From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 5 Feb 2021 17:25:21 +0000 (+0000)
Subject: Merge branch 'task/JAL-3521_Slimmed_down_build.gradle_for_debian' into releases/Relea... 
X-Git-Tag: Release_2_11_1_4~9^2~9
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=b77d6d52b7e4c25068b2d7f974225f2469a1419b;hp=dcac7508c650e40ce26902ab81f3fcbf86d709eb

Merge branch 'task/JAL-3521_Slimmed_down_build.gradle_for_debian' into releases/Release_2_11_1_4_debianpatches
---

diff --git a/build.gradle b/build.gradle
index b2e9af1..042baf5 100644
--- a/build.gradle
+++ b/build.gradle
@@ -2,37 +2,14 @@
  * For properties set within build.gradle, use camelCaseNoSpace.
  */
 import org.apache.tools.ant.filters.ReplaceTokens
-import org.gradle.internal.os.OperatingSystem
-import org.gradle.plugins.ide.eclipse.model.Output
-import org.gradle.plugins.ide.eclipse.model.Library
-import java.security.MessageDigest
-import groovy.transform.ExternalizeMethods
-import groovy.util.XmlParser
-import groovy.xml.XmlUtil
-
-
-buildscript {
-  repositories {
-    mavenCentral()
-    mavenLocal()
-  }
-}
+
+
 
 
 plugins {
   id 'java'
-  id 'application'
-  id 'eclipse'
-  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
 }
 
-repositories {
-  jcenter()
-  mavenCentral()
-  mavenLocal()
-}
 
 
 // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
@@ -45,38 +22,6 @@ ext {
   jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
   jalviewDirRelativePath = jalviewDir
 
-  // local build environment properties
-  // can be "projectDir/local.properties"
-  def localProps = "${projectDir}/local.properties"
-  def propsFile = null;
-  if (file(localProps).exists()) {
-    propsFile = localProps
-  }
-  // or "../projectDir_local.properties"
-  def dirLocalProps = projectDir.getParent() + "/" + projectDir.getName() + "_local.properties"
-  if (file(dirLocalProps).exists()) {
-    propsFile = dirLocalProps
-  }
-  if (propsFile != null) {
-    try {
-      def p = new Properties()
-      def localPropsFIS = new FileInputStream(propsFile)
-      p.load(localPropsFIS)
-      localPropsFIS.close()
-      p.each {
-        key, val -> 
-          def oldval = findProperty(key)
-          setProperty(key, val)
-          if (oldval != null) {
-            println("Overriding property '${key}' ('${oldval}') with ${file(propsFile).getName()} value '${val}'")
-          } else {
-            println("Setting unknown property '${key}' with ${file(propsFile).getName()}s value '${val}'")
-          }
-      }
-    } catch (Exception e) {
-      System.out.println("Exception reading local.properties")
-    }
-  }
 
   ////  
   // Import releaseProps from the RELEASE file
@@ -98,32 +43,6 @@ ext {
     JALVIEW_VERSION = releaseProps.get("jalview.version")
   }
   
-  // this property set when running Eclipse headlessly
-  j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
-  // this property set by Eclipse
-  eclipseApplicationProperty = string("eclipse.application")
-  // CHECK IF RUNNING FROM WITHIN ECLIPSE
-  def eclipseApplicationPropertyVal = System.properties[eclipseApplicationProperty]
-  IN_ECLIPSE = eclipseApplicationPropertyVal != null && eclipseApplicationPropertyVal.startsWith("org.eclipse.ui.")
-  // BUT WITHOUT THE HEADLESS BUILD PROPERTY SET
-  if (System.properties[j2sHeadlessBuildProperty].equals("true")) {
-    println("Setting IN_ECLIPSE to ${IN_ECLIPSE} as System.properties['${j2sHeadlessBuildProperty}'] == '${System.properties[j2sHeadlessBuildProperty]}'")
-    IN_ECLIPSE = false
-  }
-  if (IN_ECLIPSE) {
-    println("WITHIN ECLIPSE IDE")
-  } else {
-    println("HEADLESS BUILD")
-  }
-  /* *-/
-  System.properties.sort { it.key }.each {
-    key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
-  }
-  /-* *-/
-  if (false && IN_ECLIPSE) {
-    jalviewDir = jalviewDirAbsolutePath
-  }
-  */
 
   // essentials
   bareSourceDir = string(source_dir)
@@ -134,204 +53,13 @@ ext {
 
   classesDir = string("${jalviewDir}/${classes_dir}")
 
-  // clover
-  useClover = clover.equals("true")
-  cloverBuildDir = "${buildDir}/clover"
-  cloverInstrDir = file("${cloverBuildDir}/clover-instr")
-  cloverClassesDir = file("${cloverBuildDir}/clover-classes")
-  cloverReportDir = file("${buildDir}/reports/clover")
-  cloverTestInstrDir = file("${cloverBuildDir}/clover-test-instr")
-  cloverTestClassesDir = file("${cloverBuildDir}/clover-test-classes")
-  //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}")
-  buildDist = true
-
-  // the following values might be overridden by the CHANNEL switch
-  getdownChannelName = CHANNEL.toLowerCase()
-  getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
-  getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
-  getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
-  getdownAppDistDir = getdown_app_dir_alt
-  buildProperties = string("${classesDir}/${build_properties_file}")
-  reportRsyncCommand = false
-  jvlChannelName = CHANNEL.toLowerCase()
-  install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
-  install4jDSStore = "DS_Store-NON-RELEASE"
-  install4jDMGBackgroundImage = "jalview_dmg_background-NON-RELEASE.png"
-  install4jInstallerName = "${jalview_name} Non-Release Installer"
-  install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase()
-  install4jExtraScheme = "jalviewx"
-  switch (CHANNEL) {
-
-    case "BUILD":
-    // TODO: get bamboo build artifact URL for getdown artifacts
-    getdown_channel_base = bamboo_channelbase
-    getdownChannelName = string("${bamboo_planKey}/${JAVA_VERSION}")
-    getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
-    jvlChannelName += "_${getdownChannelName}"
-    // automatically add the test group Not-bamboo for exclusion 
-    if ("".equals(testng_excluded_groups)) { 
-      testng_excluded_groups = "Not-bamboo"
-    }
-    install4jExtraScheme = "jalviewb"
-    break
-
-    case "RELEASE":
-    getdownAppDistDir = getdown_app_dir_release
-    reportRsyncCommand = true
-    install4jSuffix = ""
-    install4jDSStore = "DS_Store"
-    install4jDMGBackgroundImage = "jalview_dmg_background.png"
-    install4jInstallerName = "${jalview_name} Installer"
-    break
-
-    case "ARCHIVE":
-    getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
-    getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
-    getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
-    if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
-      throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
-    } else {
-      package_dir = string("${ARCHIVEDIR}/${package_dir}")
-      buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
-      buildDist = false
-    }
-    reportRsyncCommand = true
-    install4jExtraScheme = "jalviewa"
-    break
-
-    case "ARCHIVELOCAL":
-    getdownChannelName = string("archive/${JALVIEW_VERSION}")
-    getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
-    getdownAppBase = file(getdownWebsiteDir).toURI().toString()
-    if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
-      throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
-    } else {
-      package_dir = string("${ARCHIVEDIR}/${package_dir}")
-      buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
-      buildDist = false
-    }
-    reportRsyncCommand = true
-    getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
-    install4jSuffix = "Archive"
-    install4jExtraScheme = "jalviewa"
-    break
-
-    case "DEVELOP":
-    reportRsyncCommand = true
-    
-    // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
-    JALVIEW_VERSION=JALVIEW_VERSION+"-develop"
-    
-    install4jSuffix = "Develop"
-    install4jDSStore = "DS_Store-DEVELOP"
-    install4jDMGBackgroundImage = "jalview_dmg_background-DEVELOP.png"
-    install4jExtraScheme = "jalviewd"
-    install4jInstallerName = "${jalview_name} Develop Installer"
-    break
-
-    case "TEST-RELEASE":
-    reportRsyncCommand = true
-    
-    // TEST-RELEASE is usually associated with a Jalview release series so set the version
-    JALVIEW_VERSION=JALVIEW_VERSION+"-test"
-    
-    install4jSuffix = "Test"
-    install4jDSStore = "DS_Store-TEST-RELEASE"
-    install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
-    install4jExtraScheme = "jalviewt"
-    install4jInstallerName = "${jalview_name} Test Installer"
-    break
-
-    case ~/^SCRATCH(|-[-\w]*)$/:
-    getdownChannelName = CHANNEL
-    getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
-    getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
-    reportRsyncCommand = true
-    install4jSuffix = "Scratch"
-    break
-
-    case "TEST-LOCAL":
-    if (!file("${LOCALDIR}").exists()) {
-      throw new GradleException("Must provide a LOCALDIR value to produce a local distribution")
-    } else {
-      getdownAppBase = file(file("${LOCALDIR}").getAbsolutePath()).toURI().toString()
-      getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
-    }
-    JALVIEW_VERSION = "TEST"
-    install4jSuffix = "Test-Local"
-    install4jDSStore = "DS_Store-TEST-RELEASE"
-    install4jDMGBackgroundImage = "jalview_dmg_background-TEST.png"
-    install4jExtraScheme = "jalviewt"
-    install4jInstallerName = "${jalview_name} Test Installer"
-    break
-
-    case "LOCAL":
-    getdownAppBase = file(getdownWebsiteDir).toURI().toString()
-    getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
-    install4jExtraScheme = "jalviewl"
-    break
-
-    default: // something wrong specified
-    throw new GradleException("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
-    break
 
-  }
-  // override getdownAppBase if requested
-  if (findProperty("getdown_appbase_override") != null) {
-    getdownAppBase = string(getProperty("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} ${install4jSuffix}"
-    install4jBundleId = "${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
-    def idsplitreverse = id.split("-").reverse()
-    idsplitreverse[0] = idsplitreverse[0].toInteger() + install4jSuffix.hashCode()
-    install4jWinApplicationId = idsplitreverse.reverse().join("-")
-  }
-  // sanitise folder and id names
-  // install4jApplicationFolder = e.g. "Jalview Build"
-  install4jApplicationFolder = install4jApplicationName
-                                    .replaceAll("[\"'~:/\\\\\\s]", "_") // replace all awkward filename chars " ' ~ : / \
-                                    .replaceAll("_+", "_") // collapse __
-  install4jInternalId = install4jApplicationName
-                                    .replaceAll(" ","_")
-                                    .replaceAll("[^\\w\\-\\.]", "_") // replace other non [alphanumeric,_,-,.]
-                                    .replaceAll("_+", "") // collapse __
-                                    //.replaceAll("_*-_*", "-") // collapse _-_
-  install4jUnixApplicationFolder = install4jApplicationName
-                                    .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}")
-  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}/${j11modDir}", include: ["*.jar"])
-  modules_runtimeClasspath = modules_compileClasspath
-  */
+  resourceClassesDir = classesDir
+
+  testSourceDir = testDir
+  testClassesDir = "${jalviewDir}/${test_output_dir}"
+
+  buildProperties = string("${classesDir}/${build_properties_file}")
   gitHash = string("")
   gitBranch = string("")
 
@@ -344,75 +72,25 @@ ext {
     //libDir = j8libDir
     libDir = j11libDir
     libDistDir = j8libDir
-    digestonlyDir = j8digestonlyDir
     compile_source_compatibility = 1.8
     compile_target_compatibility = 1.8
-    // these are getdown.txt properties defined dependent on the JAVA_VERSION
-    getdownAltJavaMinVersion = string(findProperty("getdown_alt_java8_min_version"))
-    getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java8_max_version"))
-    // this property is assigned below and expanded to multiple lines in the getdown task
-    getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java8_txt_multi_java_location"))
-    // this property is for the Java library used in eclipse
-    eclipseJavaRuntimeName = string("JavaSE-1.8")
   } else if (JAVA_VERSION.equals("11")) {
     JAVA_INTEGER_VERSION = string("11")
     libDir = j11libDir
     libDistDir = j11libDir
-    digestonlyDir = j11digestonlyDir
     compile_source_compatibility = 11
     compile_target_compatibility = 11
-    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")
-    /* compile without modules -- using classpath libraries
-    additional_compiler_args += [
-    '--module-path', modules_compileClasspath.asPath,
-    '--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
-    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")
-    /* compile without modules -- using classpath libraries
-    additional_compiler_args += [
-    '--module-path', modules_compileClasspath.asPath,
-    '--add-modules', j11modules
-    ]
-     */
   } else {
     throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
   }
 
 
-  // for install4j
-  JAVA_MIN_VERSION = JAVA_VERSION
-  JAVA_MAX_VERSION = JAVA_VERSION
-  def jreInstallsDir = string(jre_installs_dir)
-  if (jreInstallsDir.startsWith("~/")) {
-    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")
-  install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
-  install4jConfFileName = string("jalview-install4j-conf.install4j")
-  install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
-  install4jHomeDir = install4j_home_dir
-  if (install4jHomeDir.startsWith("~/")) {
-    install4jHomeDir = System.getProperty("user.home") + install4jHomeDir.substring(1)
-  }
-
 
 
   buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
@@ -421,28 +99,6 @@ ext {
   helpSourceDir = string("${helpParentDir}/${help_dir}")
 
 
-  relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
-  jalviewjsBuildDir = string("${relativeBuildDir}/jalviewjs")
-  jalviewjsSiteDir = string("${jalviewjsBuildDir}/${jalviewjs_site_dir}")
-  if (IN_ECLIPSE) {
-    jalviewjsTransferSiteJsDir = string(jalviewjsSiteDir)
-  } else {
-    jalviewjsTransferSiteJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_js")
-  }
-  jalviewjsTransferSiteLibDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_lib")
-  jalviewjsTransferSiteSwingJsDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_swingjs")
-  jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
-  jalviewjsJalviewCoreHtmlFile = string("")
-  jalviewjsJalviewCoreName = string(jalviewjs_core_name)
-  jalviewjsCoreClasslists = []
-  jalviewjsJalviewTemplateName = string(jalviewjs_name)
-  jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
-  jalviewjsJ2sProps = null
-
-  eclipseWorkspace = null
-  eclipseBinary = string("")
-  eclipseVersion = string("")
-  eclipseDebug = false
   // ENDEXT
 }
 
@@ -467,25 +123,6 @@ sourceSets {
     runtimeClasspath = compileClasspath
   }
 
-  clover {
-    java {
-      srcDirs cloverInstrDir
-      outputDir = cloverClassesDir
-    }
-
-    resources {
-      srcDirs = sourceSets.main.resources.srcDirs
-    }
-
-    compileClasspath = files( sourceSets.clover.java.outputDir )
-    //compileClasspath += files( testClassesDir )
-    compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
-    compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
-    compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
-
-    runtimeClasspath = compileClasspath
-  }
-
   test {
     java {
       srcDirs testSourceDir
@@ -493,11 +130,11 @@ sourceSets {
     }
 
     resources {
-      srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
+      srcDirs = sourceSets.main.resources.srcDirs
     }
 
     compileClasspath = files( sourceSets.test.java.outputDir )
-    compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
+    compileClasspath += sourceSets.main.compileClasspath
     compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
 
     runtimeClasspath = compileClasspath
@@ -506,358 +143,6 @@ sourceSets {
 }
 
 
-// eclipse project and settings files creation, also used by buildship
-eclipse {
-  project {
-    name = eclipse_project_name
-
-    natures 'org.eclipse.jdt.core.javanature',
-    'org.eclipse.jdt.groovy.core.groovyNature',
-    'org.eclipse.buildship.core.gradleprojectnature'
-
-    buildCommand 'org.eclipse.jdt.core.javabuilder'
-    buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
-  }
-
-  classpath {
-    //defaultOutputDir = sourceSets.main.java.outputDir
-    def removeThese = []
-    configurations.each{
-      if (it.isCanBeResolved()) {
-        removeThese += it
-      }
-    }
-
-    minusConfigurations += removeThese
-    plusConfigurations = [ ]
-    file {
-
-      whenMerged { cp ->
-        def removeTheseToo = []
-        HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
-        cp.entries.each { entry ->
-          // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
-          // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
-          // we add the resources and help/help dirs in as libs afterwards (see below)
-          if (entry.kind == 'src') {
-            if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
-              removeTheseToo += entry
-            } else {
-              alreadyAddedSrcPath.putAt(entry.path, true)
-            }
-          }
-
-        }
-        cp.entries.removeAll(removeTheseToo)
-
-        //cp.entries += new Output("${eclipse_bin_dir}/main")
-        if (file(helpParentDir).isDirectory()) {
-          cp.entries += new Library(fileReference(helpParentDir))
-        }
-        if (file(resourceDir).isDirectory()) {
-          cp.entries += new Library(fileReference(resourceDir))
-        }
-
-        HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
-
-        sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
-          //don't want to add outputDir as eclipse is using its own output dir in bin/main
-          if (it.isDirectory() || ! it.exists()) {
-            // don't add dirs to classpath, especially if they don't exist
-            return false // groovy "continue" in .any closure
-          }
-          def itPath = it.toString()
-          if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
-            // make relative path
-            itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
-          }
-          if (alreadyAddedLibPath.get(itPath)) {
-            //println("Not adding duplicate entry "+itPath)
-          } else {
-            //println("Adding entry "+itPath)
-            cp.entries += new Library(fileReference(itPath))
-            alreadyAddedLibPath.put(itPath, true)
-          }
-        }
-
-        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 "continue" in .any closure
-          }
-
-          def itPath = it.toString()
-          if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
-            itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
-          }
-          if (alreadyAddedLibPath.get(itPath)) {
-            // don't duplicate
-          } else {
-            def lib = new Library(fileReference(itPath))
-            lib.entryAttributes["test"] = "true"
-            cp.entries += lib
-            alreadyAddedLibPath.put(itPath, true)
-          }
-        }
-
-      } // whenMerged
-
-    } // file
-
-    containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
-
-  } // classpath
-
-  jdt {
-    // for the IDE, use java 11 compatibility
-    sourceCompatibility = compile_source_compatibility
-    targetCompatibility = compile_target_compatibility
-    javaRuntimeName = eclipseJavaRuntimeName
-
-    // add in jalview project specific properties/preferences into eclipse core preferences
-    file {
-      withProperties { props ->
-        def jalview_prefs = new Properties()
-        def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
-        jalview_prefs.load(ins)
-        ins.close()
-        jalview_prefs.forEach { t, v ->
-          if (props.getAt(t) == null) {
-            props.putAt(t, v)
-          }
-        }
-      }
-    }
-
-  } // jdt
-
-  if (IN_ECLIPSE) {
-    // Don't want these to be activated if in headless build
-    synchronizationTasks "eclipseSynchronizationTask"
-    autoBuildTasks "eclipseAutoBuildTask"
-
-  }
-}
-
-
-// clover bits
-
-
-task cleanClover {
-  doFirst {
-    delete cloverBuildDir
-    delete cloverReportDir
-  }
-}
-
-
-task cloverInstrJava(type: JavaExec) {
-  group = "Verification"
-  description = "Create clover instrumented source java files"
-
-  dependsOn cleanClover
-
-  inputs.files(sourceSets.main.allJava)
-  outputs.dir(cloverInstrDir)
-
-  //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
-  classpath = sourceSets.clover.compileClasspath
-  main = "com.atlassian.clover.CloverInstr"
-
-  def argsList = [
-    "--encoding",
-    "UTF-8",
-    "--initstring",
-    cloverDb,
-    "--destdir",
-    cloverInstrDir.getPath(),
-  ]
-  def srcFiles = sourceSets.main.allJava.files
-  argsList.addAll(
-    srcFiles.collect(
-      { file -> file.absolutePath }
-    )
-  )
-  args argsList.toArray()
-
-  doFirst {
-    delete cloverInstrDir
-    println("Clover: About to instrument "+srcFiles.size() +" files")
-  }
-}
-
-
-task cloverInstrTests(type: JavaExec) {
-  group = "Verification"
-  description = "Create clover instrumented source test files"
-
-  dependsOn cleanClover
-
-  inputs.files(testDir)
-  outputs.dir(cloverTestInstrDir)
-
-  classpath = sourceSets.clover.compileClasspath
-  main = "com.atlassian.clover.CloverInstr"
-
-  def argsList = [
-    "--encoding",
-    "UTF-8",
-    "--initstring",
-    cloverDb,
-    "--srcdir",
-    testDir,
-    "--destdir",
-    cloverTestInstrDir.getPath(),
-  ]
-  args argsList.toArray()
-
-  doFirst {
-    delete cloverTestInstrDir
-    println("Clover: About to instrument test files")
-  }
-}
-
-
-task cloverInstr {
-  group = "Verification"
-  description = "Create clover instrumented all source files"
-
-  dependsOn cloverInstrJava
-  dependsOn cloverInstrTests
-}
-
-
-cloverClasses.dependsOn cloverInstr
-
-
-task cloverConsoleReport(type: JavaExec) {
-  group = "Verification"
-  description = "Creates clover console report"
-
-  onlyIf {
-    file(cloverDb).exists()
-  }
-
-  inputs.dir cloverClassesDir
-
-  classpath = sourceSets.clover.runtimeClasspath
-  main = "com.atlassian.clover.reporters.console.ConsoleReporter"
-
-  if (cloverreport_mem.length() > 0) {
-    maxHeapSize = cloverreport_mem
-  }
-  if (cloverreport_jvmargs.length() > 0) {
-    jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
-  }
-
-  def argsList = [
-    "--alwaysreport",
-    "--initstring",
-    cloverDb,
-    "--unittests"
-  ]
-
-  args argsList.toArray()
-}
-
-
-task cloverHtmlReport(type: JavaExec) {
-  group = "Verification"
-  description = "Creates clover HTML report"
-
-  onlyIf {
-    file(cloverDb).exists()
-  }
-
-  def cloverHtmlDir = cloverReportDir
-  inputs.dir cloverClassesDir
-  outputs.dir cloverHtmlDir
-
-  classpath = sourceSets.clover.runtimeClasspath
-  main = "com.atlassian.clover.reporters.html.HtmlReporter"
-
-  if (cloverreport_mem.length() > 0) {
-    maxHeapSize = cloverreport_mem
-  }
-  if (cloverreport_jvmargs.length() > 0) {
-    jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
-  }
-
-  def argsList = [
-    "--alwaysreport",
-    "--initstring",
-    cloverDb,
-    "--outputdir",
-    cloverHtmlDir
-  ]
-
-  if (cloverreport_html_options.length() > 0) {
-    argsList += cloverreport_html_options.split(" ")
-  }
-
-  args argsList.toArray()
-}
-
-
-task cloverXmlReport(type: JavaExec) {
-  group = "Verification"
-  description = "Creates clover XML report"
-
-  onlyIf {
-    file(cloverDb).exists()
-  }
-
-  def cloverXmlFile = "${cloverReportDir}/clover.xml"
-  inputs.dir cloverClassesDir
-  outputs.file cloverXmlFile
-
-  classpath = sourceSets.clover.runtimeClasspath
-  main = "com.atlassian.clover.reporters.xml.XMLReporter"
-
-  if (cloverreport_mem.length() > 0) {
-    maxHeapSize = cloverreport_mem
-  }
-  if (cloverreport_jvmargs.length() > 0) {
-    jvmArgs Arrays.asList(cloverreport_jvmargs.split(" "))
-  }
-
-  def argsList = [
-    "--alwaysreport",
-    "--initstring",
-    cloverDb,
-    "--outfile",
-    cloverXmlFile
-  ]
-
-  if (cloverreport_xml_options.length() > 0) {
-    argsList += cloverreport_xml_options.split(" ")
-  }
-
-  args argsList.toArray()
-}
-
-
-task cloverReport {
-  group = "Verification"
-  description = "Creates clover reports"
-
-  dependsOn cloverXmlReport
-  dependsOn cloverHtmlReport
-}
-
-
-compileCloverJava {
-
-  doFirst {
-    sourceCompatibility = compile_source_compatibility
-    targetCompatibility = compile_target_compatibility
-    options.compilerArgs += additional_compiler_args
-    print ("Setting target compatibility to "+targetCompatibility+"\n")
-  }
-  //classpath += configurations.cloverRuntime
-}
-// end clover bits
 
 
 compileJava {
@@ -890,7 +175,6 @@ clean {
 
 
 cleanTest {
-  dependsOn cleanClover
   doFirst {
     delete sourceSets.test.java.outputDir
   }
@@ -1030,13 +314,6 @@ task copyHelp(type: Copy) {
 }
 
 
-task syncLib(type: Sync) {
-  def syncDir = "${resourceClassesDir}/${libDistDir}"
-  from fileTree("${jalviewDir}/${libDistDir}")
-  into syncDir
-}
-
-
 task syncResources(type: Sync) {
   from resourceDir
   include "**/*.*"
@@ -1059,11 +336,7 @@ test {
   dependsOn prepare
   //dependsOn compileJava ////? DELETE
 
-  if (useClover) {
-    dependsOn cloverClasses
-   } else { //?
-     dependsOn compileJava //?
-  }
+  dependsOn compileJava //?
 
   useTestNG() {
     includeGroups testng_groups
@@ -1091,9 +364,6 @@ test {
   jvmArgs += additional_compiler_args
 
   doFirst {
-    if (useClover) {
-      println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
-    }
   }
 }
 
@@ -1189,623 +459,3 @@ jar {
   inputs.dir(classesDir)
   outputs.file("${jalviewDir}/${package_dir}/${archiveName}")
 }
-
-
-task copyJars(type: Copy) {
-  from fileTree(dir: classesDir, include: "**/*.jar").files
-  into "${jalviewDir}/${package_dir}"
-}
-
-
-// doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
-task syncJars(type: Sync) {
-  from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
-  into "${jalviewDir}/${package_dir}"
-  preserve {
-    include jar.archiveName
-  }
-}
-
-
-task makeDist {
-  group = "build"
-  description = "Put all required libraries in dist"
-  // order of "cleanPackageDir", "copyJars", "jar" important!
-  jar.mustRunAfter cleanPackageDir
-  syncJars.mustRunAfter cleanPackageDir
-  dependsOn cleanPackageDir
-  dependsOn syncJars
-  dependsOn jar
-  outputs.dir("${jalviewDir}/${package_dir}")
-}
-
-
-task cleanDist {
-  dependsOn cleanPackageDir
-  dependsOn cleanTest
-  dependsOn clean
-}
-
-shadowJar {
-  group = "distribution"
-  if (buildDist) {
-    dependsOn makeDist
-  }
-  from ("${jalviewDir}/${libDistDir}") {
-    include("*.jar")
-  }
-  manifest {
-    attributes 'Implementation-Version': JALVIEW_VERSION
-  }
-  mainClassName = shadow_jar_main_class
-  mergeServiceFiles()
-  classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
-  minimize()
-}
-
-
-task getdownWebsite() {
-  group = "distribution"
-  description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
-  if (buildDist) {
-    dependsOn makeDist
-  }
-
-  def getdownWebsiteResourceFilenames = []
-  def getdownTextString = ""
-  def getdownResourceDir = getdownResourceDir
-  def getdownResourceFilenames = []
-
-  doFirst {
-    // clean the getdown website and files dir before creating getdown folders
-    delete getdownWebsiteDir
-    delete getdownFilesDir
-
-    copy {
-      from buildProperties
-      rename(build_properties_file, getdown_build_properties)
-      into getdownAppDir
-    }
-    getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
-
-    // set some getdown_txt_ properties then go through all properties looking for getdown_txt_...
-    def props = project.properties.sort { it.key }
-    if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
-      props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
-    }
-    if (getdownAltJavaMaxVersion != null && getdownAltJavaMaxVersion.length() > 0) {
-      props.put("getdown_txt_java_max_version", getdownAltJavaMaxVersion)
-    }
-    if (getdownAltMultiJavaLocation != null && getdownAltMultiJavaLocation.length() > 0) {
-      props.put("getdown_txt_multi_java_location", getdownAltMultiJavaLocation)
-    }
-
-    props.put("getdown_txt_title", jalview_name)
-    props.put("getdown_txt_ui.name", install4jApplicationName)
-
-    // start with appbase
-    getdownTextString += "appbase = ${getdownAppBase}\n"
-    props.each{ prop, val ->
-      if (prop.startsWith("getdown_txt_") && val != null) {
-        if (prop.startsWith("getdown_txt_multi_")) {
-          def key = prop.substring(18)
-          val.split(",").each{ v ->
-            def line = "${key} = ${v}\n"
-            getdownTextString += line
-          }
-        } else {
-          // file values rationalised
-          if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
-            def r = null
-            if (val.indexOf('/') == 0) {
-              // absolute path
-              r = file(val)
-            } else if (val.indexOf('/') > 0) {
-              // relative path (relative to jalviewDir)
-              r = file( "${jalviewDir}/${val}" )
-            }
-            if (r.exists()) {
-              val = "${getdown_resource_dir}/" + r.getName()
-              getdownWebsiteResourceFilenames += val
-              getdownResourceFilenames += r.getPath()
-            }
-          }
-          if (! prop.startsWith("getdown_txt_resource")) {
-            def line = prop.substring(12) + " = ${val}\n"
-            getdownTextString += line
-          }
-        }
-      }
-    }
-
-    getdownWebsiteResourceFilenames.each{ filename ->
-      getdownTextString += "resource = ${filename}\n"
-    }
-    getdownResourceFilenames.each{ filename ->
-      copy {
-        from filename
-        into getdownResourceDir
-      }
-    }
-
-    def codeFiles = []
-    fileTree(file(package_dir)).each{ f ->
-      if (f.isDirectory()) {
-        def files = fileTree(dir: f, include: ["*"]).getFiles()
-        codeFiles += files
-      } else if (f.exists()) {
-        codeFiles += f
-      }
-    }
-    codeFiles.sort().each{f ->
-      def name = f.getName()
-      def line = "code = ${getdownAppDistDir}/${name}\n"
-      getdownTextString += line
-      copy {
-        from f.getPath()
-        into getdownAppDir
-      }
-    }
-
-    fileTree(dir: digestonlyDir, include: ["*"]).getFiles().sort().each{f ->
-      def name = f.getName()
-      def line = "digestonly = ${getdownAppDistDir}/${name}\n"
-      getdownTextString += line
-      copy {
-        from f.getPath()
-        into getdownAppDir
-      }
-    }
-    
-    // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
-    /*
-    if (JAVA_VERSION.equals("11")) {
-    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
-    copy {
-    from f.getPath()
-    into getdownJ11libDir
-    }
-    }
-    }
-     */
-
-    // 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 = ${main_class}\n"
-    /* NOT setting these properties so that getdownappbase and getdowndistdir will default to release version
-     * getdownTextString += "jvmarg = -Dgetdowndistdir=${getdownAppDistDir}\n"
-     * getdownTextString += "jvmarg = -Dgetdownappbase=${getdownAppBase}\n"
-     */
-
-    def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
-    getdown_txt.write(getdownTextString)
-
-    def getdownLaunchJvl = getdown_launch_jvl_name + ( (jvlChannelName != null && jvlChannelName.length() > 0)?"-${jvlChannelName}":"" ) + ".jvl"
-    def launchJvl = file("${getdownWebsiteDir}/${getdownLaunchJvl}")
-    launchJvl.write("appbase=${getdownAppBase}")
-
-    copy {
-      from getdownLauncher
-      rename(file(getdownLauncher).getName(), getdown_launcher_new)
-      into getdownWebsiteDir
-    }
-
-    copy {
-      from getdownLauncher
-      if (file(getdownLauncher).getName() != getdown_launcher) {
-        rename(file(getdownLauncher).getName(), getdown_launcher)
-      }
-      into getdownWebsiteDir
-    }
-
-    if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
-      copy {
-        from getdown_txt
-        from getdownLauncher
-        from "${getdownAppDir}/${getdown_build_properties}"
-        if (file(getdownLauncher).getName() != getdown_launcher) {
-          rename(file(getdownLauncher).getName(), getdown_launcher)
-        }
-        into getdownInstallDir
-      }
-
-      copy {
-        from getdownInstallDir
-        into getdownFilesInstallDir
-      }
-    }
-
-    copy {
-      from getdown_txt
-      from launchJvl
-      from getdownLauncher
-      from "${getdownWebsiteDir}/${getdown_build_properties}"
-      if (file(getdownLauncher).getName() != getdown_launcher) {
-        rename(file(getdownLauncher).getName(), getdown_launcher)
-      }
-      into getdownFilesDir
-    }
-
-    copy {
-      from getdownResourceDir
-      into "${getdownFilesDir}/${getdown_resource_dir}"
-    }
-  }
-
-  if (buildDist) {
-    inputs.dir("${jalviewDir}/${package_dir}")
-  }
-  outputs.dir(getdownWebsiteDir)
-  outputs.dir(getdownFilesDir)
-}
-
-
-// a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
-task getdownDigestDir(type: JavaExec) {
-  group "Help"
-  description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
-
-  def digestDirPropertyName = "DIGESTDIR"
-  doFirst {
-    classpath = files(getdownLauncher)
-    def digestDir = findProperty(digestDirPropertyName)
-    if (digestDir == null) {
-      throw new GradleException("Must provide a DIGESTDIR value to produce an alternative getdown digest")
-    }
-    args digestDir
-  }
-  main = "com.threerings.getdown.tools.Digester"
-}
-
-
-task getdownDigest(type: JavaExec) {
-  group = "distribution"
-  description = "Digest the getdown website folder"
-  dependsOn getdownWebsite
-  doFirst {
-    classpath = files(getdownLauncher)
-  }
-  main = "com.threerings.getdown.tools.Digester"
-  args getdownWebsiteDir
-  inputs.dir(getdownWebsiteDir)
-  outputs.file("${getdownWebsiteDir}/digest2.txt")
-}
-
-
-task getdown() {
-  group = "distribution"
-  description = "Create the minimal and full getdown app folder for installers and website and create digest file"
-  dependsOn getdownDigest
-  doLast {
-    if (reportRsyncCommand) {
-      def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
-      def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
-      println "LIKELY RSYNC COMMAND:"
-      println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
-      if (RUNRSYNC == "true") {
-        exec {
-          commandLine "mkdir", "-p", toDir
-        }
-        exec {
-          commandLine "rsync", "-avh", "--delete", fromDir, toDir
-        }
-      }
-    }
-  }
-}
-
-
-clean {
-  doFirst {
-    delete getdownWebsiteDir
-    delete getdownFilesDir
-  }
-}
-
-
-install4j {
-  if (file(install4jHomeDir).exists()) {
-    // good to go!
-  } else if (file(System.getProperty("user.home")+"/buildtools/install4j").exists()) {
-    install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
-  } else if (file("/Applications/install4j.app/Contents/Resources/app").exists()) {
-    install4jHomeDir = "/Applications/install4j.app/Contents/Resources/app"
-  }
-  installDir(file(install4jHomeDir))
-
-  mediaTypes = Arrays.asList(install4j_media_types.split(","))
-}
-
-
-task copyInstall4jTemplate {
-  def install4jTemplateFile = file("${install4jDir}/${install4j_template}")
-  def install4jFileAssociationsFile = file("${install4jDir}/${install4j_installer_file_associations}")
-  inputs.file(install4jTemplateFile)
-  inputs.file(install4jFileAssociationsFile)
-  inputs.property("CHANNEL", { CHANNEL })
-  outputs.file(install4jConfFile)
-
-  doLast {
-    def install4jConfigXml = new XmlParser().parse(install4jTemplateFile)
-
-    // turn off code signing if no OSX_KEYPASS
-    if (OSX_KEYPASS == "") {
-      install4jConfigXml.'**'.codeSigning.each { codeSigning ->
-        codeSigning.'@macEnabled' = "false"
-      }
-      install4jConfigXml.'**'.windows.each { windows ->
-        windows.'@runPostProcessor' = "false"
-      }
-    }
-
-    // turn off checksum creation for LOCAL channel
-    def e = install4jConfigXml.application[0]
-    if (CHANNEL == "LOCAL") {
-      e.'@createChecksums' = "false"
-    } else {
-      e.'@createChecksums' = "true"
-    }
-
-    // put file association actions where placeholder action is
-    def install4jFileAssociationsText = install4jFileAssociationsFile.text
-    def fileAssociationActions = new XmlParser().parseText("<actions>${install4jFileAssociationsText}</actions>")
-    install4jConfigXml.'**'.action.any { a -> // .any{} stops after the first one that returns true
-      if (a.'@name' == 'EXTENSIONS_REPLACED_BY_GRADLE') {
-        def parent = a.parent()
-        parent.remove(a)
-        fileAssociationActions.each { faa ->
-            parent.append(faa)
-        }
-        // don't need to continue in .any loop once replacements have been made
-        return true
-      }
-    }
-
-    // use Windows Program Group with Examples folder for RELEASE, and Program Group without Examples for everything else
-    // NB we're deleting the /other/ one!
-    // Also remove the examples subdir from non-release versions
-    def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
-    // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
-    if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
-      customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
-    } else {
-      // remove the examples subdir from Full File Set
-      def files = install4jConfigXml.files[0]
-      def fileset = files.filesets.fileset.find { fs -> fs.'@customizedId' == "FULL_FILE_SET" }
-      def root = files.roots.root.find { r -> r.'@fileset' == fileset.'@id' }
-      def mountPoint = files.mountPoints.mountPoint.find { mp -> mp.'@root' == root.'@id' }
-      def dirEntry = files.entries.dirEntry.find { de -> de.'@mountPoint' == mountPoint.'@id' && de.'@subDirectory' == "examples" }
-      dirEntry.parent().remove(dirEntry)
-    }
-    install4jConfigXml.'**'.action.any { a ->
-      if (a.'@customizedId' == customizedIdToDelete) {
-        def parent = a.parent()
-        parent.remove(a)
-        return true
-      }
-    }
-
-    // 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)
-  }
-}
-
-
-clean {
-  doFirst {
-    delete install4jConfFile
-  }
-}
-
-
-task installers(type: com.install4j.gradle.Install4jTask) {
-  group = "distribution"
-  description = "Create the install4j installers"
-  dependsOn setGitVals
-  dependsOn getdown
-  dependsOn copyInstall4jTemplate
-
-  projectFile = install4jConfFile
-
-  // create an md5 for the input files to use as version for install4j conf file
-  def digest = MessageDigest.getInstance("MD5")
-  digest.update(
-    (file("${install4jDir}/${install4j_template}").text + 
-    file("${install4jDir}/${install4j_info_plist_file_associations}").text +
-    file("${install4jDir}/${install4j_installer_file_associations}").text).bytes)
-  def filesMd5 = new BigInteger(1, digest.digest()).toString(16)
-  if (filesMd5.length() >= 8) {
-    filesMd5 = filesMd5.substring(0,8)
-  }
-  def install4jTemplateVersion = "${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_DIR': "../..",
-    'OSX_KEYSTORE': OSX_KEYSTORE,
-    'JSIGN_SH': JSIGN_SH,
-    'JRE_DIR': getdown_app_dir_java,
-    'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
-    'JALVIEW_VERSION': JALVIEW_VERSION,
-    'JAVA_MIN_VERSION': JAVA_MIN_VERSION,
-    'JAVA_MAX_VERSION': JAVA_MAX_VERSION,
-    'JAVA_VERSION': JAVA_VERSION,
-    'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
-    'VERSION': JALVIEW_VERSION,
-    'MACOS_JAVA_VM_DIR': macosJavaVMDir,
-    'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
-    'LINUX_JAVA_VM_DIR': linuxJavaVMDir,
-    'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
-    'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
-    'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
-    'COPYRIGHT_MESSAGE': install4j_copyright_message,
-    'BUNDLE_ID': install4jBundleId,
-    'INTERNAL_ID': install4jInternalId,
-    'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
-    'MACOS_DS_STORE': install4jDSStore,
-    'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
-    'INSTALLER_NAME': install4jInstallerName,
-    'INSTALL4J_UTILS_DIR': install4j_utils_dir,
-    'GETDOWN_WEBSITE_DIR': getdown_website_dir,
-    'GETDOWN_FILES_DIR': getdown_files_dir,
-    'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
-    'GETDOWN_DIST_DIR': getdownAppDistDir,
-    'GETDOWN_ALT_DIR': getdown_app_dir_alt,
-    'GETDOWN_INSTALL_DIR': getdown_install_dir,
-    'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
-    'BUILD_DIR': install4jBuildDir,
-    'APPLICATION_CATEGORIES': install4j_application_categories,
-    'APPLICATION_FOLDER': install4jApplicationFolder,
-    'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
-    'EXECUTABLE_NAME': install4jExecutableName,
-    'EXTRA_SCHEME': install4jExtraScheme,
-  ]
-
-  //println("INSTALL4J VARIABLES:")
-  //variables.each{k,v->println("${k}=${v}")}
-
-  destination = "${jalviewDir}/${install4jBuildDir}"
-  buildSelected = true
-
-  if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
-    faster = true
-    disableSigning = true
-  }
-
-  if (OSX_KEYPASS) {
-    macKeystorePassword = OSX_KEYPASS
-  }
-
-  doFirst {
-    println("Using projectFile "+projectFile)
-  }
-
-  inputs.dir(getdownWebsiteDir)
-  inputs.file(install4jConfFile)
-  inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
-  inputs.dir(macosJavaVMDir)
-  inputs.dir(windowsJavaVMDir)
-  outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
-}
-
-
-task sourceDist(type: Tar) {
-  
-  def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
-  def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
-  // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09]
-  try {
-    archiveFileName = outputFileName
-  } catch (Exception e) {
-    archiveName = outputFileName
-  }
-  
-  compression Compression.GZIP
-  
-  into project.name
-
-  def EXCLUDE_FILES=[
-    "build/*",
-    "bin/*",
-    "test-output/",
-    "test-reports",
-    "tests",
-    "clover*/*",
-    ".*",
-    "benchmarking/*",
-    "**/.*",
-    "*.class",
-    "**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales",
-    "*locales/**",
-    "utils/InstallAnywhere",
-    "**/*.log",
-  ] 
-  def PROCESS_FILES=[
-    "AUTHORS",
-    "CITATION",
-    "FEATURETODO",
-    "JAVA-11-README",
-    "FEATURETODO",
-    "LICENSE",
-    "**/README",
-    "RELEASE",
-    "THIRDPARTYLIBS",
-    "TESTNG",
-    "build.gradle",
-    "gradle.properties",
-    "**/*.java",
-    "**/*.html",
-    "**/*.xml",
-    "**/*.gradle",
-    "**/*.groovy",
-    "**/*.properties",
-    "**/*.perl",
-    "**/*.sh",
-  ]
-  def INCLUDE_FILES=[
-    ".settings/org.eclipse.jdt.core.jalview.prefs",
-  ]
-
-  from(jalviewDir) {
-    exclude (EXCLUDE_FILES)
-    include (PROCESS_FILES)
-    filter(ReplaceTokens,
-      beginToken: '$$',
-      endToken: '$$',
-      tokens: [
-        'Version-Rel': JALVIEW_VERSION,
-        'Year-Rel': getDate("yyyy")
-      ]
-    )
-  }
-  from(jalviewDir) {
-    exclude (EXCLUDE_FILES)
-    exclude (PROCESS_FILES)
-    exclude ("appletlib")
-    exclude ("**/*locales")
-    exclude ("*locales/**")
-    exclude ("utils/InstallAnywhere")
-
-    exclude (getdown_files_dir)
-    exclude (getdown_website_dir)
-
-    // exluding these as not using jars as modules yet
-    exclude ("$j11modDir/**/*.jar")
-  }
-  from(jalviewDir) {
-    include(INCLUDE_FILES)
-  }
-//  from (jalviewDir) {
-//    // explicit includes for stuff that seemed to not get included
-//    include(fileTree("test/**/*."))
-//    exclude(EXCLUDE_FILES)
-//    exclude(PROCESS_FILES)
-//  }
-}
-
-
-task helppages {
-  dependsOn copyHelp
-  dependsOn pubhtmlhelp
-  
-  inputs.dir("${classesDir}/${help_dir}")
-  outputs.dir("${buildDir}/distributions/${help_dir}")
-}
-
-// LARGE AMOUNT OF JALVIEWJS STUFF DELETED HERE
-task eclipseAutoBuildTask {}
-task eclipseSynchronizationTask {}