X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=c3e89e588dad6f3018c376655becd2a32d094b48;hb=2669c44fcae1f976692d840b61bc37c80d9a4322;hp=4e50b7722fd10415da6932d2f009b9f5cb245135;hpb=6650b1dc05cddec8301d52017db0dca93b7a6c95;p=jalview.git

diff --git a/build.gradle b/build.gradle
index 4e50b77..c3e89e5 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1,3 +1,6 @@
+/* Convention for properties.  Read from gradle.properties, use lower_case_underlines for property names.
+ * 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.internal.generator.PropertiesPersistableConfigurationObject
@@ -9,7 +12,16 @@ import java.security.MessageDigest
 import groovy.transform.ExternalizeMethods
 import groovy.util.XmlParser
 import groovy.xml.XmlUtil
-
+import com.vladsch.flexmark.util.ast.Node
+import com.vladsch.flexmark.html.HtmlRenderer
+import com.vladsch.flexmark.parser.Parser
+import com.vladsch.flexmark.util.data.MutableDataSet
+import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension
+import com.vladsch.flexmark.ext.tables.TablesExtension
+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
 
 buildscript {
   repositories {
@@ -17,7 +29,7 @@ buildscript {
     mavenLocal()
   }
   dependencies {
-    classpath 'org.openclover:clover:4.4.1'
+    classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
   }
 }
 
@@ -30,6 +42,7 @@ plugins {
   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'
 }
 
 repositories {
@@ -98,7 +111,7 @@ ext {
   }
   ////
   // Set JALVIEW_VERSION if it is not already set
-  if (findProperty(JALVIEW_VERSION)==null || "".equals(JALVIEW_VERSION)) {
+  if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
     JALVIEW_VERSION = releaseProps.get("jalview.version")
   }
   
@@ -139,21 +152,23 @@ ext {
   sourceDir = string("${jalviewDir}/${bareSourceDir}")
   resourceDir = string("${jalviewDir}/${resource_dir}")
   bareTestSourceDir = string(test_source_dir)
-  testSourceDir = string("${jalviewDir}/${bareTestSourceDir}")
+  testDir = string("${jalviewDir}/${bareTestSourceDir}")
 
-  // clover
-  cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}")
-  cloverDb = string("${buildDir}/clover/clover.db")
   classesDir = string("${jalviewDir}/${classes_dir}")
-  if (clover.equals("true")) {
-    use_clover = true
-    classesDir = string("${buildDir}/${cloverClassesDir}")
-  } else {
-    use_clover = false
-    classesDir = string("${jalviewDir}/${classes_dir}")
-  }
 
-  classes = classesDir
+  // 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("${cloverBuildDir}/clover.db")
+
+  testSourceDir = useClover ? cloverTestInstrDir : testDir
+  testClassesDir = useClover ? cloverTestClassesDir : "${jalviewDir}/${test_output_dir}"
 
   getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
   buildDist = true
@@ -164,7 +179,6 @@ ext {
   getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
   getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
   getdownAppDistDir = getdown_app_dir_alt
-  buildProperties = string("${resourceDir}/${build_properties_file}")
   reportRsyncCommand = false
   jvlChannelName = CHANNEL.toLowerCase()
   install4jSuffix = CHANNEL.substring(0, 1).toUpperCase() + CHANNEL.substring(1).toLowerCase(); // BUILD -> Build
@@ -182,8 +196,8 @@ ext {
     getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
     jvlChannelName += "_${getdownChannelName}"
     // automatically add the test group Not-bamboo for exclusion 
-    if ("".equals(testngExcludedGroups)) { 
-      testngExcludedGroups = "Not-bamboo"
+    if ("".equals(testng_excluded_groups)) { 
+      testng_excluded_groups = "Not-bamboo"
     }
     install4jExtraScheme = "jalviewb"
     break
@@ -191,11 +205,6 @@ ext {
     case "RELEASE":
     getdownAppDistDir = getdown_app_dir_release
     reportRsyncCommand = true
-    // Don't ignore transpile errors for release build
-    if (jalviewjs_ignore_transpile_errors.equals("true")) {
-      jalviewjs_ignore_transpile_errors = "false"
-      println("Setting jalviewjs_ignore_transpile_errors to 'false'")
-    }
     install4jSuffix = ""
     install4jDSStore = "DS_Store"
     install4jDMGBackgroundImage = "jalview_dmg_background.png"
@@ -206,11 +215,11 @@ ext {
     getdownChannelName = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
     getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
     getdownAppBase = string("${getdown_channel_base}/${getdownDir}")
-    if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
+    if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
       throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
     } else {
-      packageDir = string("${ARCHIVEDIR}/${packageDir}")
-      buildProperties = string("${buildDir}/archive/${build_properties_file}")
+      package_dir = string("${ARCHIVEDIR}/${package_dir}")
+      buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
       buildDist = false
     }
     reportRsyncCommand = true
@@ -221,11 +230,11 @@ ext {
     getdownChannelName = string("archive/${JALVIEW_VERSION}")
     getdownDir = string("${getdownChannelName}/${JAVA_VERSION}")
     getdownAppBase = file(getdownWebsiteDir).toURI().toString()
-    if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
+    if (!file("${ARCHIVEDIR}/${package_dir}").exists()) {
       throw new GradleException("Must provide an ARCHIVEDIR value to produce an archive distribution")
     } else {
-      packageDir = string("${ARCHIVEDIR}/${packageDir}")
-      buildProperties = string("${buildDir}/archive/${build_properties_file}")
+      package_dir = string("${ARCHIVEDIR}/${package_dir}")
+      buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
       buildDist = false
     }
     reportRsyncCommand = true
@@ -240,11 +249,19 @@ ext {
     // DEVELOP-RELEASE is usually associated with a Jalview release series so set the version
     JALVIEW_VERSION=JALVIEW_VERSION+"-develop"
     
+    channelPropertiesFile = string("${channel_properties_dir}/develop_properties")
+    getdownImagesDir = "${getdown_images_dir}/develop"
+    getdownBgColour = "000000"
+    getdownFgColour = "FFFFFF"
+    getdownLightFgColour = "CCCCFF"
     install4jSuffix = "Develop"
     install4jDSStore = "DS_Store-DEVELOP"
     install4jDMGBackgroundImage = "jalview_dmg_background-DEVELOP.png"
     install4jExtraScheme = "jalviewd"
     install4jInstallerName = "${jalview_name} Develop Installer"
+    install4jMacIconsFile = string("${install4j_utils_dir}/develop/${install4j_mac_icons_file}")
+    install4jWindowsIconsFile = string("${install4j_utils_dir}/develop/${install4j_windows_icons_file}")
+    install4jPngIconFile = string("${install4j_utils_dir}/develop/${install4j_png_icon_file}")
     break
 
     case "TEST-RELEASE":
@@ -347,8 +364,9 @@ ext {
   modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
   modules_runtimeClasspath = modules_compileClasspath
   */
-  gitHash = string("")
-  gitBranch = string("")
+  def details = versionDetails()
+  gitHash = details.gitHash
+  gitBranch = details.branchName
 
   println("Using a ${CHANNEL} profile.")
 
@@ -426,12 +444,16 @@ 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")
 
-
-  buildingHTML = string("${jalviewDir}/${docDir}/building.html")
-  helpFile = string("${classesDir}/${help_dir}/help.jhm")
+  buildProperties = string("${resourcesBuildDir}/${build_properties_file}")
+  buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
   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())
@@ -469,33 +491,31 @@ sourceSets {
     }
 
     resources {
-      srcDirs resourceDir
-      srcDirs += helpParentDir
+      srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
     }
 
-    jar.destinationDir = file("${jalviewDir}/${packageDir}")
-
     compileClasspath = files(sourceSets.main.java.outputDir)
-    //compileClasspath += files(sourceSets.main.resources.srcDirs)
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 
     runtimeClasspath = compileClasspath
+    runtimeClasspath += files(sourceSets.main.resources.srcDirs)
   }
 
   clover {
     java {
-      srcDirs = [ cloverInstrDir ]
-      outputDir = file("${buildDir}/${cloverClassesDir}")
+      srcDirs cloverInstrDir
+      outputDir = cloverClassesDir
     }
 
     resources {
       srcDirs = sourceSets.main.resources.srcDirs
     }
-    compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir )
-    compileClasspath += files(sourceSets.main.java.outputDir)
-    compileClasspath += sourceSets.main.compileClasspath
-    compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["**/*.jar"])
+
+    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
   }
@@ -503,42 +523,21 @@ sourceSets {
   test {
     java {
       srcDirs testSourceDir
-      outputDir = file("${jalviewDir}/${testOutputDir}")
+      outputDir = file(testClassesDir)
     }
 
     resources {
-      srcDirs = sourceSets.main.resources.srcDirs
+      srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
     }
 
     compileClasspath = files( sourceSets.test.java.outputDir )
-
-    if (use_clover) {
-      compileClasspath = sourceSets.clover.compileClasspath
-    } else {
-      compileClasspath += files(sourceSets.main.java.outputDir)
-    }
-
-    compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
-    compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testnglibs", include: ["**/*.jar"])
-    compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testlibs", include: ["**/*.jar"])
+    compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
+    compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
 
     runtimeClasspath = compileClasspath
+    runtimeClasspath += files(sourceSets.test.resources.srcDirs)
   }
-}
-
 
-// clover bits
-dependencies {
-  if (use_clover) {
-    cloverCompile 'org.openclover:clover:4.4.1'
-    testCompile 'org.openclover:clover:4.4.1'
-  }
-}
-
-
-configurations {
-  cloverRuntime
-  cloverRuntime.extendsFrom cloverCompile
 }
 
 
@@ -557,14 +556,12 @@ 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 {
 
@@ -652,7 +649,6 @@ eclipse {
     javaRuntimeName = eclipseJavaRuntimeName
 
     // add in jalview project specific properties/preferences into eclipse core preferences
-    // and also the codestyle XML file
     file {
       withProperties { props ->
         def jalview_prefs = new Properties()
@@ -751,61 +747,209 @@ eclipseGroovyCorePreferences.mustRunAfter eclipseJdt
 /* end of eclipse preferences hack */
 
 
-task cloverInstr {
-  // only instrument source, we build test classes as normal
-  inputs.files files (sourceSets.main.allJava,sourceSets.test.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
-  outputs.dir cloverInstrDir
+// clover bits
+
 
+task cleanClover {
   doFirst {
-    delete cloverInstrDir
-    def argsList = [
-      "--initstring",
-      cloverDb,
-      "-d",
-      cloverInstrDir.getPath(),
-    ]
-    argsList.addAll(
-      inputs.files.files.collect(
-        { file -> file.absolutePath }
-      )
+    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 }
     )
-    String[] args = argsList.toArray()
-    println("About to instrument "+args.length +" files")
-    com.atlassian.clover.CloverInstr.mainImpl(args)
+  )
+  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 cloverReport {
+task cloverConsoleReport(type: JavaExec) {
   group = "Verification"
-  description = "Creates the Clover report"
-  inputs.dir "${buildDir}/clover"
-  outputs.dir "${reportsDir}/clover"
+  description = "Creates clover console report"
+
   onlyIf {
     file(cloverDb).exists()
   }
-  doFirst {
-    def argsList = [
-      "--initstring",
-      cloverDb,
-      "-o",
-      "${reportsDir}/clover"
-    ]
-    String[] args = argsList.toArray()
-    com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
 
-    // and generate ${reportsDir}/clover/clover.xml
-    args = [
-      "--initstring",
-      cloverDb,
-      "-o",
-      "${reportsDir}/clover/clover.xml"
-    ].toArray()
-    com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
+  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
 }
 
 
@@ -817,15 +961,7 @@ compileCloverJava {
     options.compilerArgs += additional_compiler_args
     print ("Setting target compatibility to "+targetCompatibility+"\n")
   }
-  classpath += configurations.cloverRuntime
-}
-
-
-task cleanClover {
-  doFirst {
-    delete cloverInstrDir
-    delete cloverDb
-  }
+  //classpath += configurations.cloverRuntime
 }
 // end clover bits
 
@@ -837,23 +973,17 @@ compileJava {
   options.compilerArgs = additional_compiler_args
   options.encoding = "UTF-8"
   doFirst {
-    print ("Setting target compatibility to "+targetCompatibility+"\n")
+    print ("Setting target compatibility to "+compile_target_compatibility+"\n")
   }
 
 }
 
 
 compileTestJava {
-  if (use_clover) {
-    dependsOn compileCloverJava
-    classpath += configurations.cloverRuntime
-  } else {
-    classpath += sourceSets.main.runtimeClasspath
-  }
+  sourceCompatibility = compile_source_compatibility
+  targetCompatibility = compile_target_compatibility
+  options.compilerArgs = additional_compiler_args
   doFirst {
-    sourceCompatibility = compile_source_compatibility
-    targetCompatibility = compile_target_compatibility
-    options.compilerArgs = additional_compiler_args
     print ("Setting target compatibility to "+targetCompatibility+"\n")
   }
 }
@@ -881,112 +1011,179 @@ def getDate(format) {
 }
 
 
-task setGitVals {
-  def hashStdOut = new ByteArrayOutputStream()
-  exec {
-    commandLine "git", "rev-parse", "--short", "HEAD"
-    standardOutput = hashStdOut
-    ignoreExitValue true
-  }
+def convertMdToHtml (FileTree mdFiles, File cssFile) {
+  MutableDataSet options = new MutableDataSet()
 
-  def branchStdOut = new ByteArrayOutputStream()
-  exec {
-    commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
-    standardOutput = branchStdOut
-    ignoreExitValue true
+  def extensions = new ArrayList<>()
+  extensions.add(AnchorLinkExtension.create()) 
+  extensions.add(AutolinkExtension.create())
+  extensions.add(StrikethroughExtension.create())
+  extensions.add(TaskListExtension.create())
+  extensions.add(TablesExtension.create())
+  extensions.add(TocExtension.create())
+  
+  options.set(Parser.EXTENSIONS, extensions)
+
+  // set GFM table parsing options
+  options.set(TablesExtension.WITH_CAPTION, false)
+  options.set(TablesExtension.COLUMN_SPANS, false)
+  options.set(TablesExtension.MIN_HEADER_ROWS, 1)
+  options.set(TablesExtension.MAX_HEADER_ROWS, 1)
+  options.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
+  options.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
+  options.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
+  // GFM anchor links
+  options.set(AnchorLinkExtension.ANCHORLINKS_SET_ID, false)
+  options.set(AnchorLinkExtension.ANCHORLINKS_ANCHOR_CLASS, "anchor")
+  options.set(AnchorLinkExtension.ANCHORLINKS_SET_NAME, true)
+  options.set(AnchorLinkExtension.ANCHORLINKS_TEXT_PREFIX, "<span class=\"octicon octicon-link\"></span>")
+
+  Parser parser = Parser.builder(options).build()
+  HtmlRenderer renderer = HtmlRenderer.builder(options).build()
+
+  mdFiles.each { mdFile ->
+    // add table of contents
+    def mdText = "[TOC]\n"+mdFile.text
+
+    // grab the first top-level title
+    def title = null
+    def titleRegex = /(?m)^#(\s+|([^#]))(.*)/
+    def matcher = mdText =~ titleRegex
+    if (matcher.size() > 0) {
+      // matcher[0][2] is the first character of the title if there wasn't any whitespace after the #
+      title = (matcher[0][2] != null ? matcher[0][2] : "")+matcher[0][3]
+    }
+    // or use the filename if none found
+    if (title == null) {
+      title = mdFile.getName()
+    }
+
+    Node document = parser.parse(mdText)
+    String htmlBody = renderer.render(document)
+    def htmlText = '''<html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <meta http-equiv="Content-Style-Type" content="text/css" />
+    <meta name="generator" content="flexmark" />
+'''
+    htmlText += ((title != null) ? "  <title>${title}</title>" : '' )
+    htmlText += '''
+    <style type="text/css">code{white-space: pre;}</style>
+'''
+    htmlText += ((cssFile != null) ? cssFile.text : '')
+    htmlText += '''</head>
+  <body>
+'''
+    htmlText += htmlBody
+    htmlText += '''
+  </body>
+</html>
+'''
+
+    def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".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
 
-  gitHash = hashStdOut.toString().trim()
-  gitBranch = branchStdOut.toString().trim()
-
-  outputs.upToDateWhen { false }
+  inputs.dir(inputDir)
+  outputs.dir(outputDir)
 }
 
 
-task createBuildProperties(type: WriteProperties) {
-  group = "build"
-  description = "Create the ${buildProperties} file"
-  
-  dependsOn setGitVals
-  inputs.dir(sourceDir)
-  inputs.dir(resourceDir)
-  file(buildProperties).getParentFile().mkdirs()
-  outputFile (buildProperties)
-  // taking time specific comment out to allow better incremental builds
-  comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
-  //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
-  property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
-  property "VERSION", JALVIEW_VERSION
-  property "INSTALLATION", INSTALLATION+" git-commit:"+gitHash+" ["+gitBranch+"]"
-  outputs.file(outputFile)
-}
-
+task convertMdFiles {
+  dependsOn copyDocs
+  def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
+  def cssFile = file("${jalviewDir}/${flexmark_css}")
 
-clean {
-  doFirst {
-    delete buildProperties
+  doLast {
+    convertMdToHtml(mdFiles, cssFile)
   }
-}
 
+  inputs.files(mdFiles)
+  inputs.file(cssFile)
 
-task cleanBuildingHTML(type: Delete) {
-  doFirst {
-    delete buildingHTML
+  def htmlFiles = []
+  mdFiles.each { mdFile ->
+    def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
+    htmlFiles.add(file(htmlFilePath))
   }
+  outputs.files(htmlFiles)
 }
 
 
-task convertBuildingMD(type: Exec) {
-  dependsOn cleanBuildingHTML
-  def buildingMD = "${jalviewDir}/${docDir}/building.md"
-  def css = "${jalviewDir}/${docDir}/github.css"
-
-  def pandoc = null
-  pandoc_exec.split(",").each {
-    if (file(it.trim()).exists()) {
-      pandoc = it.trim()
-      return true
-    }
-  }
-
-  def buildtoolsPandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
-  if ((pandoc == null || ! file(pandoc).exists()) && file(buildtoolsPandoc).exists()) {
-    pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
+task copyHelp(type: Copy) {
+  def inputDir = helpSourceDir
+  def outputDir = "${helpBuildDir}/${help_dir}"
+  from(inputDir) {
+    include('**/*.txt')
+    include('**/*.md')
+    include('**/*.html')
+    include('**/*.hs')
+    include('**/*.xml')
+    include('**/*.jhm')
+    filter(ReplaceTokens,
+      beginToken: '$$',
+      endToken: '$$',
+      tokens: [
+        'Version-Rel': JALVIEW_VERSION,
+        'Year-Rel': getDate("yyyy")
+      ]
+    )
   }
-
-  doFirst {
-    if (pandoc != null && file(pandoc).exists()) {
-        commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
-    } else {
-        println("Cannot find pandoc. Skipping convert building.md to HTML")
-        throw new StopExecutionException("Cannot find pandoc. Skipping convert building.md to HTML")
-    }
+  from(inputDir) {
+    exclude('**/*.txt')
+    exclude('**/*.md')
+    exclude('**/*.html')
+    exclude('**/*.hs')
+    exclude('**/*.xml')
+    exclude('**/*.jhm')
   }
+  into outputDir
 
-  ignoreExitValue true
-
-  inputs.file(buildingMD)
-  inputs.file(css)
-  outputs.file(buildingHTML)
-}
-
-
-task syncDocs(type: Sync) {
-  dependsOn convertBuildingMD
-  def syncDir = "${classesDir}/${docDir}"
-  from fileTree("${jalviewDir}/${docDir}")
-  into syncDir
-
+  inputs.dir(inputDir)
+  outputs.files(helpFile)
+  outputs.dir(outputDir)
 }
 
 
-task copyHelp(type: Copy) {
-  def inputDir = helpSourceDir
-  def outputDir = "${classesDir}/${help_dir}"
+task copyResources(type: Copy) {
+  def inputDir = resourceDir
+  def outputDir = resourcesBuildDir
   from(inputDir) {
-    exclude '**/*.gif'
-    exclude '**/*.jpg'
-    exclude '**/*.png'
+    include('**/*.txt')
+    include('**/*.md')
+    include('**/*.html')
+    include('**/*.xml')
     filter(ReplaceTokens,
       beginToken: '$$',
       endToken: '$$',
@@ -997,58 +1194,84 @@ task copyHelp(type: Copy) {
     )
   }
   from(inputDir) {
-    include '**/*.gif'
-    include '**/*.jpg'
-    include '**/*.png'
+    exclude('**/*.txt')
+    exclude('**/*.md')
+    exclude('**/*.html')
+    exclude('**/*.xml')
   }
   into outputDir
 
   inputs.dir(inputDir)
-  outputs.files(helpFile)
   outputs.dir(outputDir)
 }
 
 
-task syncLib(type: Sync) {
-  def syncDir = "${classesDir}/${libDistDir}"
-  from fileTree("${jalviewDir}/${libDistDir}")
-  into syncDir
+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+"]"
+  outputs.file(outputFile)
 }
 
 
-task syncResources(type: Sync) {
-  dependsOn createBuildProperties
-  from resourceDir
-  include "**/*.*"
-  into "${classesDir}"
-  preserve {
-    include "**"
-  }
+task buildIndices(type: JavaExec) {
+  dependsOn copyHelp
+  classpath = sourceSets.main.compileClasspath
+  main = "com.sun.java.help.search.Indexer"
+  workingDir = "${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 prepare {
-  dependsOn syncResources
-  dependsOn syncDocs
+  dependsOn copyResources
+  dependsOn copyDocs
   dependsOn copyHelp
+  dependsOn createBuildProperties
+  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
-  if (use_clover) {
-    dependsOn cloverInstr
-  }
 
-  if (use_clover) {
-    print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
+  if (useClover) {
+    dependsOn cloverClasses
+   } else { //?
+    dependsOn compileJava //?
   }
 
   useTestNG() {
-    includeGroups testngGroups
-    excludeGroups testngExcludedGroups
+    includeGroups testng_groups
+    excludeGroups testng_excluded_groups
     preserveOrder true
     useDefaultListeners=true
   }
@@ -1056,55 +1279,45 @@ 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
+  }
   sourceCompatibility = compile_source_compatibility
   targetCompatibility = compile_target_compatibility
   jvmArgs += additional_compiler_args
 
-}
-
-
-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")
+  doFirst {
+    if (useClover) {
+      println("Running tests " + (useClover?"WITH":"WITHOUT") + " clover")
+    }
+  }
 }
 
 
 task compileLinkCheck(type: JavaCompile) {
   options.fork = true
-  classpath = files("${jalviewDir}/${utilsDir}")
-  destinationDir = file("${jalviewDir}/${utilsDir}")
-  source = fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
+  classpath = files("${jalviewDir}/${utils_dir}")
+  destinationDir = file("${jalviewDir}/${utils_dir}")
+  source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
 
-  inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
-  inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
-  outputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.class")
-  outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class")
+  inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
+  inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
+  outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
+  outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
 }
 
 
 task linkCheck(type: JavaExec) {
-  dependsOn prepare, compileLinkCheck
+  dependsOn prepare
+  dependsOn compileLinkCheck
 
-  def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out")
-  classpath = files("${jalviewDir}/${utilsDir}")
+  def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
+  classpath = files("${jalviewDir}/${utils_dir}")
   main = "HelpLinksChecker"
   workingDir = jalviewDir
-  args = [ "${classesDir}/${help_dir}", "-nointernet" ]
+  args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
 
   def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
   def errFOS = outFOS
@@ -1115,37 +1328,38 @@ task linkCheck(type: JavaExec) {
     outFOS,
     errorOutput)
 
-  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.importBuild "${utilsDir}/publishHelp.xml"
+ant.properties.helpBuildDir = "${helpBuildDir}/${help_dir}"
+ant.importBuild "${utils_dir}/publishHelp.xml"
 
 
 task cleanPackageDir(type: Delete) {
   doFirst {
-    delete fileTree(dir: "${jalviewDir}/${packageDir}", include: "*.jar")
+    delete fileTree(dir: "${jalviewDir}/${package_dir}", include: "*.jar")
   }
 }
 
 
 jar {
+  dependsOn prepare
   dependsOn linkCheck
-  dependsOn buildIndices
-  dependsOn createBuildProperties
 
   manifest {
-    attributes "Main-Class": mainClass,
+    attributes "Main-Class": main_class,
     "Permissions": "all-permissions",
-    "Application-Name": "Jalview Desktop",
-    "Codebase": application_codebase
+    "Application-Name": install4jApplicationName,
+    "Codebase": application_codebase,
+    "Implementation-Version": JALVIEW_VERSION
   }
 
-  destinationDir = file("${jalviewDir}/${packageDir}")
-  archiveName = rootProject.name+".jar"
+  destinationDirectory = file("${jalviewDir}/${package_dir}")
+  archiveFileName = rootProject.name+".jar"
 
   exclude "cache*/**"
   exclude "*.jar"
@@ -1153,23 +1367,27 @@ jar {
   exclude "**/*.jar"
   exclude "**/*.jar.*"
 
-  inputs.dir(classesDir)
-  outputs.file("${jalviewDir}/${packageDir}/${archiveName}")
+  inputs.dir(sourceSets.main.java.outputDir)
+  sourceSets.main.resources.srcDirs.each{ dir ->
+    inputs.dir(dir)
+  }
+  outputs.file("${destinationDirectory}/${archiveFileName}")
 }
 
 
 task copyJars(type: Copy) {
   from fileTree(dir: classesDir, include: "**/*.jar").files
-  into "${jalviewDir}/${packageDir}"
+  into "${jalviewDir}/${package_dir}"
 }
 
 
 // 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 "${jalviewDir}/${packageDir}"
+  into "${jalviewDir}/${package_dir}"
   preserve {
-    include jar.archiveName
+    include jar.archiveFileName.getOrNull()
   }
 }
 
@@ -1183,7 +1401,7 @@ task makeDist {
   dependsOn cleanPackageDir
   dependsOn syncJars
   dependsOn jar
-  outputs.dir("${jalviewDir}/${packageDir}")
+  outputs.dir("${jalviewDir}/${package_dir}")
 }
 
 
@@ -1193,8 +1411,10 @@ task cleanDist {
   dependsOn clean
 }
 
+
 shadowJar {
   group = "distribution"
+  description = "Create a single jar file with all dependency libraries merged. Can be run with java -jar"
   if (buildDist) {
     dependsOn makeDist
   }
@@ -1202,9 +1422,10 @@ shadowJar {
     include("*.jar")
   }
   manifest {
-    attributes 'Implementation-Version': JALVIEW_VERSION
+    attributes "Implementation-Version": JALVIEW_VERSION,
+    "Application-Name": install4jApplicationName
   }
-  mainClassName = shadowJarMainClass
+  mainClassName = shadow_jar_main_class
   mergeServiceFiles()
   classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
   minimize()
@@ -1296,7 +1517,7 @@ task getdownWebsite() {
     }
 
     def codeFiles = []
-    fileTree(file(packageDir)).each{ f ->
+    fileTree(file(package_dir)).each{ f ->
       if (f.isDirectory()) {
         def files = fileTree(dir: f, include: ["*"]).getFiles()
         codeFiles += files
@@ -1333,7 +1554,7 @@ 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 = ${mainClass}\n"
+    getdownTextString += "class = ${main_class}\n"
 
     def getdown_txt = file("${getdownWebsiteDir}/getdown.txt")
     getdown_txt.write(getdownTextString)
@@ -1391,7 +1612,7 @@ task getdownWebsite() {
   }
 
   if (buildDist) {
-    inputs.dir("${jalviewDir}/${packageDir}")
+    inputs.dir("${jalviewDir}/${package_dir}")
   }
   outputs.dir(getdownWebsiteDir)
   outputs.dir(getdownFilesDir)
@@ -1400,8 +1621,10 @@ task getdownWebsite() {
 
 // 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"
-  description = "Digest a local dir (-P${digestDirPropertyName}=...) for getdown"
   doFirst {
     classpath = files(getdownLauncher)
     def digestDir = findProperty(digestDirPropertyName)
@@ -1568,7 +1791,6 @@ clean {
 task installers(type: com.install4j.gradle.Install4jTask) {
   group = "distribution"
   description = "Create the install4j installers"
-  dependsOn setGitVals
   dependsOn getdown
   dependsOn copyInstall4jTemplate
 
@@ -1667,15 +1889,14 @@ spotless {
 
 
 task sourceDist(type: Tar) {
+  group "distribution"
+  description "Create a source .tar.gz file for distribution"
   
+  dependsOn convertMdFiles
+
   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
-  }
+  archiveFileName = outputFileName
   
   compression Compression.GZIP
   
@@ -1765,7 +1986,7 @@ task helppages {
   dependsOn copyHelp
   dependsOn pubhtmlhelp
   
-  inputs.dir("${classesDir}/${help_dir}")
+  inputs.dir("${helpBuildDir}/${help_dir}")
   outputs.dir("${buildDir}/distributions/${help_dir}")
 }
 
@@ -2442,7 +2663,7 @@ def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inpu
       beginToken: '_',
       endToken: '_',
       tokens: [
-        'MAIN': '"'+mainClass+'"',
+        'MAIN': '"'+main_class+'"',
         'CODE': "null",
         'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
         'COREKEY': jalviewjs_core_key,
@@ -2569,11 +2790,7 @@ task jalviewjsSiteTar(type: Tar) {
   description "Creates a tar.gz file for the website"
   dependsOn jalviewjsBuildSite
   def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
-  try {
-    archiveFileName = outputFilename
-  } catch (Exception e) {
-    archiveName = outputFilename
-  }
+  archiveFileName = outputFilename
 
   compression Compression.GZIP
 
@@ -2662,10 +2879,25 @@ task jalviewjsIDE_checkJ2sPlugin {
     if (eclipseHome == null || ! IN_ECLIPSE) {
       throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
     }
-    def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
-    def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
-    if (!eclipseJ2sPluginFile.exists()) {
-      def msg = "Eclipse J2S Plugin is not installed (could not find '${eclipseJ2sPlugin}')\nTry running task jalviewjsIDE_copyJ2sPlugin"
+    def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
+    def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
+    if (altPluginsDir != null && file(altPluginsDir).exists()) {
+      eclipseJ2sPluginDirs += altPluginsDir
+    }
+    def foundPlugin = false
+    def j2sPluginFileName = j2sPluginFile.getName()
+    def eclipseJ2sPlugin
+    def eclipseJ2sPluginFile
+    eclipseJ2sPluginDirs.any { dir ->
+      eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
+      eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
+      if (eclipseJ2sPluginFile.exists()) {
+        foundPlugin = true
+        return true
+      }
+    }
+    if (!foundPlugin) {
+      def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
       System.err.println(msg)
       throw new StopExecutionException(msg)
     }
@@ -2683,7 +2915,7 @@ task jalviewjsIDE_checkJ2sPlugin {
       System.err.println(msg)
       throw new StopExecutionException(msg)
     } else {
-      def msg = "Eclipse J2S Plugin is the same as '${j2sPlugin}' (this is good)"
+      def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
       println(msg)
     }
   }
@@ -2743,7 +2975,7 @@ task jalviewjsIDE_PrepareSite {
   description "Sync libs and resources to site dir, but not closure cores"
 
   dependsOn jalviewjsIDE_SyncSiteAll
-  dependsOn cleanJalviewjsTransferSite
+  //dependsOn cleanJalviewjsTransferSite // not sure why this clean is here -- will slow down a re-run of this task
 }