From a7818bc128f2dd28fbbde47b938266691fac1063 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 4 Mar 2022 15:41:06 +0000
Subject: [PATCH] =?utf8?q?JAL-3608=20JAL-3830=20tweaked=20the=20what=E2=80=99?=
 =?utf8?q?s=20new=20text=20and=20updated=20helpTOC?=
MIME-Version: 1.0
Content-Type: text/plain; charset=utf8
Content-Transfer-Encoding: 8bit

---
 help/help/help.jhm           |    1 +
 help/help/helpTOC.xml        |    5 +++--
 help/help/html/whatsNew.html |   10 ++++------
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/help/help/help.jhm b/help/help/help.jhm
index 78eaa70..6b06d36 100755
--- 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
--- 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
--- 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>
-- 
1.7.10.2