+@@ -1031,85 +236,6 @@
+ }
+
+
+-def convertMdToHtml (FileTree mdFiles, File cssFile) {
+- MutableDataSet options = new MutableDataSet()
+-
+- 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}/${doc_dir}"
+@@ -1140,27 +266,6 @@
+ }
+
+
+-task convertMdFiles {
+- dependsOn copyDocs
+- def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
+- def cssFile = file("${jalviewDir}/${flexmark_css}")
+-
+- doLast {
+- convertMdToHtml(mdFiles, cssFile)
+- }
+-
+- inputs.files(mdFiles)
+- inputs.file(cssFile)
+-
+- def htmlFiles = []
+- mdFiles.each { mdFile ->
+- def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
+- htmlFiles.add(file(htmlFilePath))
+- }
+- outputs.files(htmlFiles)
+-}
+-
+-
+ task copyHelp(type: Copy) {
+ def inputDir = helpSourceDir
+ def outputDir = "${helpBuildDir}/${help_dir}"
+@@ -1242,24 +347,15 @@
+ outputs.dir(outputDir)
+ }
+
+-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+"]"
+- if (getdownSetAppBaseProperty) {
+- property "GETDOWNAPPBASE", getdownAppBase
+- property "GETDOWNAPPDISTDIR", getdownAppDistDir
+- }
++task createBuildProperties(type: Copy) {
++ // using the build_properties already included in the source tarball
++ def inputFile = "build_properties"
++ def outputFile = buildProperties
++ from inputFile
++ into file(outputFile).getParent()
++ rename(file(inputFile).getName(), file(outputFile).getName())
++
++ inputs.file(inputFile)
+ outputs.file(outputFile)
+ }
+
+@@ -1293,7 +389,6 @@
+ dependsOn buildResources
+ dependsOn copyDocs
+ dependsOn copyHelp
+- dependsOn convertMdFiles
+ dependsOn buildIndices
+ }
+
+@@ -1306,12 +401,7 @@