-d${buildDate}"
     
     install4jSuffix = "Develop"
-    install4jDSStore = "DS_Store-DEVELOP"
-    install4jDMGBackgroundImage = "jalview_dmg_background-DEVELOP.png"
     install4jExtraScheme = "jalviewd"
     install4jInstallerName = "${jalview_name} Develop Installer"
     break
 
     case "TEST-RELEASE":
     reportRsyncCommand = true
+    getdownSetAppBaseProperty = true
     // Don't ignore transpile errors for release build
     if (jalviewjs_ignore_transpile_errors.equals("true")) {
       jalviewjs_ignore_transpile_errors = "false"
@@ -268,8 +308,6 @@ ext {
     }
     JALVIEW_VERSION = JALVIEW_VERSION+"-test"
     install4jSuffix = "Test"
-    install4jDSStore = "DS_Store-TEST-RELEASE"
-    install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
     install4jExtraScheme = "jalviewt"
     install4jInstallerName = "${jalview_name} Test Installer"
     break
@@ -293,17 +331,17 @@ ext {
     }
     JALVIEW_VERSION = "TEST"
     install4jSuffix = "Test-Local"
-    install4jDSStore = "DS_Store-TEST-RELEASE"
-    install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
     install4jExtraScheme = "jalviewt"
     install4jInstallerName = "${jalview_name} Test Installer"
     break
 
-    case "LOCAL":
+    case [ "LOCAL", "JALVIEWJS" ]:
     JALVIEW_VERSION = "TEST"
-    getdownAppBase = file(getdownWebsiteDir).toURI().toString()
+    getdownAppBase = file(getdownAppBaseDir).toURI().toString()
+    getdownArchiveAppBase = file("${jalviewDir}/${getdown_archive_dir}").toURI().toString()
     getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
     install4jExtraScheme = "jalviewl"
+    install4jCheckSums = false
     break
 
     default: // something wrong specified
@@ -311,20 +349,31 @@ ext {
     break
 
   }
+  JALVIEW_VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
+  hugoDataJsonFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_data_installers_dir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
+  hugoArchiveMdFile = file("${jalviewDir}/${hugo_build_dir}/${hugo_version_archive_dir}/Version-${JALVIEW_VERSION_UNDERSCORES}/_index.md")
   // override getdownAppBase if requested
   if (findProperty("getdown_appbase_override") != null) {
-    getdownAppBase = string(getProperty("getdown_appbase_override"))
+    // revert to LOCAL if empty string
+    if (string(getdown_appbase_override) == "") {
+      getdownAppBase = file(getdownAppBaseDir).toURI().toString()
+      getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+    } else if (string(getdown_appbase_override).startsWith("file://")) {
+      getdownAppBase = string(getdown_appbase_override)
+      getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
+    } else {
+      getdownAppBase = string(getdown_appbase_override)
+    }
     println("Overriding getdown appbase with '${getdownAppBase}'")
   }
   // sanitise file name for jalview launcher file for this channel
   jvlChannelName = jvlChannelName.replaceAll("[^\\w\\-]+", "_")
   // install4j application and folder names
   if (install4jSuffix == "") {
-    install4jApplicationName = "${jalview_name}"
     install4jBundleId = "${install4j_bundle_id}"
     install4jWinApplicationId = install4j_release_win_application_id
   } else {
-    install4jApplicationName = "${jalview_name} ${install4jSuffix}"
+    applicationName = "${jalview_name} ${install4jSuffix}"
     install4jBundleId = "${install4j_bundle_id}-" + install4jSuffix.toLowerCase()
     // add int hash of install4jSuffix to the last part of the application_id
     def id = install4j_release_win_application_id
@@ -334,34 +383,47 @@ ext {
   }
   // sanitise folder and id names
   // install4jApplicationFolder = e.g. "Jalview Build"
-  install4jApplicationFolder = install4jApplicationName
+  install4jApplicationFolder = applicationName
                                     .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
                                     .replaceAll("_+", "_") // collapse __
-  install4jInternalId = install4jApplicationName
+  install4jInternalId = applicationName
                                     .replaceAll(" ","_")
                                     .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
                                     .replaceAll("_+", "") // collapse __
                                     //.replaceAll("_*-_*", "-") // collapse _-_
-  install4jUnixApplicationFolder = install4jApplicationName
+  install4jUnixApplicationFolder = applicationName
                                     .replaceAll(" ","_")
                                     .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
                                     .replaceAll("_+", "_") // collapse __
                                     .replaceAll("_*-_*", "-") // collapse _-_
                                     .toLowerCase()
 
-  getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
-  //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
-  getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
-  getdownInstallDir = string("${getdownWebsiteDir}/${getdown_install_dir}")
+  getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
+  getdownAppDir = string("${getdownAppBaseDir}/${getdownAppDistDir}")
+  //getdownJ11libDir = "${getdownAppBaseDir}/${getdown_j11lib_dir}"
+  getdownResourceDir = string("${getdownAppBaseDir}/${getdown_resource_dir}")
+  getdownInstallDir = string("${getdownAppBaseDir}/${getdown_install_dir}")
   getdownFilesDir = string("${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/")
   getdownFilesInstallDir = string("${getdownFilesDir}/${getdown_install_dir}")
   /* compile without modules -- using classpath libraries
   modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
   modules_runtimeClasspath = modules_compileClasspath
   */
-  def details = versionDetails()
-  gitHash = details.gitHash
-  gitBranch = details.branchName
+
+  gitHash = "SOURCE"
+  gitBranch = "Source"
+  try {
+    apply plugin: "com.palantir.git-version"
+    def details = versionDetails()
+    gitHash = details.gitHash
+    gitBranch = details.branchName
+  } catch(org.gradle.api.internal.plugins.PluginApplicationException e) {
+    println("Not in a git repository. Using git values from RELEASE properties file.")
+    gitHash = releaseProps.getProperty("git.hash")
+    gitBranch = releaseProps.getProperty("git.branch")
+  } catch(java.lang.RuntimeException e1) {
+    throw new GradleException("Error with git-version plugin.  Directory '.git' exists but versionDetails() cannot be found.")
+  }
 
   println("Using a ${CHANNEL} profile.")
 
@@ -397,16 +459,16 @@ ext {
     '--add-modules', j11modules
     ]
      */
-  } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
-    JAVA_INTEGER_VERSION = JAVA_VERSION
-    libDir = j11libDir
-    libDistDir = j11libDir
-    compile_source_compatibility = JAVA_VERSION
-    compile_target_compatibility = JAVA_VERSION
+  } else if (JAVA_VERSION.equals("17")) {
+    JAVA_INTEGER_VERSION = string("17")
+    libDir = j17libDir
+    libDistDir = j17libDir
+    compile_source_compatibility = 17
+    compile_target_compatibility = 17
     getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
     getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
     getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
-    eclipseJavaRuntimeName = string("JavaSE-11")
+    eclipseJavaRuntimeName = string("JavaSE-17")
     /* compile without modules -- using classpath libraries
     additional_compiler_args += [
     '--module-path', modules_compileClasspath.asPath,
@@ -426,11 +488,11 @@ ext {
     jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
   }
   macosJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-mac-x64/jre")
-  macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-mac-x64.tar.gz")
   windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre")
-  windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-windows-x64.tar.gz")
   linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre")
-  linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre-${JAVA_INTEGER_VERSION}-linux-x64.tar.gz")
+  macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_mac_x64.tar.gz")
+  windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_windows_x64.tar.gz")
+  linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_linux_x64.tar.gz")
   install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
   install4jConfFileName = string("jalview-install4j-conf.install4j")
   install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
@@ -439,12 +501,18 @@ ext {
     install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
   }
 
+  resourceBuildDir = string("${buildDir}/resources")
+  resourcesBuildDir = string("${resourceBuildDir}/resources_build")
+  helpBuildDir = string("${resourceBuildDir}/help_build")
+  docBuildDir = string("${resourceBuildDir}/doc_build")
 
-
+  if (buildProperties == null) {
+    buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
+  }
   buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
-  helpFile = string("${resourceClassesDir}/${help_dir}/help.jhm")
   helpParentDir = string("${jalviewDir}/${help_parent_dir}")
   helpSourceDir = string("${helpParentDir}/${help_dir}")
+  helpFile = string("${helpBuildDir}/${help_dir}/help.jhm")
 
 
   relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
@@ -463,6 +531,7 @@ ext {
   jalviewjsCoreClasslists = []
   jalviewjsJalviewTemplateName = string(jalviewjs_name)
   jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
+  jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
   jalviewjsJ2sProps = null
   jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
 
@@ -482,16 +551,14 @@ sourceSets {
     }
 
     resources {
-      srcDirs resourceDir
-      srcDirs += helpParentDir
+      srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
     }
 
-    jar.destinationDir = file("${jalviewDir}/${package_dir}")
-
     compileClasspath = files(sourceSets.main.java.outputDir)
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 
     runtimeClasspath = compileClasspath
+    runtimeClasspath += files(sourceSets.main.resources.srcDirs)
   }
 
   clover {
@@ -528,6 +595,7 @@ sourceSets {
     compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
 
     runtimeClasspath = compileClasspath
+    runtimeClasspath += files(sourceSets.test.resources.srcDirs)
   }
 
 }
@@ -548,14 +616,12 @@ eclipse {
 
   classpath {
     //defaultOutputDir = sourceSets.main.java.outputDir
-    def removeThese = []
-    configurations.each{
-      if (it.isCanBeResolved()) {
-        removeThese += it
+    configurations.each{ c->
+      if (c.isCanBeResolved()) {
+        minusConfigurations += [c]
       }
     }
 
-    minusConfigurations += removeThese
     plusConfigurations = [ ]
     file {
 
@@ -1000,43 +1066,10 @@ cleanTest {
 
 // format is a string like date.format("dd MMMM yyyy")
 def getDate(format) {
-  def date = new Date()
   return date.format(format)
 }
 
 
-task createBuildProperties(type: WriteProperties) {
-  group = "build"
-  description = "Create the ${buildProperties} file"
-  
-  inputs.dir(sourceDir)
-  inputs.dir(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")
-  //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
-  property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
-  property "VERSION", JALVIEW_VERSION
-  property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
-  outputs.file(outputFile)
-}
-
-
-clean {
-  doFirst {
-    delete buildProperties
-  }
-}
-
-
-task cleanBuildingHTML(type: Delete) {
-  doFirst {
-    delete buildingHTML
-  }
-}
-
-
 def convertMdToHtml (FileTree mdFiles, File cssFile) {
   MutableDataSet options = new MutableDataSet()
 
@@ -1110,14 +1143,45 @@ def convertMdToHtml (FileTree mdFiles, File cssFile) {
 
     def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
     def htmlFile = file(htmlFilePath)
+    println("Creating ${htmlFilePath}")
     htmlFile.text = htmlText
   }
 }
 
 
+task copyDocs(type: Copy) {
+  def inputDir = "${jalviewDir}/${doc_dir}"
+  def outputDir = "${docBuildDir}/${doc_dir}"
+  from(inputDir) {
+    include('**/*.txt')
+    include('**/*.md')
+    include('**/*.html')
+    include('**/*.xml')
+    filter(ReplaceTokens,
+      beginToken: '$$',
+      endToken: '$$',
+      tokens: [
+        'Version-Rel': JALVIEW_VERSION,
+        'Year-Rel': getDate("yyyy")
+      ]
+    )
+  }
+  from(inputDir) {
+    exclude('**/*.txt')
+    exclude('**/*.md')
+    exclude('**/*.html')
+    exclude('**/*.xml')
+  }
+  into outputDir
+
+  inputs.dir(inputDir)
+  outputs.dir(outputDir)
+}
+
+
 task convertMdFiles {
-  dependsOn cleanBuildingHTML
-  def mdFiles = fileTree(dir: "${jalviewDir}/${doc_dir}", include: "*.md")
+  dependsOn copyDocs
+  def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
   def cssFile = file("${jalviewDir}/${flexmark_css}")
 
   doLast {
@@ -1136,21 +1200,224 @@ task convertMdFiles {
 }
 
 
-task syncDocs(type: Sync) {
-  dependsOn convertMdFiles
-  def syncDir = "${classesDir}/${doc_dir}"
-  from fileTree("${jalviewDir}/${doc_dir}")
-  into syncDir
+def hugoTemplateSubstitutions(String input, Map extras=null) {
+  def replacements = [
+    DATE: getDate("yyyy-MM-dd"),
+    CHANNEL: propertiesChannelName,
+    APPLICATION_NAME: applicationName,
+    GIT_HASH: gitHash,
+    GIT_BRANCH: gitBranch,
+    VERSION: JALVIEW_VERSION,
+    JAVA_VERSION: JAVA_VERSION,
+    VERSION_UNDERSCORES: JALVIEW_VERSION_UNDERSCORES,
+    DRAFT: "false",
+    JVL_HEADER: ""
+  ]
+  def output = input
+  if (extras != null) {
+    extras.each{ k, v ->
+      output = output.replaceAll("__${k}__", ((v == null)?"":v))
+    }
+  }
+  replacements.each{ k, v ->
+    output = output.replaceAll("__${k}__", ((v == null)?"":v))
+  }
+  return output
+}
+
+def mdFileComponents(File mdFile, def dateOnly=false) {
+  def map = [:]
+  def content = ""
+  if (mdFile.exists()) {
+    def inFrontMatter = false
+    def firstLine = true
+    mdFile.eachLine { line ->
+      if (line.matches("---")) {
+        def prev = inFrontMatter
+        inFrontMatter = firstLine
+        if (inFrontMatter != prev)
+          return false
+      }
+      if (inFrontMatter) {
+        def m = null
+        if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) {
+          map["date"] = new Date().parse("yyyy-MM-dd HH:mm:ss", m[0][1])
+        } else if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2})/) {
+          map["date"] = new Date().parse("yyyy-MM-dd", m[0][1])
+        } else if (m = line =~ /^channel:\s*(\S+)/) {
+          map["channel"] = m[0][1]
+        } else if (m = line =~ /^version:\s*(\S+)/) {
+          map["version"] = m[0][1]
+        } else if (m = line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) {
+          map[ m[0][1] ] = m[0][2]
+        }
+        if (dateOnly && map["date"] != null) {
+          return false
+        }
+      } else {
+        if (dateOnly)
+          return false
+        content += line+"\n"
+      }
+      firstLine = false
+    }
+  }
+  return dateOnly ? map["date"] : [map, content]
+}
+
+task hugoTemplates {
+  group "website"
+  description "Create partially populated md pages for hugo website build"
+
+  def hugoTemplatesDir = file("${jalviewDir}/${hugo_templates_dir}")
+  def hugoBuildDir = "${jalviewDir}/${hugo_build_dir}"
+  def templateFiles = fileTree(dir: hugoTemplatesDir)
+  def releaseMdFile = file("${jalviewDir}/${releases_dir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
+  def whatsnewMdFile = file("${jalviewDir}/${whatsnew_dir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
+  def oldJvlFile = file("${jalviewDir}/${hugo_old_jvl}")
+  def jalviewjsFile = file("${jalviewDir}/${hugo_jalviewjs}")
+
+  doFirst {
+    // specific release template for version archive
+    def changes = ""
+    def whatsnew = null
+    def givenDate = null
+    def givenChannel = null
+    def givenVersion = null
+    if (CHANNEL == "RELEASE") {
+      def (map, content) = mdFileComponents(releaseMdFile)
+      givenDate = map.date
+      givenChannel = map.channel
+      givenVersion = map.version
+      changes = content
+      if (givenVersion != null && givenVersion != JALVIEW_VERSION) {
+        throw new GradleException("'version' header (${givenVersion}) found in ${releaseMdFile} does not match JALVIEW_VERSION (${JALVIEW_VERSION})")
+      }
+
+      if (whatsnewMdFile.exists())
+        whatsnew = whatsnewMdFile.text
+    }
+
+    def oldJvl = oldJvlFile.exists() ? oldJvlFile.collect{it} : []
+    def jalviewjsLink = jalviewjsFile.exists() ? jalviewjsFile.collect{it} : []
+
+    def changesHugo = null
+    if (changes != null) {
+      changesHugo = '<div class="release_notes">\n\n'
+      def inSection = false
+      changes.eachLine { line ->
+        def m = null
+        if (m = line =~ /^##([^#].*)$/) {
+          if (inSection) {
+            changesHugo += "</div>\n\n"
+          }
+          def section = m[0][1].trim()
+          section = section.toLowerCase()
+          section = section.replaceAll(/ +/, "_")
+          section = section.replaceAll(/[^a-z0-9_\-]/, "")
+          changesHugo += "<div class=\"${section}\">\n\n"
+          inSection = true
+        } else if (m = line =~ /^(\s*-\s*)<!--([^>]+)-->(.*?)(<br\/?>)?\s*$/) {
+          def comment = m[0][2].trim()
+          if (comment != "") {
+            comment = comment.replaceAll('"', "&quot;")
+            def issuekeys = []
+            comment.eachMatch(/JAL-\d+/) { jal -> issuekeys += jal }
+            def newline = m[0][1]
+            if (comment.trim() != "")
+              newline += "{{<comment>}}${comment}{{</comment>}}  "
+            newline += m[0][3].trim()
+            if (issuekeys.size() > 0)
+              newline += "  {{< jal issue=\"${issuekeys.join(",")}\" alt=\"${comment}\" >}}"
+            if (m[0][4] != null)
+              newline += m[0][4]
+            line = newline
+          }
+        }
+        changesHugo += line+"\n"
+      }
+      if (inSection) {
+        changesHugo += "\n</div>\n\n"
+      }
+      changesHugo += '</div>'
+    }
+
+    templateFiles.each{ templateFile ->
+      def newFileName = string(hugoTemplateSubstitutions(templateFile.getName()))
+      def relPath = hugoTemplatesDir.toPath().relativize(templateFile.toPath()).getParent()
+      def newRelPathName = hugoTemplateSubstitutions( relPath.toString() )
+
+      def outPathName = string("${hugoBuildDir}/$newRelPathName")
+
+      copy {
+        from templateFile
+        rename(templateFile.getName(), newFileName)
+        into outPathName
+      }
+
+      def newFile = file("${outPathName}/${newFileName}".toString())
+      def content = newFile.text
+      newFile.text = hugoTemplateSubstitutions(content,
+        [
+          WHATSNEW: whatsnew,
+          CHANGES: changesHugo,
+          DATE: givenDate == null ? "" : givenDate.format("yyyy-MM-dd"),
+          DRAFT: givenDate == null ? "true" : "false",
+          JALVIEWJSLINK: jalviewjsLink.contains(JALVIEW_VERSION) ? "true" : "false",
+          JVL_HEADER: oldJvl.contains(JALVIEW_VERSION) ? "jvl: true" : ""
+        ]
+      )
+    }
+
+  }
+
+  inputs.file(oldJvlFile)
+  inputs.dir(hugoTemplatesDir)
+  inputs.property("JALVIEW_VERSION", { JALVIEW_VERSION })
+  inputs.property("CHANNEL", { CHANNEL })
+}
+
+def getMdDate(File mdFile) {
+  return mdFileComponents(mdFile, true)
+}
+
+def getMdSections(String content) {
+  def sections = [:]
+  def sectionContent = ""
+  def sectionName = null
+  content.eachLine { line ->
+    def m = null
+    if (m = line =~ /^##([^#].*)$/) {
+      if (sectionName != null) {
+        sections[sectionName] = sectionContent
+        sectionName = null
+        sectionContent = ""
+      }
+      sectionName = m[0][1].trim()
+      sectionName = sectionName.toLowerCase()
+      sectionName = sectionName.replaceAll(/ +/, "_")
+      sectionName = sectionName.replaceAll(/[^a-z0-9_\-]/, "")
+    } else if (sectionName != null) {
+      sectionContent += line+"\n"
+    }
+  }
+  if (sectionContent != null) {
+    sections[sectionName] = sectionContent
+  }
+  return sections
 }
 
 
 task copyHelp(type: Copy) {
   def inputDir = helpSourceDir
-  def outputDir = "${resourceClassesDir}/${help_dir}"
+  def outputDir = "${helpBuildDir}/${help_dir}"
   from(inputDir) {
-    exclude '**/*.gif'
-    exclude '**/*.jpg'
-    exclude '**/*.png'
+    include('**/*.txt')
+    include('**/*.md')
+    include('**/*.html')
+    include('**/*.hs')
+    include('**/*.xml')
+    include('**/*.jhm')
     filter(ReplaceTokens,
       beginToken: '$$',
       endToken: '$$',
@@ -1161,9 +1428,12 @@ task copyHelp(type: Copy) {
     )
   }
   from(inputDir) {
-    include '**/*.gif'
-    include '**/*.jpg'
-    include '**/*.png'
+    exclude('**/*.txt')
+    exclude('**/*.md')
+    exclude('**/*.html')
+    exclude('**/*.hs')
+    exclude('**/*.xml')
+    exclude('**/*.jhm')
   }
   into outputDir
 
@@ -1173,40 +1443,258 @@ task copyHelp(type: Copy) {
 }
 
 
-task syncLib(type: Sync) {
-  def syncDir = "${resourceClassesDir}/${libDistDir}"
-  from fileTree("${jalviewDir}/${libDistDir}")
-  into syncDir
+task releasesTemplates {
+  group "help"
+  description "Recreate whatsNew.html and releases.html from markdown files and templates in help"
+
+  dependsOn copyHelp
+
+  def releasesTemplateFile = file("${jalviewDir}/${releases_template}")
+  def whatsnewTemplateFile = file("${jalviewDir}/${whatsnew_template}")
+  def releasesHtmlFile = file("${helpBuildDir}/${help_dir}/${releases_html}")
+  def whatsnewHtmlFile = file("${helpBuildDir}/${help_dir}/${whatsnew_html}")
+  def releasesMdDir = "${jalviewDir}/${releases_dir}"
+  def whatsnewMdDir = "${jalviewDir}/${whatsnew_dir}"
+
+  doFirst {
+    def releaseMdFile = file("${releasesMdDir}/release-${JALVIEW_VERSION_UNDERSCORES}.md")
+    def whatsnewMdFile = file("${whatsnewMdDir}/whatsnew-${JALVIEW_VERSION_UNDERSCORES}.md")
+
+    if (CHANNEL == "RELEASE") {
+      if (!releaseMdFile.exists()) {
+        throw new GradleException("File ${releaseMdFile} must be created for RELEASE")
+      }
+      if (!whatsnewMdFile.exists()) {
+        throw new GradleException("File ${whatsnewMdFile} must be created for RELEASE")
+      }
+    }
+
+    def releaseFiles = fileTree(dir: releasesMdDir, include: "release-*.md")
+    def releaseFilesDates = releaseFiles.collectEntries {
+      [(it): getMdDate(it)]
+    }
+    releaseFiles = releaseFiles.sort { a,b -> releaseFilesDates[a].compareTo(releaseFilesDates[b]) }
+
+    def releasesTemplate = releasesTemplateFile.text
+    def m = releasesTemplate =~ /(?s)__VERSION_LOOP_START__(.*)__VERSION_LOOP_END__/
+    def versionTemplate = m[0][1]
+
+    MutableDataSet options = new MutableDataSet()
+
+    def extensions = new ArrayList<>()
+    options.set(Parser.EXTENSIONS, extensions)
+    options.set(Parser.HTML_BLOCK_COMMENT_ONLY_FULL_LINE, true)
+
+    Parser parser = Parser.builder(options).build()
+    HtmlRenderer renderer = HtmlRenderer.builder(options).build()
+
+    def actualVersions = releaseFiles.collect { rf ->
+      def (rfMap, rfContent) = mdFileComponents(rf)
+      return rfMap.version
+    }
+    def versionsHtml = ""
+    def linkedVersions = []
+    releaseFiles.reverse().each { rFile ->
+      def (rMap, rContent) = mdFileComponents(rFile)
+
+      def versionLink = ""
+      def partialVersion = ""
+      def firstPart = true
+      rMap.version.split("\\.").each { part ->
+        def displayPart = ( firstPart ? "" : "." ) + part
+        partialVersion += displayPart
+        if (
+            linkedVersions.contains(partialVersion)
+            || ( actualVersions.contains(partialVersion) && partialVersion != rMap.version )
+            ) {
+          versionLink += displayPart
+        } else {
+          versionLink += "<a id=\"Jalview.${partialVersion}\">${displayPart}</a>"
+          linkedVersions += partialVersion
+        }
+        firstPart = false
+      }
+      def displayDate = releaseFilesDates[rFile].format("dd/MM/yyyy")
+
+      def lm = null
+      def rContentProcessed = ""
+      rContent.eachLine { line ->
+        if (lm = line =~ /^(\s*-)(\s*<!--[^>]*?-->)(.*)$/) {
+          line = "${lm[0][1]}${lm[0][3]}${lm[0][2]}"
+      } else if (lm = line =~ /^###([^#]+.*)$/) {
+          line = "_${lm[0][1].trim()}_"
+        }
+        rContentProcessed += line + "\n"
+      }
+
+      def rContentSections = getMdSections(rContentProcessed)
+      def rVersion = versionTemplate
+      if (rVersion != "") {
+        def rNewFeatures = rContentSections["new_features"]
+        def rIssuesResolved = rContentSections["issues_resolved"]
+        Node newFeaturesNode = parser.parse(rNewFeatures)
+        String newFeaturesHtml = renderer.render(newFeaturesNode)
+        Node issuesResolvedNode = parser.parse(rIssuesResolved)
+        String issuesResolvedHtml = renderer.render(issuesResolvedNode)
+        rVersion = hugoTemplateSubstitutions(rVersion,
+          [
+            VERSION: rMap.version,
+            VERSION_LINK: versionLink,
+            DISPLAY_DATE: displayDate,
+            NEW_FEATURES: newFeaturesHtml,
+            ISSUES_RESOLVED: issuesResolvedHtml
+          ]
+        )
+        versionsHtml += rVersion
+      }
+    }
+
+    releasesTemplate = releasesTemplate.replaceAll("(?s)__VERSION_LOOP_START__.*__VERSION_LOOP_END__", versionsHtml)
+    releasesTemplate = hugoTemplateSubstitutions(releasesTemplate)
+    releasesHtmlFile.text = releasesTemplate
+
+    if (whatsnewMdFile.exists()) {
+      def wnDisplayDate = releaseFilesDates[releaseMdFile] != null ? releaseFilesDates[releaseMdFile].format("dd MMMM yyyy") : ""
+      def whatsnewMd = hugoTemplateSubstitutions(whatsnewMdFile.text)
+      Node whatsnewNode = parser.parse(whatsnewMd)
+      String whatsnewHtml = renderer.render(whatsnewNode)
+      whatsnewHtml = whatsnewTemplateFile.text.replaceAll("__WHATS_NEW__", whatsnewHtml)
+      whatsnewHtmlFile.text = hugoTemplateSubstitutions(whatsnewHtml,
+        [
+          DISPLAY_DATE: wnDisplayDate
+        ]
+      )
+    } else if (gradle.taskGraph.hasTask(":linkCheck")) {
+      whatsnewHtmlFile.text = "Development build " + getDate("yyyy-MM-dd HH:mm:ss")
+    }
+
+  }
+
+  inputs.file(releasesTemplateFile)
+  inputs.file(whatsnewTemplateFile)
+  inputs.dir(releasesMdDir)
+  inputs.dir(whatsnewMdDir)
+  outputs.file(releasesHtmlFile)
+  outputs.file(whatsnewHtmlFile)
 }
 
 
-task syncResources(type: Sync) {
-  dependsOn createBuildProperties
-  from resourceDir
-  include "**/*.*"
-  into "${resourceClassesDir}"
-  preserve {
-    include "**"
+task copyResources(type: Copy) {
+  group = "build"
+  description = "Copy (and make text substitutions in) the resources dir to the build area"
+
+  def inputDir = resourceDir
+  def outputDir = resourcesBuildDir
+  from(inputDir) {
+    include('**/*.txt')
+    include('**/*.md')
+    include('**/*.html')
+    include('**/*.xml')
+    filter(ReplaceTokens,
+      beginToken: '$$',
+      endToken: '$$',
+      tokens: [
+        'Version-Rel': JALVIEW_VERSION,
+        'Year-Rel': getDate("yyyy")
+      ]
+    )
+  }
+  from(inputDir) {
+    exclude('**/*.txt')
+    exclude('**/*.md')
+    exclude('**/*.html')
+    exclude('**/*.xml')
+  }
+  into outputDir
+
+  inputs.dir(inputDir)
+  outputs.dir(outputDir)
+}
+
+task copyChannelResources(type: Copy) {
+  dependsOn copyResources
+  group = "build"
+  description = "Copy the channel resources dir to the build resources area"
+
+  def inputDir = "${channelDir}/${resource_dir}"
+  def outputDir = resourcesBuildDir
+  from inputDir
+  into outputDir
+
+  inputs.dir(inputDir)
+  outputs.dir(outputDir)
+}
+
+task createBuildProperties(type: WriteProperties) {
+  dependsOn copyResources
+  group = "build"
+  description = "Create the ${buildProperties} file"
+  
+  inputs.dir(sourceDir)
+  inputs.dir(resourcesBuildDir)
+  outputFile (buildProperties)
+  // taking time specific comment out to allow better incremental builds
+  comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
+  //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
+  property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
+  property "VERSION", JALVIEW_VERSION
+  property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
+  if (getdownSetAppBaseProperty) {
+    property "GETDOWNAPPBASE", getdownAppBase
+    property "GETDOWNAPPDISTDIR", getdownAppDistDir
   }
+  outputs.file(outputFile)
+}
+
+
+task buildIndices(type: JavaExec) {
+  dependsOn copyHelp
+  classpath = sourceSets.main.compileClasspath
+  main = "com.sun.java.help.search.Indexer"
+  workingDir = "${helpBuildDir}/${help_dir}"
+  def argDir = "html"
+  args = [ argDir ]
+  inputs.dir("${workingDir}/${argDir}")
+
+  outputs.dir("${classesDir}/doc")
+  outputs.dir("${classesDir}/help")
+  outputs.file("${workingDir}/JavaHelpSearch/DOCS")
+  outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
+  outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
+  outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
+  outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
+  outputs.file("${workingDir}/JavaHelpSearch/TMAP")
 }
 
+task buildResources {
+  dependsOn copyResources
+  dependsOn copyChannelResources
+  dependsOn createBuildProperties
+}
 
 task prepare {
-  dependsOn syncResources
-  dependsOn syncDocs
+  dependsOn buildResources
+  dependsOn copyDocs
   dependsOn copyHelp
+  dependsOn releasesTemplates
+  dependsOn convertMdFiles
+  dependsOn buildIndices
 }
 
 
+compileJava.dependsOn prepare
+run.dependsOn compileJava
+//run.dependsOn prepare
+
+
 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
 test {
   dependsOn prepare
-  //dependsOn compileJava ////? DELETE
 
   if (useClover) {
     dependsOn cloverClasses
    } else { //?
-     dependsOn compileJava //?
+    dependsOn compileJava //?
   }
 
   useTestNG() {
@@ -1219,12 +1707,16 @@ test {
   maxHeapSize = "1024m"
 
   workingDir = jalviewDir
-  //systemProperties 'clover.jar' System.properties.clover.jar
   def testLaf = project.findProperty("test_laf")
   if (testLaf != null) {
     println("Setting Test LaF to '${testLaf}'")
     systemProperty "laf", testLaf
   }
+  def testHiDPIScale = project.findProperty("test_HiDPIScale")
+  if (testHiDPIScale != null) {
+    println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
+    systemProperty "sun.java2d.uiScale", testHiDPIScale
+  }
   sourceCompatibility = compile_source_compatibility
   targetCompatibility = compile_target_compatibility
   jvmArgs += additional_compiler_args
@@ -1237,26 +1729,6 @@ test {
 }
 
 
-task buildIndices(type: JavaExec) {
-  dependsOn copyHelp
-  classpath = sourceSets.main.compileClasspath
-  main = "com.sun.java.help.search.Indexer"
-  workingDir = "${classesDir}/${help_dir}"
-  def argDir = "html"
-  args = [ argDir ]
-  inputs.dir("${workingDir}/${argDir}")
-
-  outputs.dir("${classesDir}/doc")
-  outputs.dir("${classesDir}/help")
-  outputs.file("${workingDir}/JavaHelpSearch/DOCS")
-  outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
-  outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
-  outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
-  outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
-  outputs.file("${workingDir}/JavaHelpSearch/TMAP")
-}
-
-
 task compileLinkCheck(type: JavaCompile) {
   options.fork = true
   classpath = files("${jalviewDir}/${utils_dir}")
@@ -1271,30 +1743,31 @@ task compileLinkCheck(type: JavaCompile) {
 
 
 task linkCheck(type: JavaExec) {
-  dependsOn prepare, compileLinkCheck
+  dependsOn prepare
+  dependsOn compileLinkCheck
 
   def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
   classpath = files("${jalviewDir}/${utils_dir}")
   main = "HelpLinksChecker"
-  workingDir = jalviewDir
-  args = [ "${classesDir}/${help_dir}", "-nointernet" ]
+  workingDir = "${helpBuildDir}"
+  args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
 
   def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
-  def errFOS = outFOS
   standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
     outFOS,
-    standardOutput)
+    System.out)
   errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
     outFOS,
-    errorOutput)
+    System.err)
 
-  inputs.dir("${classesDir}/${help_dir}")
+  inputs.dir(helpBuildDir)
   outputs.file(helpLinksCheckerOutFile)
 }
 
+
 // import the pubhtmlhelp target
 ant.properties.basedir = "${jalviewDir}"
-ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${help_dir}"
+ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
 ant.importBuild "${utils_dir}/publishHelp.xml"
 
 
@@ -1306,19 +1779,22 @@ task cleanPackageDir(type: Delete) {
 
 
 jar {
+  dependsOn prepare
   dependsOn linkCheck
-  dependsOn buildIndices
-  dependsOn createBuildProperties
 
   manifest {
     attributes "Main-Class": main_class,
     "Permissions": "all-permissions",
-    "Application-Name": "Jalview Desktop",
-    "Codebase": application_codebase
+    "Application-Name": applicationName,
+    "Codebase": application_codebase,
+    "Implementation-Version": JALVIEW_VERSION
   }
 
-  destinationDir = file("${jalviewDir}/${package_dir}")
-  archiveName = rootProject.name+".jar"
+  def outputDir = "${jalviewDir}/${package_dir}"
+  destinationDirectory = file(outputDir)
+  archiveFileName = rootProject.name+".jar"
+  duplicatesStrategy "EXCLUDE"
+
 
   exclude "cache*/**"
   exclude "*.jar"
@@ -1326,8 +1802,11 @@ jar {
   exclude "**/*.jar"
   exclude "**/*.jar.*"
 
-  inputs.dir(classesDir)
-  outputs.file("${jalviewDir}/${package_dir}/${archiveName}")
+  inputs.dir(sourceSets.main.java.outputDir)
+  sourceSets.main.resources.srcDirs.each{ dir ->
+    inputs.dir(dir)
+  }
+  outputs.file("${outputDir}/${archiveFileName}")
 }
 
 
@@ -1339,10 +1818,11 @@ task copyJars(type: Copy) {
 
 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
 task syncJars(type: Sync) {
+  dependsOn jar
   from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
   into "${jalviewDir}/${package_dir}"
   preserve {
-    include jar.archiveName
+    include jar.archiveFileName.getOrNull()
   }
 }
 
@@ -1366,6 +1846,7 @@ task cleanDist {
   dependsOn clean
 }
 
+
 shadowJar {
   group = "distribution"
   description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
@@ -1376,8 +1857,12 @@ shadowJar {
     include("*.jar")
   }
   manifest {
-    attributes 'Implementation-Version': JALVIEW_VERSION
+    attributes "Implementation-Version": JALVIEW_VERSION,
+    "Application-Name": applicationName
   }
+
+  duplicatesStrategy "INCLUDE"
+
   mainClassName = shadow_jar_main_class
   mergeServiceFiles()
   classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
@@ -1393,23 +1878,28 @@ task getdownWebsite() {
   }
 
   def getdownWebsiteResourceFilenames = []
-  def getdownTextString = ""
   def getdownResourceDir = getdownResourceDir
   def getdownResourceFilenames = []
 
   doFirst {
     // clean the getdown website and files dir before creating getdown folders
-    delete getdownWebsiteDir
+    delete getdownAppBaseDir
     delete getdownFilesDir
 
     copy {
       from buildProperties
-      rename(build_properties_file, getdown_build_properties)
+      rename(file(buildProperties).getName(), getdown_build_properties)
       into getdownAppDir
     }
     getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
 
-    // set some getdown_txt_ properties then go through all properties looking for getdown_txt_...
+    copy {
+      from channelPropsFile
+      into getdownAppBaseDir
+    }
+    getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
+
+    // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
     def props = project.properties.sort { it.key }
     if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
       props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
@@ -1420,19 +1910,27 @@ task getdownWebsite() {
     if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
       props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
     }
+    if (getdownImagesDir != null && file(getdownImagesDir).exists()) {
+      props.put("getdown_txt_ui.background_image", "${getdownImagesDir}/${getdown_background_image}")
+      props.put("getdown_txt_ui.instant_background_image", "${getdownImagesDir}/${getdown_instant_background_image}")
+      props.put("getdown_txt_ui.error_background", "${getdownImagesDir}/${getdown_error_background}")
+      props.put("getdown_txt_ui.progress_image", "${getdownImagesDir}/${getdown_progress_image}")
+      props.put("getdown_txt_ui.icon", "${getdownImagesDir}/${getdown_icon}")
+      props.put("getdown_txt_ui.mac_dock_icon", "${getdownImagesDir}/${getdown_mac_dock_icon}")
+    }
 
     props.put("getdown_txt_title", jalview_name)
-    props.put("getdown_txt_ui.name", install4jApplicationName)
+    props.put("getdown_txt_ui.name", applicationName)
 
     // start with appbase
-    getdownTextString += "appbase = ${getdownAppBase}\n"
+    getdownTextLines += "appbase = ${getdownAppBase}"
     props.each{ prop, val ->
       if (prop.startsWith("getdown_txt_") && val != null) {
         if (prop.startsWith("getdown_txt_multi_")) {
           def key = prop.substring(18)
           val.split(",").each{ v ->
-            def line = "${key} = ${v}\n"
-            getdownTextString += line
+            def line = "${key} = ${v}"
+            getdownTextLines += line
           }
         } else {
           // file values rationalised
@@ -1452,15 +1950,15 @@ task getdownWebsite() {
             }
           }
           if (! prop.startsWith("getdown_txt_resource")) {
-            def line = prop.substring(12) + " = ${val}\n"
-            getdownTextString += line
+            def line = prop.substring(12) + " = ${val}"
+            getdownTextLines += line
           }
         }
       }
     }
 
     getdownWebsiteResourceFilenames.each{ filename ->
-      getdownTextString += "resource = ${filename}\n"
+      getdownTextLines += "resource = ${filename}"
     }
     getdownResourceFilenames.each{ filename ->
       copy {
@@ -1468,6 +1966,18 @@ task getdownWebsite() {
         into getdownResourceDir
       }
     }
+    
+    def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
+    getdownWrapperScripts.each{ script ->
+      def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
+      if (s.exists()) {
+        copy {
+          from s
+          into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
+        }
+        getdownTextLines += "resource = ${getdown_wrapper_script_dir}/${script}"
+      }
+    }
 
     def codeFiles = []
     fileTree(file(package_dir)).each{ f ->
@@ -1478,10 +1988,12 @@ task getdownWebsite() {
         codeFiles += f
       }
     }
-    codeFiles.sort().each{f ->
+    def jalviewJar = jar.archiveFileName.getOrNull()
+    // put jalview.jar first for CLASSPATH and .properties files reasons
+    codeFiles.sort{a, b -> ( a.getName() == jalviewJar ? -1 : ( b.getName() == jalviewJar ? 1 : a <=> b ) ) }.each{f ->
       def name = f.getName()
-      def line = "code = ${getdownAppDistDir}/${name}\n"
-      getdownTextString += line
+      def line = "code = ${getdownAppDistDir}/${name}"
+      getdownTextLines += line
       copy {
         from f.getPath()
         into getdownAppDir
@@ -1494,8 +2006,8 @@ task getdownWebsite() {
     def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
     j11libFiles.sort().each{f ->
     def name = f.getName()
-    def line = "code = ${getdown_j11lib_dir}/${name}\n"
-    getdownTextString += line
+    def line = "code = ${getdown_j11lib_dir}/${name}"
+    getdownTextLines += line
     copy {
     from f.getPath()
     into getdownJ11libDir
@@ -1505,59 +2017,71 @@ task getdownWebsite() {
      */
 
     // getdown-launcher.jar should not be in main application class path so the main application can move it when updated.  Listed as a resource so it gets updated.
-    //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
-    getdownTextString += "resource = ${getdown_launcher_new}\n"
-    getdownTextString += "class = ${main_class}\n"
+    //getdownTextLines += "class = " + file(getdownLauncher).getName()
+    getdownTextLines += "resource = ${getdown_launcher_new}"
+    getdownTextLines += "class = ${main_class}"
+    // Not setting these properties in general so that getdownappbase and getdowndistdir will default to release version in jalview.bin.Cache
+    if (getdownSetAppBaseProperty) {
+      getdownTextLines += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}"
+      getdownTextLines += "jvmarg = -Dgetdownappbase=${getdownAppBase}"
+    }
 
-    def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
-    getdown_txt.write(getdownTextString)
+    def getdownTxt = file("${getdownAppBaseDir}/getdown.txt")
+    getdownTxt.write(getdownTextLines.join("\n"))
 
-    def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
-    def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}")
+    getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
+    def launchJvl = file("${getdownAppBaseDir}/${getdownLaunchJvl}")
     launchJvl.write("appbase=${getdownAppBase}")
 
+    // files going into the getdown website dir: getdown-launcher.jar
     copy {
       from getdownLauncher
       rename(file(getdownLauncher).getName(), getdown_launcher_new)
-      into getdownWebsiteDir
+      into getdownAppBaseDir
     }
 
+    // files going into the getdown website dir: getdown-launcher(-local).jar
     copy {
       from getdownLauncher
       if (file(getdownLauncher).getName() != getdown_launcher) {
         rename(file(getdownLauncher).getName(), getdown_launcher)
       }
-      into getdownWebsiteDir
+      into getdownAppBaseDir
     }
 
+    // files going into the getdown website dir: ./install dir and files
     if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
       copy {
-        from getdown_txt
+        from getdownTxt
         from getdownLauncher
-        from "${getdownWebsiteDir}/${getdown_build_properties}"
+        from "${getdownAppDir}/${getdown_build_properties}"
         if (file(getdownLauncher).getName() != getdown_launcher) {
           rename(file(getdownLauncher).getName(), getdown_launcher)
         }
         into getdownInstallDir
       }
 
+      // and make a copy in the getdown files dir (these are not downloaded by getdown)
       copy {
         from getdownInstallDir
         into getdownFilesInstallDir
       }
     }
 
+    // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
     copy {
-      from getdown_txt
+      from getdownTxt
       from launchJvl
       from getdownLauncher
-      from "${getdownWebsiteDir}/${getdown_build_properties}"
+      from "${getdownAppBaseDir}/${getdown_build_properties}"
+      from "${getdownAppBaseDir}/${channel_props}"
       if (file(getdownLauncher).getName() != getdown_launcher) {
         rename(file(getdownLauncher).getName(), getdown_launcher)
       }
       into getdownFilesDir
     }
 
+    // and ./resource (not all downloaded by getdown)
     copy {
       from getdownResourceDir
       into "${getdownFilesDir}/${getdown_resource_dir}"
@@ -1567,7 +2091,7 @@ task getdownWebsite() {
   if (buildDist) {
     inputs.dir("${jalviewDir}/${package_dir}")
   }
-  outputs.dir(getdownWebsiteDir)
+  outputs.dir(getdownAppBaseDir)
   outputs.dir(getdownFilesDir)
 }
 
@@ -1598,9 +2122,9 @@ task getdownDigest(type: JavaExec) {
     classpath = files(getdownLauncher)
   }
   main = "com.threerings.getdown.tools.Digester"
-  args getdownWebsiteDir
-  inputs.dir(getdownWebsiteDir)
-  outputs.file("${getdownWebsiteDir}/digest2.txt")
+  args getdownAppBaseDir
+  inputs.dir(getdownAppBaseDir)
+  outputs.file("${getdownAppBaseDir}/digest2.txt")
 }
 
 
@@ -1610,7 +2134,7 @@ task getdown() {
   dependsOn getdownDigest
   doLast {
     if (reportRsyncCommand) {
-      def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
+      def fromDir = getdownAppBaseDir + (getdownAppBaseDir.endsWith('/')?'':'/')
       def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
       println "LIKELY RSYNC COMMAND:"
       println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
@@ -1627,6 +2151,106 @@ task getdown() {
 }
 
 
+task getdownArchiveBuild() {
+  group = "distribution"
+  description = "Put files in the archive dir to go on the website"
+
+  dependsOn getdownWebsite
+
+  def v = "v${JALVIEW_VERSION_UNDERSCORES}"
+  def vDir = "${getdownArchiveDir}/${v}"
+  getdownFullArchiveDir = "${vDir}/getdown"
+  getdownVersionLaunchJvl = "${vDir}/jalview-${v}.jvl"
+
+  def vAltDir = "alt_${v}"
+  def archiveImagesDir = "${jalviewDir}/${channel_properties_dir}/old/images"
+
+  doFirst {
+    // cleanup old "old" dir
+    delete getdownArchiveDir
+
+    def getdownArchiveTxt = file("${getdownFullArchiveDir}/getdown.txt")
+    getdownArchiveTxt.getParentFile().mkdirs()
+    def getdownArchiveTextLines = []
+    def getdownFullArchiveAppBase = "${getdownArchiveAppBase}${getdownArchiveAppBase.endsWith("/")?"":"/"}${v}/getdown/"
+
+    // the libdir
+    copy {
+      from "${getdownAppBaseDir}/${getdownAppDistDir}"
+      into "${getdownFullArchiveDir}/${vAltDir}"
+    }
+
+    getdownTextLines.each { line ->
+      line = line.replaceAll("^(?<s>appbase\\s*=\\s*).*", '${s}'+getdownFullArchiveAppBase)
+      line = line.replaceAll("^(?<s>(resource|code)\\s*=\\s*)${getdownAppDistDir}/", '${s}'+vAltDir+"/")
+      line = line.replaceAll("^(?<s>ui.background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background.png")
+      line = line.replaceAll("^(?<s>ui.instant_background_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_initialising.png")
+      line = line.replaceAll("^(?<s>ui.error_background\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_background_error.png")
+      line = line.replaceAll("^(?<s>ui.progress_image\\s*=\\s*).*\\.png", '${s}'+"${getdown_resource_dir}/jalview_archive_getdown_progress_bar.png")
+      // remove the existing resource = resource/ or bin/ lines
+      if (! line.matches("resource\\s*=\\s*(resource|bin)/.*")) {
+        getdownArchiveTextLines += line
+      }
+    }
+
+    // the resource dir -- add these files as resource lines in getdown.txt
+    copy {
+      from "${archiveImagesDir}"
+      into "${getdownFullArchiveDir}/${getdown_resource_dir}"
+      eachFile { file ->
+        getdownArchiveTextLines += "resource = ${getdown_resource_dir}/${file.getName()}"
+      }
+    }
+
+    getdownArchiveTxt.write(getdownArchiveTextLines.join("\n"))
+
+    def vLaunchJvl = file(getdownVersionLaunchJvl)
+    vLaunchJvl.getParentFile().mkdirs()
+    vLaunchJvl.write("appbase=${getdownFullArchiveAppBase}\n")
+    def vLaunchJvlPath = vLaunchJvl.toPath().toAbsolutePath()
+    def jvlLinkPath = file("${vDir}/jalview.jvl").toPath().toAbsolutePath()
+    // for some reason filepath.relativize(fileInSameDirPath) gives a path to "../" which is wrong
+    //java.nio.file.Files.createSymbolicLink(jvlLinkPath, jvlLinkPath.relativize(vLaunchJvlPath));
+    java.nio.file.Files.createSymbolicLink(jvlLinkPath, java.nio.file.Paths.get(".",vLaunchJvl.getName()));
+
+    // files going into the getdown files dir: getdown.txt, getdown-launcher.jar, channel-launch.jvl, build_properties
+    copy {
+      from getdownLauncher
+      from "${getdownAppBaseDir}/${getdownLaunchJvl}"
+      from "${getdownAppBaseDir}/${getdown_launcher_new}"
+      from "${getdownAppBaseDir}/${channel_props}"
+      if (file(getdownLauncher).getName() != getdown_launcher) {
+        rename(file(getdownLauncher).getName(), getdown_launcher)
+      }
+      into getdownFullArchiveDir
+    }
+
+  }
+}
+
+task getdownArchiveDigest(type: JavaExec) {
+  group = "distribution"
+  description = "Digest the getdown archive folder"
+
+  dependsOn getdownArchiveBuild
+
+  doFirst {
+    classpath = files(getdownLauncher)
+    args getdownFullArchiveDir
+  }
+  main = "com.threerings.getdown.tools.Digester"
+  inputs.dir(getdownFullArchiveDir)
+  outputs.file("${getdownFullArchiveDir}/digest2.txt")
+}
+
+task getdownArchive() {
+  group = "distribution"
+  description = "Build the website archive dir with getdown digest"
+
+  dependsOn getdownArchiveBuild
+  dependsOn getdownArchiveDigest
+}
+
 tasks.withType(JavaCompile) {
 	options.encoding = 'UTF-8'
 }
@@ -1634,8 +2258,9 @@ tasks.withType(JavaCompile) {
 
 clean {
   doFirst {
-    delete getdownWebsiteDir
+    delete getdownAppBaseDir
     delete getdownFilesDir
+    delete getdownArchiveDir
   }
 }
 
@@ -1675,13 +2300,15 @@ task copyInstall4jTemplate {
       }
     }
 
+    // disable install screen for OSX dmg (for 2.11.2.0)
+    install4jConfigXml.'**'.macosArchive.each { macosArchive -> 
+      macosArchive.attributes().remove('executeSetupApp')
+      macosArchive.attributes().remove('setupAppId')
+    }
+
     // turn off checksum creation for LOCAL channel
     def e = install4jConfigXml.application[0]
-    if (CHANNEL == "LOCAL") {
-      e.'@createChecksums' = "false"
-    } else {
-      e.'@createChecksums' = "true"
-    }
+    e.'@createChecksums' = string(install4jCheckSums)
 
     // put file association actions where placeholder action is
     def install4jFileAssociationsText = install4jFileAssociationsFile.text
@@ -1722,12 +2349,6 @@ task copyInstall4jTemplate {
       }
     }
 
-    // remove the "Uninstall Old Jalview (optional)" symlink from DMG for non-release DS_Stores
-    if (! (CHANNEL == "RELEASE" || CHANNEL == "TEST-RELEASE" ) ) {
-      def symlink = install4jConfigXml.'**'.topLevelFiles.symlink.find { sl -> sl.'@name' == "Uninstall Old Jalview (optional).app" }
-      symlink.parent().remove(symlink)
-    }
-
     // write install4j file
     install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
   }
@@ -1740,12 +2361,23 @@ clean {
   }
 }
 
+task cleanInstallersDataFiles {
+  def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
+  def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
+  def hugoDataJsonFile = file("${jalviewDir}/${install4jBuildDir}/installers-${JALVIEW_VERSION_UNDERSCORES}.json")
+  doFirst {
+    delete installersOutputTxt
+    delete installersSha256
+    delete hugoDataJsonFile
+  }
+}
 
-task installers(type: com.install4j.gradle.Install4jTask) {
+task installerFiles(type: com.install4j.gradle.Install4jTask) {
   group = "distribution"
   description = "Create the install4j installers"
   dependsOn getdown
   dependsOn copyInstall4jTemplate
+  dependsOn cleanInstallersDataFiles
 
   projectFile = install4jConfFile
 
@@ -1760,14 +2392,14 @@ task installers(type: com.install4j.gradle.Install4jTask) {
     filesMd5 = filesMd5.substring(0,8)
   }
   def install4jTemplateVersion = "${JALVIEW_VERSION}_F${filesMd5}_C${gitHash}"
-  // make install4jBuildDir relative to jalviewDir
-  def install4jBuildDir = "${install4j_build_dir}/${JAVA_VERSION}"
 
   variables = [
     'JALVIEW_NAME': jalview_name,
-    'JALVIEW_APPLICATION_NAME': install4jApplicationName,
+    'JALVIEW_APPLICATION_NAME': applicationName,
     'JALVIEW_DIR': "../..",
     'OSX_KEYSTORE': OSX_KEYSTORE,
+    'OSX_APPLEID': OSX_APPLEID,
+    'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
     'JSIGN_SH': JSIGN_SH,
     'JRE_DIR': getdown_app_dir_java,
     'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
@@ -1787,11 +2419,15 @@ task installers(type: com.install4j.gradle.Install4jTask) {
     'BUNDLE_ID': install4jBundleId,
     'INTERNAL_ID': install4jInternalId,
     'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
-    'MACOS_DS_STORE': install4jDSStore,
+    'MACOS_DMG_DS_STORE': install4jDMGDSStore,
     'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
+    'WRAPPER_LINK': getdownWrapperLink,
+    'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
+    'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
+    'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
     'INSTALLER_NAME': install4jInstallerName,
     'INSTALL4J_UTILS_DIR': install4j_utils_dir,
-    'GETDOWN_WEBSITE_DIR': getdown_website_dir,
+    'GETDOWN_CHANNEL_DIR': getdownChannelDir,
     'GETDOWN_FILES_DIR': getdown_files_dir,
     'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
     'GETDOWN_DIST_DIR': getdownAppDistDir,
@@ -1804,6 +2440,11 @@ task installers(type: com.install4j.gradle.Install4jTask) {
     'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
     'EXECUTABLE_NAME': install4jExecutableName,
     'EXTRA_SCHEME': install4jExtraScheme,
+    'MAC_ICONS_FILE': install4jMacIconsFile,
+    'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
+    'PNG_ICON_FILE': install4jPngIconFile,
+    'BACKGROUND': install4jBackground,
+
   ]
 
   //println("INSTALL4J VARIABLES:")
@@ -1815,17 +2456,27 @@ task installers(type: com.install4j.gradle.Install4jTask) {
   if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
     faster = true
     disableSigning = true
+    disableNotarization = true
   }
 
   if (OSX_KEYPASS) {
     macKeystorePassword = OSX_KEYPASS
+  } 
+  
+  if (OSX_ALTOOLPASS) {
+    appleIdPassword = OSX_ALTOOLPASS
+    disableNotarization = false
+  } else {
+    disableNotarization = true
   }
 
   doFirst {
     println("Using projectFile "+projectFile)
+    if (!disableNotarization) { println("Will notarize OSX App DMG") }
   }
+  //verbose=true
 
-  inputs.dir(getdownWebsiteDir)
+  inputs.dir(getdownAppBaseDir)
   inputs.file(install4jConfFile)
   inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
   inputs.dir(macosJavaVMDir)
@@ -1833,6 +2484,84 @@ task installers(type: com.install4j.gradle.Install4jTask) {
   outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
 }
 
+def getDataHash(File myFile) {
+  HashCode hash = Files.asByteSource(myFile).hash(Hashing.sha256())
+  return myFile.exists()
+  ? [
+      "file" : myFile.getName(),
+      "filesize" : myFile.length(),
+      "sha256" : hash.toString()
+    ]
+  : null
+}
+
+def writeDataJsonFile(File installersOutputTxt, File installersSha256, File dataJsonFile) {
+  def hash = [
+    "channel" : getdownChannelName,
+    "date" : getDate("yyyy-MM-dd HH:mm:ss"),
+    "git-commit" : "${gitHash} [${gitBranch}]",
+    "version" : JALVIEW_VERSION
+  ]
+  // install4j installer files
+  if (installersOutputTxt.exists()) {
+    def idHash = [:]
+    installersOutputTxt.readLines().each { def line ->
+      if (line.startsWith("#")) {
+        return;
+      }
+      line.replaceAll("\n","")
+      def vals = line.split("\t")
+      def filename = vals[3]
+      def filesize = file(filename).length()
+      filename = filename.replaceAll(/^.*\//, "")
+      hash[vals[0]] = [ "id" : vals[0], "os" : vals[1], "name" : vals[2], "file" : filename, "filesize" : filesize ]
+      idHash."${filename}" = vals[0]
+    }
+    if (install4jCheckSums && installersSha256.exists()) {
+      installersSha256.readLines().each { def line ->
+        if (line.startsWith("#")) {
+          return;
+        }
+        line.replaceAll("\n","")
+        def vals = line.split(/\s+\*?/)
+        def filename = vals[1]
+        def innerHash = (hash.(idHash."${filename}"))."sha256" = vals[0]
+      }
+    }
+  }
+
+  [
+    "JAR": shadowJar.archiveFile, // executable JAR
+    "JVL": getdownVersionLaunchJvl, // version JVL
+    "SOURCE": sourceDist.archiveFile // source TGZ
+  ].each { key, value ->
+    def file = file(value)
+    if (file.exists()) {
+      def fileHash = getDataHash(file)
+      if (fileHash != null) {
+        hash."${key}" = fileHash;
+      }
+    }
+  }
+  return dataJsonFile.write(new JsonBuilder(hash).toPrettyString())
+}
+
+task staticMakeInstallersJsonFile {
+  doFirst {
+    def output = findProperty("i4j_output")
+    def sha256 = findProperty("i4j_sha256")
+    def json = findProperty("i4j_json")
+    if (output == null || sha256 == null || json == null) {
+      throw new GradleException("Must provide paths to all of output.txt, sha256sums, and output.json with '-Pi4j_output=... -Pi4j_sha256=... -Pi4j_json=...")
+    }
+    writeDataJsonFile(file(output), file(sha256), file(json))
+  }
+}
+
+task installers {
+  dependsOn installerFiles
+}
+
 
 spotless {
   java {
@@ -1840,21 +2569,35 @@ spotless {
   }
 }
 
+task createSourceReleaseProperties(type: WriteProperties) {
+  group = "distribution"
+  description = "Create the source RELEASE properties file"
+  
+  def sourceTarBuildDir = "${buildDir}/sourceTar"
+  def sourceReleasePropertiesFile = "${sourceTarBuildDir}/RELEASE"
+  outputFile (sourceReleasePropertiesFile)
+
+  doFirst {
+    releaseProps.each{ key, val -> property key, val }
+    property "git.branch", gitBranch
+    property "git.hash", gitHash
+  }
+
+  outputs.file(outputFile)
+}
 
 task sourceDist(type: Tar) {
   group "distribution"
   description "Create a source .tar.gz file for distribution"
-  
+
+  dependsOn createBuildProperties
   dependsOn convertMdFiles
+  dependsOn eclipseAllPreferences
+  dependsOn createSourceReleaseProperties
 
-  def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
-  def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
-  // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09]
-  try {
-    archiveFileName = outputFileName
-  } catch (Exception e) {
-    archiveName = outputFileName
-  }
+
+  def outputFileName = "${project.name}_${JALVIEW_VERSION_UNDERSCORES}.tar.gz"
+  archiveFileName = outputFileName
   
   compression Compression.GZIP
   
@@ -1875,6 +2618,7 @@ task sourceDist(type: Tar) {
     "*locales/**",
     "utils/InstallAnywhere",
     "**/*.log",
+    "RELEASE",
   ] 
   def PROCESS_FILES=[
     "AUTHORS",
@@ -1884,7 +2628,6 @@ task sourceDist(type: Tar) {
     "FEATURETODO",
     "LICENSE",
     "**/README",
-    "RELEASE",
     "THIRDPARTYLIBS",
     "TESTNG",
     "build.gradle",
@@ -1899,7 +2642,9 @@ task sourceDist(type: Tar) {
     "**/*.sh",
   ]
   def INCLUDE_FILES=[
-    ".settings/org.eclipse.jdt.core.jalview.prefs",
+    ".classpath",
+    ".settings/org.eclipse.buildship.core.prefs",
+    ".settings/org.eclipse.jdt.core.prefs"
   ]
 
   from(jalviewDir) {
@@ -1923,7 +2668,9 @@ task sourceDist(type: Tar) {
     exclude ("utils/InstallAnywhere")
 
     exclude (getdown_files_dir)
-    exclude (getdown_website_dir)
+    // getdown_website_dir and getdown_archive_dir moved to build/website/docroot/getdown
+    //exclude (getdown_website_dir)
+    //exclude (getdown_archive_dir)
 
     // exluding these as not using jars as modules yet
     exclude ("${j11modDir}/**/*.jar")
@@ -1937,14 +2684,64 @@ task sourceDist(type: Tar) {
 //    exclude(EXCLUDE_FILES)
 //    exclude(PROCESS_FILES)
 //  }
+
+  from(file(buildProperties).getParent()) {
+    include(file(buildProperties).getName())
+    rename(file(buildProperties).getName(), "build_properties")
+    filter({ line ->
+      line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
+    })
+  }
+
+  def sourceTarBuildDir = "${buildDir}/sourceTar"
+  from(sourceTarBuildDir) {
+    // this includes the appended RELEASE properties file
+  }
 }
 
+task dataInstallersJson {
+  group "website"
+  description "Create the installers-VERSION.json data file for installer files created"
+
+  mustRunAfter installers
+  mustRunAfter shadowJar
+  mustRunAfter sourceDist
+  mustRunAfter getdownArchive
+
+  def installersOutputTxt = file("${jalviewDir}/${install4jBuildDir}/output.txt")
+  def installersSha256 = file("${jalviewDir}/${install4jBuildDir}/sha256sums")
+
+  if (installersOutputTxt.exists()) {
+    inputs.file(installersOutputTxt)
+  }
+  if (install4jCheckSums && installersSha256.exists()) {
+    inputs.file(installersSha256)
+  }
+  [
+    shadowJar.archiveFile, // executable JAR
+    getdownVersionLaunchJvl, // version JVL
+    sourceDist.archiveFile // source TGZ
+  ].each { fileName ->
+    if (file(fileName).exists()) {
+      inputs.file(fileName)
+    }
+  }
+
+  outputs.file(hugoDataJsonFile)
+
+  doFirst {
+    writeDataJsonFile(installersOutputTxt, installersSha256, hugoDataJsonFile)
+  }
+}
 
 task helppages {
+  group "help"
+  description "Copies all help pages to build dir. Runs ant task 'pubhtmlhelp'."
+
   dependsOn copyHelp
   dependsOn pubhtmlhelp
   
-  inputs.dir("${classesDir}/${help_dir}")
+  inputs.dir("${helpBuildDir}/${help_dir}")
   outputs.dir("${buildDir}/distributions/${help_dir}")
 }
 
@@ -1956,6 +2753,33 @@ task j2sSetHeadlessBuild {
 }
 
 
+task jalviewjsEnableAltFileProperty(type: WriteProperties) {
+  group "jalviewjs"
+  description "Enable the alternative J2S Config file for headless build"
+
+  outputFile = jalviewjsJ2sSettingsFileName
+  def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
+  def j2sProps = new Properties()
+  if (j2sPropsFile.exists()) {
+    try {
+      def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
+      j2sProps.load(j2sPropsFileFIS)
+      j2sPropsFileFIS.close()
+
+      j2sProps.each { prop, val ->
+        property(prop, val)
+      }
+    } catch (Exception e) {
+      println("Exception reading ${jalviewjsJ2sSettingsFileName}")
+      e.printStackTrace()
+    }
+  }
+  if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
+    property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
+  }
+}
+
+
 task jalviewjsSetEclipseWorkspace {
   def propKey = "jalviewjs_eclipse_workspace"
   def propVal = null
@@ -2168,7 +2992,7 @@ task jalviewjsTransferUnzipAllLibs {
 
 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
   group "JalviewJS"
-  description "Create the .j2s file from the j2s.* properties"
+  description "Create the alternative j2s file from the j2s.* properties"
 
   jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
   def siteDirProperty = "j2s.site.directory"
@@ -2187,11 +3011,11 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) {
       property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
     }
   }
-  outputFile = jalviewjsJ2sSettingsFileName
+  outputFile = jalviewjsJ2sAltSettingsFileName
 
   if (! IN_ECLIPSE) {
     inputs.properties(jalviewjsJ2sProps)
-    outputs.file(jalviewjsJ2sSettingsFileName)
+    outputs.file(jalviewjsJ2sAltSettingsFileName)
   }
 }
 
@@ -2219,13 +3043,19 @@ task jalviewjsSyncAllLibs (type: Sync) {
   preserve {
     include "**"
   }
+
+  // should this be exclude really ?
+  duplicatesStrategy "INCLUDE"
+
   outputs.files outputFiles
   inputs.files inputFiles
 }
 
 
 task jalviewjsSyncResources (type: Sync) {
-  def inputFiles = fileTree(dir: resourceDir)
+  dependsOn buildResources
+
+  def inputFiles = fileTree(dir: resourcesBuildDir)
   def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
 
   from inputFiles
@@ -2307,6 +3137,7 @@ task jalviewjsProjectImport(type: Exec) {
   args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
   if (!IN_ECLIPSE) {
     args += [ "-D${j2sHeadlessBuildProperty}=true" ]
+    args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
   }
 
   inputs.file("${jalviewDir}/.project")
@@ -2320,6 +3151,9 @@ task jalviewjsTranspile(type: Exec) {
   dependsOn jalviewjsEclipseSetup 
   dependsOn jalviewjsProjectImport
   dependsOn jalviewjsEclipsePaths
+  if (!IN_ECLIPSE) {
+    dependsOn jalviewjsEnableAltFileProperty
+  }
 
   doFirst {
     // do not run a headless transpile when we claim to be in Eclipse
@@ -2339,6 +3173,7 @@ task jalviewjsTranspile(type: Exec) {
   args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
   if (!IN_ECLIPSE) {
     args += [ "-D${j2sHeadlessBuildProperty}=true" ]
+    args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
   }
 
   def stdout
@@ -2366,12 +3201,12 @@ DEBUG: ${eclipseDebug}
         new org.apache.tools.ant.util.TeeOutputStream(
           logOutFOS,
           stdout),
-        standardOutput)
+        System.out)
       errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
         new org.apache.tools.ant.util.TeeOutputStream(
           logErrFOS,
           stderr),
-        errorOutput)
+        System.err)
     } else {
       standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
         logOutFOS,
@@ -2459,7 +3294,7 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin
           new org.apache.tools.ant.util.TeeOutputStream(
             logErrFOS,
             stderr),
-          errorOutput)
+          System.err)
     } else {
       standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
         logOutFOS,
@@ -2748,11 +3583,7 @@ task jalviewjsSiteTar(type: Tar) {
   description "Creates a tar.gz file for the website"
   dependsOn jalviewjsBuildSite
   def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
-  try {
-    archiveFileName = outputFilename
-  } catch (Exception e) {
-    archiveName = outputFilename
-  }
+  archiveFileName = outputFilename
 
   compression Compression.GZIP
 
@@ -2770,7 +3601,13 @@ task jalviewjsServer {
   def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
   doLast {
 
-    SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
+    def factory
+    try {
+      def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
+      factory = f.newInstance()
+    } catch (ClassNotFoundException e) {
+      throw new GradleException("Unable to create SimpleHttpFileServerFactory")
+    }
     def port = Integer.valueOf(jalviewjs_server_port)
     def start = port
     def running = false
@@ -2823,7 +3660,7 @@ task cleanJalviewjsAll {
     if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
       delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
     }
-    delete "${jalviewDir}/${jalviewjs_j2s_settings}"
+    delete jalviewjsJ2sAltSettingsFileName
   }
 
   outputs.upToDateWhen( { false } )