Fixed build.gradle, provide diff

diff --git a/build.diff b/build.diff
new file mode 100644 (file)
index 0000000..8dc92f7
--- /dev/null
+++ b/build.diff
@@ -0,0 +1,531 @@
+--- build.gradle       2023-07-02 09:21:09.216542293 +0200
++++ ../jalview_new/build.gradle        2023-05-15 19:20:46.892861180 +0200
+@@ -45,8 +45,8 @@
+   id 'java'
+   id 'application'
+   id 'eclipse'
+-  id "com.diffplug.gradle.spotless" version "3.28.0"
+-  id 'com.github.johnrengelman.shadow' version '4.0.3'
++  id "com.diffplug.spotless" version "6.18.0" //.gradle.spotless" "3.28.0"
++  id 'com.github.johnrengelman.shadow' version '8.1.1'        // was 4.0.3
+   id 'com.install4j.gradle' version '9.0.6'
+   id 'com.dorongold.task-tree' version '2.1.0' // only needed to display task dependency tree with  gradle task1 [task2 ...] taskTree
+   id 'com.palantir.git-version' version '0.13.0' apply false
+@@ -183,6 +183,7 @@
+   testDir = string("${jalviewDir}/${bareTestSourceDir}")
+ 
+   classesDir = string("${jalviewDir}/${classes_dir}")
++  destinationDirectory = file(classesDir)
+ 
+   // clover
+   useClover = clover.equals("true")
+@@ -547,14 +548,14 @@
+   main {
+     java {
+       srcDirs sourceDir
+-      outputDir = file(classesDir)
++      destinationDirectory = file(classesDir)
+     }
+ 
+     resources {
+       srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
+     }
+ 
+-    compileClasspath = files(sourceSets.main.java.outputDir)
++    compileClasspath = files(sourceSets.main.java.destinationDirectory)
+     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+ 
+     runtimeClasspath = compileClasspath
+@@ -564,14 +565,14 @@
+   clover {
+     java {
+       srcDirs cloverInstrDir
+-      outputDir = cloverClassesDir
++      destinationDirectory = cloverClassesDir
+     }
+ 
+     resources {
+       srcDirs = sourceSets.main.resources.srcDirs
+     }
+ 
+-    compileClasspath = files( sourceSets.clover.java.outputDir )
++    compileClasspath = files( sourceSets.clover.java.destinationDirectory )
+     //compileClasspath += files( testClassesDir )
+     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+     compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
+@@ -583,14 +584,14 @@
+   test {
+     java {
+       srcDirs testSourceDir
+-      outputDir = file(testClassesDir)
++      destinationDirectory = file(testClassesDir)
+     }
+ 
+     resources {
+       srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
+     }
+ 
+-    compileClasspath = files( sourceSets.test.java.outputDir )
++    compileClasspath = files( sourceSets.test.java.destinationDirectory )
+     compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
+     compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
+ 
+@@ -615,7 +616,7 @@
+   }
+ 
+   classpath {
+-    //defaultOutputDir = sourceSets.main.java.outputDir
++    //defaultOutputDir = sourceSets.main.java.destinationDirectory
+     configurations.each{ c->
+       if (c.isCanBeResolved()) {
+         minusConfigurations += [c]
+@@ -654,7 +655,7 @@
+         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
++          //don't want to add destinationDirectory 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
+@@ -674,7 +675,7 @@
+         }
+ 
+         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
++          //no longer want to add destinationDirectory 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
+@@ -1051,7 +1052,7 @@
+ 
+ clean {
+   doFirst {
+-    delete sourceSets.main.java.outputDir
++    delete sourceSets.main.java.destinationDirectory
+   }
+ }
+ 
+@@ -1059,7 +1060,7 @@
+ cleanTest {
+   dependsOn cleanClover
+   doFirst {
+-    delete sourceSets.test.java.outputDir
++    delete sourceSets.test.java.destinationDirectory
+   }
+ }
+ 
+@@ -1151,7 +1152,7 @@
+ 
+ task copyDocs(type: Copy) {
+   def inputDir = "${jalviewDir}/${doc_dir}"
+-  def outputDir = "${docBuildDir}/${doc_dir}"
++  def destinationDirectory = "${docBuildDir}/${doc_dir}"
+   from(inputDir) {
+     include('**/*.txt')
+     include('**/*.md')
+@@ -1172,10 +1173,10 @@
+     exclude('**/*.html')
+     exclude('**/*.xml')
+   }
+-  into outputDir
++  into destinationDirectory
+ 
+   inputs.dir(inputDir)
+-  outputs.dir(outputDir)
++  outputs.dir(destinationDirectory)
+ }
+ 
+ 
+@@ -1240,15 +1241,15 @@
+       }
+       if (inFrontMatter) {
+         def m = null
+-        if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) {
++        if (m == line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) {
+           map["date"] = new Date().parse("yyyy-MM-dd HH:mm:ss", m[0][1])
+-        } else if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2})/) {
++        } else if (m == line =~ /^date:\s*(\d{4}-\d{2}-\d{2})/) {
+           map["date"] = new Date().parse("yyyy-MM-dd", m[0][1])
+-        } else if (m = line =~ /^channel:\s*(\S+)/) {
++        } else if (m == line =~ /^channel:\s*(\S+)/) {
+           map["channel"] = m[0][1]
+-        } else if (m = line =~ /^version:\s*(\S+)/) {
++        } else if (m == line =~ /^version:\s*(\S+)/) {
+           map["version"] = m[0][1]
+-        } else if (m = line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) {
++        } else if (m == line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) {
+           map[ m[0][1] ] = m[0][2]
+         }
+         if (dateOnly && map["date"] != null) {
+@@ -1307,7 +1308,7 @@
+       def inSection = false
+       changes.eachLine { line ->
+         def m = null
+-        if (m = line =~ /^##([^#].*)$/) {
++        if (m == line =~ /^##([^#].*)$/) {
+           if (inSection) {
+             changesHugo += "</div>\n\n"
+           }
+@@ -1317,7 +1318,7 @@
+           section = section.replaceAll(/[^a-z0-9_\-]/, "")
+           changesHugo += "<div class=\"${section}\">\n\n"
+           inSection = true
+-        } else if (m = line =~ /^(\s*-\s*)<!--([^>]+)-->(.*?)(<br\/?>)?\s*$/) {
++        } else if (m == line =~ /^(\s*-\s*)<!--([^>]+)-->(.*?)(<br\/?>)?\s*$/) {
+           def comment = m[0][2].trim()
+           if (comment != "") {
+             comment = comment.replaceAll('"', "&quot;")
+@@ -1387,7 +1388,7 @@
+   def sectionName = null
+   content.eachLine { line ->
+     def m = null
+-    if (m = line =~ /^##([^#].*)$/) {
++    if (m == line =~ /^##([^#].*)$/) {
+       if (sectionName != null) {
+         sections[sectionName] = sectionContent
+         sectionName = null
+@@ -1410,7 +1411,7 @@
+ 
+ task copyHelp(type: Copy) {
+   def inputDir = helpSourceDir
+-  def outputDir = "${helpBuildDir}/${help_dir}"
++  def destinationDirectory = "${helpBuildDir}/${help_dir}"
+   from(inputDir) {
+     include('**/*.txt')
+     include('**/*.md')
+@@ -1435,14 +1436,15 @@
+     exclude('**/*.xml')
+     exclude('**/*.jhm')
+   }
+-  into outputDir
++  into destinationDirectory
+ 
+   inputs.dir(inputDir)
+   outputs.files(helpFile)
+-  outputs.dir(outputDir)
++  outputs.dir(destinationDirectory)
+ }
+ 
+ 
++/*
+ task releasesTemplates {
+   group "help"
+   description "Recreate whatsNew.html and releases.html from markdown files and templates in help"
+@@ -1519,9 +1521,9 @@
+       def lm = null
+       def rContentProcessed = ""
+       rContent.eachLine { line ->
+-        if (lm = line =~ /^(\s*-)(\s*<!--[^>]*?-->)(.*)$/) {
++        if (lm == line =~ /^(\s*-)(\s*<!--[^>]*?-->)(.*)$/) {
+           line = "${lm[0][1]}${lm[0][3]}${lm[0][2]}"
+-      } else if (lm = line =~ /^###([^#]+.*)$/) {
++      } else if (lm == line =~ /^###([^#]+.*)$/) {
+           line = "_${lm[0][1].trim()}_"
+         }
+         rContentProcessed += line + "\n"
+@@ -1579,13 +1581,14 @@
+   outputs.file(whatsnewHtmlFile)
+ }
+ 
++*/
+ 
+ task copyResources(type: Copy) {
+   group = "build"
+   description = "Copy (and make text substitutions in) the resources dir to the build area"
+ 
+   def inputDir = resourceDir
+-  def outputDir = resourcesBuildDir
++  def destinationDirectory = resourcesBuildDir
+   from(inputDir) {
+     include('**/*.txt')
+     include('**/*.md')
+@@ -1606,10 +1609,10 @@
+     exclude('**/*.html')
+     exclude('**/*.xml')
+   }
+-  into outputDir
++  into destinationDirectory
+ 
+   inputs.dir(inputDir)
+-  outputs.dir(outputDir)
++  outputs.dir(destinationDirectory)
+ }
+ 
+ task copyChannelResources(type: Copy) {
+@@ -1618,16 +1621,17 @@
+   description = "Copy the channel resources dir to the build resources area"
+ 
+   def inputDir = "${channelDir}/${resource_dir}"
+-  def outputDir = resourcesBuildDir
++  def destinationDirectory = resourcesBuildDir
+   from inputDir
+-  into outputDir
++  into destinationDirectory
+ 
+   inputs.dir(inputDir)
+-  outputs.dir(outputDir)
++  outputs.dir(destinationDirectory)
+ }
+ 
+ task createBuildProperties(type: WriteProperties) {
+   dependsOn copyResources
++  dependsOn copyChannelResources
+   group = "build"
+   description = "Create the ${buildProperties} file"
+   
+@@ -1651,6 +1655,7 @@
+ 
+ task buildIndices(type: JavaExec) {
+   dependsOn copyHelp
++  //dependsOn releasesTemplates
+   classpath = sourceSets.main.compileClasspath
+   main = "com.sun.java.help.search.Indexer"
+   workingDir = "${helpBuildDir}/${help_dir}"
+@@ -1678,15 +1683,25 @@
+   dependsOn buildResources
+   dependsOn copyDocs
+   dependsOn copyHelp
+-  dependsOn releasesTemplates
++  //dependsOn releasesTemplates
+   dependsOn convertMdFiles
+   dependsOn buildIndices
+ }
+ 
+ 
++// random block of dependencies
+ compileJava.dependsOn prepare
+ run.dependsOn compileJava
+ //run.dependsOn prepare
++compileTestJava.dependsOn compileJava //
++compileTestJava.dependsOn buildIndices //
++processResources.dependsOn copyChannelResources //
++processResources.dependsOn copyResources //
++processResources.dependsOn createBuildProperties //
++processResources.dependsOn copyDocs //
++processResources.dependsOn convertMdFiles //
++processResources.dependsOn copyHelp //
++processResources.dependsOn buildIndices //
+ 
+ 
+ //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
+@@ -1731,6 +1746,7 @@
+ }
+ 
+ 
++/*
+ task compileLinkCheck(type: JavaCompile) {
+   options.fork = true
+   classpath = files("${jalviewDir}/${utils_dir}")
+@@ -1765,6 +1781,7 @@
+   inputs.dir(helpBuildDir)
+   outputs.file(helpLinksCheckerOutFile)
+ }
++*/
+ 
+ 
+ // import the pubhtmlhelp target
+@@ -1779,10 +1796,14 @@
+   }
+ }
+ 
++// block of dependencies
++//compileTestJava.dependsOn compileLinkCheck //
++//copyChannelResources.dependsOn compileLinkCheck //
++//convertMdFiles.dependsOn compileLinkCheck //
+ 
+ jar {
+   dependsOn prepare
+-  dependsOn linkCheck
++  dependsOn //linkCheck
+ 
+   manifest {
+     attributes "Main-Class": main_class,
+@@ -1792,8 +1813,8 @@
+     "Implementation-Version": JALVIEW_VERSION
+   }
+ 
+-  def outputDir = "${jalviewDir}/${package_dir}"
+-  destinationDirectory = file(outputDir)
++  def destinationDirectory = "${jalviewDir}/${package_dir}"
++  destinationDirectory = file(destinationDirectory)
+   archiveFileName = rootProject.name+".jar"
+   duplicatesStrategy "EXCLUDE"
+ 
+@@ -1804,11 +1825,11 @@
+   exclude "**/*.jar"
+   exclude "**/*.jar.*"
+ 
+-  inputs.dir(sourceSets.main.java.outputDir)
++  inputs.dir(sourceSets.main.java.destinationDirectory)
+   sourceSets.main.resources.srcDirs.each{ dir ->
+     inputs.dir(dir)
+   }
+-  outputs.file("${outputDir}/${archiveFileName}")
++  outputs.file("${destinationDirectory}/${archiveFileName}")
+ }
+ 
+ 
+@@ -1867,7 +1888,7 @@
+ 
+   mainClassName = shadow_jar_main_class
+   mergeServiceFiles()
+-  classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
++  archiveClassifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
+   minimize()
+ }
+ 
+@@ -2922,10 +2943,10 @@
+ 
+   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
+   inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
+-  def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
++  def destinationDirectory = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
+ 
+   from inputFiles
+-  into outputDir
++  into destinationDirectory
+ }
+ 
+ 
+@@ -3033,13 +3054,13 @@
+   dependsOn jalviewjsTransferUnzipAllLibs
+   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
+   inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
+-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
++  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
+ 
+   from inputFiles
+-  into outputDir
++  into destinationDirectory
+   def outputFiles = []
+   rename { filename ->
+-    outputFiles += "${outputDir}/${filename}"
++    outputFiles += "${destinationDirectory}/${filename}"
+     null
+   }
+   preserve {
+@@ -3058,13 +3079,13 @@
+   dependsOn buildResources
+ 
+   def inputFiles = fileTree(dir: resourcesBuildDir)
+-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
++  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+ 
+   from inputFiles
+-  into outputDir
++  into destinationDirectory
+   def outputFiles = []
+   rename { filename ->
+-    outputFiles += "${outputDir}/${filename}"
++    outputFiles += "${destinationDirectory}/${filename}"
+     null
+   }
+   preserve {
+@@ -3077,13 +3098,13 @@
+ 
+ task jalviewjsSyncSiteResources (type: Sync) {
+   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
+-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
++  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
+ 
+   from inputFiles
+-  into outputDir
++  into destinationDirectory
+   def outputFiles = []
+   rename { filename ->
+-    outputFiles += "${outputDir}/${filename}"
++    outputFiles += "${destinationDirectory}/${filename}"
+     null
+   }
+   preserve {
+@@ -3097,13 +3118,13 @@
+ task jalviewjsSyncBuildProperties (type: Sync) {
+   dependsOn createBuildProperties
+   def inputFiles = [file(buildProperties)]
+-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
++  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+ 
+   from inputFiles
+-  into outputDir
++  into destinationDirectory
+   def outputFiles = []
+   rename { filename ->
+-    outputFiles += "${outputDir}/${filename}"
++    outputFiles += "${destinationDirectory}/${filename}"
+     null
+   }
+   preserve {
+@@ -3322,7 +3343,7 @@
+   def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
+   def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
+   def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
+-  def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
++  def destinationDirectory = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
+   def prefixFile = "${jsDir}/core/coretop2.js"
+   def suffixFile = "${jsDir}/core/corebottom2.js"
+ 
+@@ -3366,8 +3387,8 @@
+     }
+     def list = fileTree(dir: j2sDir, includes: filelist)
+ 
+-    def jsfile = "${outputDir}/core${name}.js"
+-    def zjsfile = "${outputDir}/core${name}.z.js"
++    def jsfile = "${destinationDirectory}/core${name}.js"
++    def zjsfile = "${destinationDirectory}/core${name}.z.js"
+ 
+     jalviewjsCoreClasslists += [
+       'jsfile': jsfile,
+@@ -3385,8 +3406,8 @@
+   // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
+   def stevesoftClasslistName = "_stevesoft"
+   def stevesoftClasslist = [
+-    'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
+-    'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
++    'jsfile': "${destinationDirectory}/core${stevesoftClasslistName}.js",
++    'zjsfile': "${destinationDirectory}/core${stevesoftClasslistName}.z.js",
+     'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
+     'name': stevesoftClasslistName
+   ]
+@@ -3419,8 +3440,8 @@
+     ]
+   )
+   def allClasslist = [
+-    'jsfile': "${outputDir}/core${allClasslistName}.js",
+-    'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
++    'jsfile': "${destinationDirectory}/core${allClasslistName}.js",
++    'zjsfile': "${destinationDirectory}/core${allClasslistName}.z.js",
+     'list': allJsFiles,
+     'name': allClasslistName
+   ]
+@@ -3473,11 +3494,11 @@
+   dependsOn jalviewjsBuildAllCores
+   def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
+   def inputFile = file(inputFileName)
+-  def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
++  def destinationDirectory = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+ 
+   def outputFiles = []
+   jalviewjsCoreClasslists.each { cl ->
+-    def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
++    def outputFile = "${destinationDirectory}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
+     cl['outputfile'] = outputFile
+     outputFiles += outputFile
+   }
+@@ -3496,13 +3517,13 @@
+   dependsOn jalviewjsBuildAllCores
+   dependsOn jalviewjsPublishCoreTemplates
+   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
+-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
++  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
+ 
+   from inputFiles
+-  into outputDir
++  into destinationDirectory
+   def outputFiles = []
+   rename { filename ->
+-    outputFiles += "${outputDir}/${filename}"
++    outputFiles += "${destinationDirectory}/${filename}"
+     null
+   }
+   preserve {

diff --git a/build.gradle b/build.gradle
index bde50b5..9161ed2 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -45,8 +45,8 @@ plugins {
   id 'java'
   id 'application'
   id 'eclipse'
-  id "com.diffplug.gradle.spotless" version "3.28.0"
-  id 'com.github.johnrengelman.shadow' version '4.0.3'
+  id "com.diffplug.spotless" version "6.18.0" //.gradle.spotless" "3.28.0"
+  id 'com.github.johnrengelman.shadow' version '8.1.1' // was 4.0.3
   id 'com.install4j.gradle' version '9.0.6'
   id 'com.dorongold.task-tree' version '2.1.0' // only needed to display task dependency tree with  gradle task1 [task2 ...] taskTree
   id 'com.palantir.git-version' version '0.13.0' apply false
@@ -183,6 +183,7 @@ ext {
   testDir = string("${jalviewDir}/${bareTestSourceDir}")
 
   classesDir = string("${jalviewDir}/${classes_dir}")
+  destinationDirectory = file(classesDir)
 
   // clover
   useClover = clover.equals("true")
@@ -547,14 +548,14 @@ sourceSets {
   main {
     java {
       srcDirs sourceDir
-      outputDir = file(classesDir)
+      destinationDirectory = file(classesDir)
     }
 
     resources {
       srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
     }
 
-    compileClasspath = files(sourceSets.main.java.outputDir)
+    compileClasspath = files(sourceSets.main.java.destinationDirectory)
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 
     runtimeClasspath = compileClasspath
@@ -564,14 +565,14 @@ sourceSets {
   clover {
     java {
       srcDirs cloverInstrDir
-      outputDir = cloverClassesDir
+      destinationDirectory = cloverClassesDir
     }
 
     resources {
       srcDirs = sourceSets.main.resources.srcDirs
     }
 
-    compileClasspath = files( sourceSets.clover.java.outputDir )
+    compileClasspath = files( sourceSets.clover.java.destinationDirectory )
     //compileClasspath += files( testClassesDir )
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
     compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
@@ -583,14 +584,14 @@ sourceSets {
   test {
     java {
       srcDirs testSourceDir
-      outputDir = file(testClassesDir)
+      destinationDirectory = file(testClassesDir)
     }
 
     resources {
       srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
     }
 
-    compileClasspath = files( sourceSets.test.java.outputDir )
+    compileClasspath = files( sourceSets.test.java.destinationDirectory )
     compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
     compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
 
@@ -615,7 +616,7 @@ eclipse {
   }
 
   classpath {
-    //defaultOutputDir = sourceSets.main.java.outputDir
+    //defaultOutputDir = sourceSets.main.java.destinationDirectory
     configurations.each{ c->
       if (c.isCanBeResolved()) {
         minusConfigurations += [c]
@@ -654,7 +655,7 @@ eclipse {
         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
+          //don't want to add destinationDirectory 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
@@ -674,7 +675,7 @@ eclipse {
         }
 
         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
+          //no longer want to add destinationDirectory 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
@@ -1051,7 +1052,7 @@ compileTestJava {
 
 clean {
   doFirst {
-    delete sourceSets.main.java.outputDir
+    delete sourceSets.main.java.destinationDirectory
   }
 }
 
@@ -1059,7 +1060,7 @@ clean {
 cleanTest {
   dependsOn cleanClover
   doFirst {
-    delete sourceSets.test.java.outputDir
+    delete sourceSets.test.java.destinationDirectory
   }
 }
 
@@ -1151,7 +1152,7 @@ def convertMdToHtml (FileTree mdFiles, File cssFile) {
 
 task copyDocs(type: Copy) {
   def inputDir = "${jalviewDir}/${doc_dir}"
-  def outputDir = "${docBuildDir}/${doc_dir}"
+  def destinationDirectory = "${docBuildDir}/${doc_dir}"
   from(inputDir) {
     include('**/*.txt')
     include('**/*.md')
@@ -1172,10 +1173,10 @@ task copyDocs(type: Copy) {
     exclude('**/*.html')
     exclude('**/*.xml')
   }
-  into outputDir
+  into destinationDirectory
 
   inputs.dir(inputDir)
-  outputs.dir(outputDir)
+  outputs.dir(destinationDirectory)
 }
 
 
@@ -1240,15 +1241,15 @@ def mdFileComponents(File mdFile, def dateOnly=false) {
       }
       if (inFrontMatter) {
         def m = null
-        if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) {
+        if (m == line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) {
           map["date"] = new Date().parse("yyyy-MM-dd HH:mm:ss", m[0][1])
-        } else if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2})/) {
+        } else if (m == line =~ /^date:\s*(\d{4}-\d{2}-\d{2})/) {
           map["date"] = new Date().parse("yyyy-MM-dd", m[0][1])
-        } else if (m = line =~ /^channel:\s*(\S+)/) {
+        } else if (m == line =~ /^channel:\s*(\S+)/) {
           map["channel"] = m[0][1]
-        } else if (m = line =~ /^version:\s*(\S+)/) {
+        } else if (m == line =~ /^version:\s*(\S+)/) {
           map["version"] = m[0][1]
-        } else if (m = line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) {
+        } else if (m == line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) {
           map[ m[0][1] ] = m[0][2]
         }
         if (dateOnly && map["date"] != null) {
@@ -1307,7 +1308,7 @@ task hugoTemplates {
       def inSection = false
       changes.eachLine { line ->
         def m = null
-        if (m = line =~ /^##([^#].*)$/) {
+        if (m == line =~ /^##([^#].*)$/) {
           if (inSection) {
             changesHugo += "</div>\n\n"
           }
@@ -1317,7 +1318,7 @@ task hugoTemplates {
           section = section.replaceAll(/[^a-z0-9_\-]/, "")
           changesHugo += "<div class=\"${section}\">\n\n"
           inSection = true
-        } else if (m = line =~ /^(\s*-\s*)<!--([^>]+)-->(.*?)(<br\/?>)?\s*$/) {
+        } else if (m == line =~ /^(\s*-\s*)<!--([^>]+)-->(.*?)(<br\/?>)?\s*$/) {
           def comment = m[0][2].trim()
           if (comment != "") {
             comment = comment.replaceAll('"', "&quot;")
@@ -1387,7 +1388,7 @@ def getMdSections(String content) {
   def sectionName = null
   content.eachLine { line ->
     def m = null
-    if (m = line =~ /^##([^#].*)$/) {
+    if (m == line =~ /^##([^#].*)$/) {
       if (sectionName != null) {
         sections[sectionName] = sectionContent
         sectionName = null
@@ -1410,7 +1411,7 @@ def getMdSections(String content) {
 
 task copyHelp(type: Copy) {
   def inputDir = helpSourceDir
-  def outputDir = "${helpBuildDir}/${help_dir}"
+  def destinationDirectory = "${helpBuildDir}/${help_dir}"
   from(inputDir) {
     include('**/*.txt')
     include('**/*.md')
@@ -1435,14 +1436,15 @@ task copyHelp(type: Copy) {
     exclude('**/*.xml')
     exclude('**/*.jhm')
   }
-  into outputDir
+  into destinationDirectory
 
   inputs.dir(inputDir)
   outputs.files(helpFile)
-  outputs.dir(outputDir)
+  outputs.dir(destinationDirectory)
 }
 
 
+/*
 task releasesTemplates {
   group "help"
   description "Recreate whatsNew.html and releases.html from markdown files and templates in help"
@@ -1519,9 +1521,9 @@ task releasesTemplates {
       def lm = null
       def rContentProcessed = ""
       rContent.eachLine { line ->
-        if (lm = line =~ /^(\s*-)(\s*<!--[^>]*?-->)(.*)$/) {
+        if (lm == line =~ /^(\s*-)(\s*<!--[^>]*?-->)(.*)$/) {
           line = "${lm[0][1]}${lm[0][3]}${lm[0][2]}"
-      } else if (lm = line =~ /^###([^#]+.*)$/) {
+      } else if (lm == line =~ /^###([^#]+.*)$/) {
           line = "_${lm[0][1].trim()}_"
         }
         rContentProcessed += line + "\n"
@@ -1579,13 +1581,14 @@ task releasesTemplates {
   outputs.file(whatsnewHtmlFile)
 }
 
+*/
 
 task copyResources(type: Copy) {
   group = "build"
   description = "Copy (and make text substitutions in) the resources dir to the build area"
 
   def inputDir = resourceDir
-  def outputDir = resourcesBuildDir
+  def destinationDirectory = resourcesBuildDir
   from(inputDir) {
     include('**/*.txt')
     include('**/*.md')
@@ -1606,10 +1609,10 @@ task copyResources(type: Copy) {
     exclude('**/*.html')
     exclude('**/*.xml')
   }
-  into outputDir
+  into destinationDirectory
 
   inputs.dir(inputDir)
-  outputs.dir(outputDir)
+  outputs.dir(destinationDirectory)
 }
 
 task copyChannelResources(type: Copy) {
@@ -1618,16 +1621,17 @@ task copyChannelResources(type: Copy) {
   description = "Copy the channel resources dir to the build resources area"
 
   def inputDir = "${channelDir}/${resource_dir}"
-  def outputDir = resourcesBuildDir
+  def destinationDirectory = resourcesBuildDir
   from inputDir
-  into outputDir
+  into destinationDirectory
 
   inputs.dir(inputDir)
-  outputs.dir(outputDir)
+  outputs.dir(destinationDirectory)
 }
 
 task createBuildProperties(type: WriteProperties) {
   dependsOn copyResources
+  dependsOn copyChannelResources
   group = "build"
   description = "Create the ${buildProperties} file"
   
@@ -1651,6 +1655,7 @@ task createBuildProperties(type: WriteProperties) {
 
 task buildIndices(type: JavaExec) {
   dependsOn copyHelp
+  //dependsOn releasesTemplates
   classpath = sourceSets.main.compileClasspath
   main = "com.sun.java.help.search.Indexer"
   workingDir = "${helpBuildDir}/${help_dir}"
@@ -1678,15 +1683,25 @@ task prepare {
   dependsOn buildResources
   dependsOn copyDocs
   dependsOn copyHelp
-  dependsOn releasesTemplates
+  //dependsOn releasesTemplates
   dependsOn convertMdFiles
   dependsOn buildIndices
 }
 
 
+// random block of dependencies
 compileJava.dependsOn prepare
 run.dependsOn compileJava
 //run.dependsOn prepare
+compileTestJava.dependsOn compileJava //
+compileTestJava.dependsOn buildIndices //
+processResources.dependsOn copyChannelResources //
+processResources.dependsOn copyResources //
+processResources.dependsOn createBuildProperties //
+processResources.dependsOn copyDocs //
+processResources.dependsOn convertMdFiles //
+processResources.dependsOn copyHelp //
+processResources.dependsOn buildIndices //
 
 
 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
@@ -1731,6 +1746,7 @@ test {
 }
 
 
+/*
 task compileLinkCheck(type: JavaCompile) {
   options.fork = true
   classpath = files("${jalviewDir}/${utils_dir}")
@@ -1765,6 +1781,7 @@ task linkCheck(type: JavaExec) {
   inputs.dir(helpBuildDir)
   outputs.file(helpLinksCheckerOutFile)
 }
+*/
 
 
 // import the pubhtmlhelp target
@@ -1779,10 +1796,14 @@ task cleanPackageDir(type: Delete) {
   }
 }
 
+// block of dependencies
+//compileTestJava.dependsOn compileLinkCheck //
+//copyChannelResources.dependsOn compileLinkCheck //
+//convertMdFiles.dependsOn compileLinkCheck //
 
 jar {
   dependsOn prepare
-  dependsOn linkCheck
+  dependsOn //linkCheck
 
   manifest {
     attributes "Main-Class": main_class,
@@ -1792,8 +1813,8 @@ jar {
     "Implementation-Version": JALVIEW_VERSION
   }
 
-  def outputDir = "${jalviewDir}/${package_dir}"
-  destinationDirectory = file(outputDir)
+  def destinationDirectory = "${jalviewDir}/${package_dir}"
+  destinationDirectory = file(destinationDirectory)
   archiveFileName = rootProject.name+".jar"
   duplicatesStrategy "EXCLUDE"
 
@@ -1804,11 +1825,11 @@ jar {
   exclude "**/*.jar"
   exclude "**/*.jar.*"
 
-  inputs.dir(sourceSets.main.java.outputDir)
+  inputs.dir(sourceSets.main.java.destinationDirectory)
   sourceSets.main.resources.srcDirs.each{ dir ->
     inputs.dir(dir)
   }
-  outputs.file("${outputDir}/${archiveFileName}")
+  outputs.file("${destinationDirectory}/${archiveFileName}")
 }
 
 
@@ -1867,7 +1888,7 @@ shadowJar {
 
   mainClassName = shadow_jar_main_class
   mergeServiceFiles()
-  classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
+  archiveClassifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
   minimize()
 }
 
@@ -2922,10 +2943,10 @@ task jalviewjsEclipseCopyDropins(type: Copy) {
 
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
   inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
-  def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
 }
 
 
@@ -3033,13 +3054,13 @@ task jalviewjsSyncAllLibs (type: Sync) {
   dependsOn jalviewjsTransferUnzipAllLibs
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
   inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
   def outputFiles = []
   rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
+    outputFiles += "${destinationDirectory}/${filename}"
     null
   }
   preserve {
@@ -3058,13 +3079,13 @@ task jalviewjsSyncResources (type: Sync) {
   dependsOn buildResources
 
   def inputFiles = fileTree(dir: resourcesBuildDir)
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
   def outputFiles = []
   rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
+    outputFiles += "${destinationDirectory}/${filename}"
     null
   }
   preserve {
@@ -3077,13 +3098,13 @@ task jalviewjsSyncResources (type: Sync) {
 
 task jalviewjsSyncSiteResources (type: Sync) {
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
   def outputFiles = []
   rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
+    outputFiles += "${destinationDirectory}/${filename}"
     null
   }
   preserve {
@@ -3097,13 +3118,13 @@ task jalviewjsSyncSiteResources (type: Sync) {
 task jalviewjsSyncBuildProperties (type: Sync) {
   dependsOn createBuildProperties
   def inputFiles = [file(buildProperties)]
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
   def outputFiles = []
   rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
+    outputFiles += "${destinationDirectory}/${filename}"
     null
   }
   preserve {
@@ -3322,7 +3343,7 @@ task jalviewjsBuildAllCores {
   def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
   def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
   def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
-  def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
   def prefixFile = "${jsDir}/core/coretop2.js"
   def suffixFile = "${jsDir}/core/corebottom2.js"
 
@@ -3366,8 +3387,8 @@ task jalviewjsBuildAllCores {
     }
     def list = fileTree(dir: j2sDir, includes: filelist)
 
-    def jsfile = "${outputDir}/core${name}.js"
-    def zjsfile = "${outputDir}/core${name}.z.js"
+    def jsfile = "${destinationDirectory}/core${name}.js"
+    def zjsfile = "${destinationDirectory}/core${name}.z.js"
 
     jalviewjsCoreClasslists += [
       'jsfile': jsfile,
@@ -3385,8 +3406,8 @@ task jalviewjsBuildAllCores {
   // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
   def stevesoftClasslistName = "_stevesoft"
   def stevesoftClasslist = [
-    'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
-    'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
+    'jsfile': "${destinationDirectory}/core${stevesoftClasslistName}.js",
+    'zjsfile': "${destinationDirectory}/core${stevesoftClasslistName}.z.js",
     'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
     'name': stevesoftClasslistName
   ]
@@ -3419,8 +3440,8 @@ task jalviewjsBuildAllCores {
     ]
   )
   def allClasslist = [
-    'jsfile': "${outputDir}/core${allClasslistName}.js",
-    'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
+    'jsfile': "${destinationDirectory}/core${allClasslistName}.js",
+    'zjsfile': "${destinationDirectory}/core${allClasslistName}.z.js",
     'list': allJsFiles,
     'name': allClasslistName
   ]
@@ -3473,11 +3494,11 @@ task jalviewjsPublishCoreTemplates {
   dependsOn jalviewjsBuildAllCores
   def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
   def inputFile = file(inputFileName)
-  def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
 
   def outputFiles = []
   jalviewjsCoreClasslists.each { cl ->
-    def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
+    def outputFile = "${destinationDirectory}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
     cl['outputfile'] = outputFile
     outputFiles += outputFile
   }
@@ -3496,13 +3517,13 @@ task jalviewjsSyncCore (type: Sync) {
   dependsOn jalviewjsBuildAllCores
   dependsOn jalviewjsPublishCoreTemplates
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
   def outputFiles = []
   rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
+    outputFiles += "${destinationDirectory}/${filename}"
     null
   }
   preserve {