mend

diff --git a/build.diff b/build.diff
deleted file mode 100644 (file)
index 313b266..0000000
--- a/build.diff
+++ /dev/null
@@ -1,515 +0,0 @@
---- build.gradle.orig  2024-05-22 09:14:54.544344630 +0200
-+++ build.gradle       2024-05-22 09:45:40.809642258 +0200
-@@ -51,8 +51,8 @@
-   id 'java'
-   id 'application'
-   id 'eclipse'
--  id "com.diffplug.gradle.spotless" version "3.28.0"
--  id 'com.github.johnrengelman.shadow' version '6.0.0'
-+  id "com.diffplug.spotless" version "6.18.0"
-+  id 'com.github.johnrengelman.shadow' version '8.1.1'
-   id 'com.install4j.gradle' version '10.0.3'
-   id 'com.dorongold.task-tree' version '2.1.1' // only needed to display task dependency tree with  gradle task1 [task2 ...] taskTree
-   id 'com.palantir.git-version' version '0.13.0' apply false
-@@ -193,6 +193,7 @@
-   testDir = string("${jalviewDir}/${bareTestSourceDir}")
- 
-   classesDir = string("${jalviewDir}/${classes_dir}")
-+  destinationDirectory = file(classesDir)
- 
-   // clover
-   useClover = clover.equals("true")
-@@ -590,14 +591,14 @@
-   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
-@@ -607,14 +608,14 @@
-   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"])
-@@ -626,14 +627,14 @@
-   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"])
- 
-@@ -658,7 +659,7 @@
-   }
- 
-   classpath {
--    //defaultOutputDir = sourceSets.main.java.outputDir
-+    //defaultOutputDir = sourceSets.main.java.destinationDirectory
-     configurations.each{ c->
-       if (c.isCanBeResolved()) {
-         minusConfigurations += [c]
-@@ -697,7 +698,7 @@
-         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
-@@ -717,7 +718,7 @@
-         }
- 
-         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
-@@ -1094,7 +1095,7 @@
- 
- clean {
-   doFirst {
--    delete sourceSets.main.java.outputDir
-+    delete sourceSets.main.java.destinationDirectory
-   }
- }
- 
-@@ -1102,7 +1103,7 @@
- cleanTest {
-   dependsOn cleanClover
-   doFirst {
--    delete sourceSets.test.java.outputDir
-+    delete sourceSets.test.java.destinationDirectory
-   }
- }
- 
-@@ -1194,7 +1195,7 @@
- 
- 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')
-@@ -1215,10 +1216,10 @@
-     exclude('**/*.html')
-     exclude('**/*.xml')
-   }
--  into outputDir
-+  into destinationDirectory
- 
-   inputs.dir(inputDir)
--  outputs.dir(outputDir)
-+  outputs.dir(destinationDirectory)
- }
- 
- 
-@@ -1283,15 +1284,15 @@
-       }
-       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) {
-@@ -1350,7 +1351,7 @@
-       def inSection = false
-       changes.eachLine { line ->
-         def m = null
--        if (m = line =~ /^##([^#].*)$/) {
-+        if (m == line =~ /^##([^#].*)$/) {
-           if (inSection) {
-             changesHugo += "</div>\n\n"
-           }
-@@ -1360,7 +1361,7 @@
-           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*$/) {
-           def comment = m[0][2].trim()
-           if (comment != "") {
-             comment = comment.replaceAll('"', "&quot;")
-@@ -1430,7 +1431,7 @@
-   def sectionName = null
-   content.eachLine { line ->
-     def m = null
--    if (m = line =~ /^##([^#].*)$/) {
-+    if (m == line =~ /^##([^#].*)$/) {
-       if (sectionName != null) {
-         sections[sectionName] = sectionContent
-         sectionName = null
-@@ -1453,7 +1454,7 @@
- 
- task copyHelp(type: Copy) {
-   def inputDir = helpSourceDir
--  def outputDir = "${helpBuildDir}/${help_dir}"
-+  def destinationDirectory = "${helpBuildDir}/${help_dir}"
-   from(inputDir) {
-     include('**/*.txt')
-     include('**/*.md')
-@@ -1478,14 +1479,15 @@
-     exclude('**/*.xml')
-     exclude('**/*.jhm')
-   }
--  into outputDir
-+  into destinationDirectory
- 
-   inputs.dir(inputDir)
-   outputs.files(helpFile)
--  outputs.dir(outputDir)
-+  outputs.dir(destinationDirectory)
- }
- 
- 
-+/*
- task releasesTemplates {
-   group "help"
-   description "Recreate whatsNew.html and releases.html from markdown files and templates in help"
-@@ -1562,9 +1564,9 @@
-       def lm = null
-       def rContentProcessed = ""
-       rContent.eachLine { line ->
--        if (lm = line =~ /^(\s*-)(\s*<!--[^>]*?-->)(.*)$/) {
-+        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"
-@@ -1622,13 +1624,14 @@
-   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')
-@@ -1649,10 +1652,10 @@
-     exclude('**/*.html')
-     exclude('**/*.xml')
-   }
--  into outputDir
-+  into destinationDirectory
- 
-   inputs.dir(inputDir)
--  outputs.dir(outputDir)
-+  outputs.dir(destinationDirectory)
- }
- 
- task copyChannelResources(type: Copy) {
-@@ -1683,6 +1686,7 @@
- 
- task createBuildProperties(type: WriteProperties) {
-   dependsOn copyResources
-+  dependsOn copyChannelResources
-   group = "build"
-   description = "Create the ${buildProperties} file"
-   
-@@ -1706,6 +1710,7 @@
- 
- task buildIndices(type: JavaExec) {
-   dependsOn copyHelp
-+  //dependsOn releasesTemplates
-   classpath = sourceSets.main.compileClasspath
-   main = "com.sun.java.help.search.Indexer"
-   workingDir = "${helpBuildDir}/${help_dir}"
-@@ -1733,7 +1738,7 @@
-   dependsOn buildResources
-   dependsOn copyDocs
-   dependsOn copyHelp
--  dependsOn releasesTemplates
-+  //dependsOn releasesTemplates
-   dependsOn convertMdFiles
-   dependsOn buildIndices
- }
-@@ -1742,6 +1747,14 @@
- compileJava.dependsOn prepare
- run.dependsOn compileJava
- compileTestJava.dependsOn compileJava
-+compileTestJava.dependsOn buildIndices
-+processResources.dependsOn copyChannelResources
-+processResources.dependsOn copyResources
-+processResources.dependsOn createBuildProperties
-+processResources.dependsOn copyDocs
-+processResources.dependsOn convertMdFiles
-+processResources.dependsOn copyHelp
-+processResources.dependsOn buildIndices
- 
- 
- 
-@@ -2037,6 +2050,7 @@
- /* END of test tasks results summary */
- 
- 
-+/*
- task compileLinkCheck(type: JavaCompile) {
-   options.fork = true
-   classpath = files("${jalviewDir}/${utils_dir}")
-@@ -2071,6 +2085,7 @@
-   inputs.dir(helpBuildDir)
-   outputs.file(helpLinksCheckerOutFile)
- }
-+*/
- 
- 
- // import the pubhtmlhelp target
-@@ -2085,10 +2100,14 @@
-   }
- }
- 
-+// block of dependencies
-+//compileTestJava.dependsOn compileLinkCheck //
-+//copyChannelResources.dependsOn compileLinkCheck //
-+//convertMdFiles.dependsOn compileLinkCheck //
- 
- jar {
-   dependsOn prepare
--  dependsOn linkCheck
-+  dependsOn //linkCheck
- 
-   manifest {
-     attributes "Main-Class": main_class,
-@@ -2098,8 +2117,8 @@
-     "Implementation-Version": JALVIEW_VERSION
-   }
- 
--  def outputDir = "${jalviewDir}/${package_dir}"
--  destinationDirectory = file(outputDir)
-+  def destinationDirectory = "${jalviewDir}/${package_dir}"
-+  destinationDirectory = file(destinationDirectory)
-   archiveFileName = rootProject.name+".jar"
-   duplicatesStrategy "EXCLUDE"
- 
-@@ -2110,11 +2129,11 @@
-   exclude "**/*.jar"
-   exclude "**/*.jar.*"
- 
--  inputs.dir(sourceSets.main.java.outputDir)
-+  inputs.dir(sourceSets.main.java.destinationDirectory)
-   sourceSets.main.resources.srcDirs.each{ dir ->
-     inputs.dir(dir)
-   }
--  outputs.file("${outputDir}/${archiveFileName}")
-+  outputs.file("${destinationDirectory}/${archiveFileName}")
- }
- 
- 
-@@ -2207,7 +2226,7 @@
-   // this mainClassName is mandatory but gets ignored due to manifest created in doFirst{}. Set the Main-Class as an attribute in launcherJar instead
-   mainClassName = shadow_jar_main_class
-   mergeServiceFiles()
--  classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
-+  archiveClassifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
-   minimize()
- }
- 
-@@ -3388,10 +3407,10 @@
- 
-   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
-   inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
--  def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
-+  def destinationDirectory = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
- 
-   from inputFiles
--  into outputDir
-+  into destinationDirectory
- }
- 
- 
-@@ -3499,13 +3518,13 @@
-   dependsOn jalviewjsTransferUnzipAllLibs
-   def inputFiles = fileTree(dir: "${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}/${filename}"
-     null
-   }
-   preserve {
-@@ -3524,13 +3543,13 @@
-   dependsOn buildResources
- 
-   def inputFiles = fileTree(dir: resourcesBuildDir)
--  def outputDir = "${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}/${filename}"
-     null
-   }
-   preserve {
-@@ -3543,13 +3562,13 @@
- 
- task jalviewjsSyncSiteResources (type: Sync) {
-   def inputFiles = fileTree(dir: "${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}/${filename}"
-     null
-   }
-   preserve {
-@@ -3563,13 +3582,13 @@
- task jalviewjsSyncBuildProperties (type: Sync) {
-   dependsOn createBuildProperties
-   def inputFiles = [file(buildProperties)]
--  def outputDir = "${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}/${filename}"
-     null
-   }
-   preserve {
-@@ -3788,7 +3807,7 @@
-   def swingJ2sDir = "${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"
- 
-@@ -3832,8 +3851,8 @@
-     }
-     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,
-@@ -3851,8 +3870,8 @@
-   // _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
-   ]
-@@ -3885,8 +3904,8 @@
-     ]
-   )
-   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
-   ]
-@@ -3939,11 +3958,11 @@
-   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
-   }
-@@ -3962,13 +3981,13 @@
-   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 {