Merge branch 'JAL-3322_getdown_speed_improvement' of https://source.jalview.org/git...

parallel dev

diff --combined build.gradle
index 5099841,81c2751..165c05e
--- 1/build.gradle
--- 2/build.gradle
+++ b/build.gradle
@@@ -594,10 -594,13 +594,13 @@@ task convertBuildingMD(type: Exec) 
      pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
    }
  
-   if (pandoc != null && file(pandoc).exists()) {
-     commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
-   } else {
-     commandLine "true"
+   doFirst {
+     if (false && 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()
+     }
    }
  
    ignoreExitValue true
@@@ -721,7 -724,7 +724,7 @@@ task compileLinkCheck(type: JavaCompile
    outputs.file("$jalviewDir/$utilsDir/BufferedLineReader.class")
  }
  
 -def helplinkscheckeroutputfile = file("$jalviewDir/$utilsDir/HelpLinksChecker.out")
 +def helplinkscheckertouchfile = file("$jalviewDir/$utilsDir/HelpLinksChecker.touch")
  task linkCheck(type: JavaExec) {
    dependsOn prepare, compileLinkCheck
    classpath = files("$jalviewDir/$utilsDir")
@@@ -730,12 -733,12 +733,12 @@@
    def help = "$classes/$helpDir"
    args = [ "$classes/$helpDir", "-nointernet" ]
  
 -  doFirst {
 -    helplinkscheckeroutputfile.createNewFile()
 -    standardOutput new FileOutputStream(helplinkscheckeroutputfile, false)
 +  doLast {
 +    helplinkscheckertouchfile.createNewFile()
    }
  
 -  outputs.file(helplinkscheckeroutputfile)
 +  inputs.dir("$classes/$helpDir")
 +  outputs.file(helplinkscheckertouchfile)
  }
  
  task cleanPackageDir(type: Delete) {