Merge branch 'develop' into releases/Release_2_11_2_Branch

diff --git a/help/help/help.jhm b/help/help/help.jhm
index 78eaa70..6b06d36 100755 (executable)
--- a/help/help/help.jhm
+++ b/help/help/help.jhm
@@ -63,6 +63,7 @@
    <mapID target="startupprefs" url="html/features/preferences.html#startup"/>     
    <mapID target="strucprefs" url="html/features/preferences.html#structure"/>     
    <mapID target="commandline" url="html/features/commandline.html"/>
+   <mapID target="jalviewcltool" url="html/features/commandline.html#script"/>
    <mapID target="clarguments" url="html/features/clarguments.html"/>
    <mapID target="jvlfiles" url="html/features/jvlfiles.html"/>
    <mapID target="io" url="html/io/index.html"/>

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index cbef398..a9b9788 100755 (executable)
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -24,11 +24,12 @@
        <tocitem text="Jalview Documentation" target="home" expand="true">
                        <tocitem text="What's new" target="new" expand="true">
                                <tocitem text="Latest Release Notes" target="release"/>
-        <tocitem text="Support for ChimeraX" target="chimera"/>
+                       <tocitem text="Support for ChimeraX" target="chimera"/>
                                <tocitem text="Support for Pymol" target="pymol"/>
                                <tocitem text="Structures via 3D Beacons" target="structuresvia3dbeacons" />
                                <tocitem text="Startup Memory Settings" target="startupprefs" />
-        <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
+                       <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
+                       <tocitem text="Command line launch scripts" target="jalviewcltool"/>
                </tocitem>
                
                <tocitem text="Editing Alignments" target="edit" />

diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html
index d849aa2..c8d0fa9 100755 (executable)
--- a/help/help/html/whatsNew.html
+++ b/help/help/html/whatsNew.html
@@ -74,14 +74,13 @@
           allocation</a></strong></li>
     <li>Import of annotated DNA and RNA loci via GenBank and EMBL
       style flatfile</li>
-    <li>New <strong>command line launcher scripts</strong> (.sh, .ps1, .bat) usable on
-            macOS, Linux/Unix, Windows and documentation in Help
+    <li>Scripts for <a href="features/commandline.html">running
+        Jalview via the command line</a> on macOS, Linux/Unix and Windows.
     </li>
+  </ul>
 
 
-
-
-    <p>
+  <p>
       For the full release notes, see <a
         href="releases.html#Jalview.2.11.2.0">the Jalview 2.11.2.0
         release notes</a>.
@@ -90,6 +89,5 @@
       <strong>Known Issues</strong>
     </p>
     <p></p>
-  </ul>
 </body>
 </html>