Merge branch 'releases/Release_2_11_3_Branch'

[jalview.git] / help / help / helpTOC.xml

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index 877c758..6d7c948 100755 (executable)
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -23,13 +23,10 @@
 <!-- DO NOT WRAP THESE LINES - help2Website relies on each item being on one line! -->
        <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 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="Command line launch scripts" target="jalviewcltool"/>
+                       <tocitem text="Latest Release Notes" target="release"/>
+                       <tocitem text="Next Generation Command Line Interface" target="clarguments" />
+                       <tocitem text="AlphaFold PAE Matrices" target="workingwithpae" />
+                       <tocitem text="Nucleotide Ambiguity colours" target="colours.nucleotideambiguity" />                            
                </tocitem>
                
                <tocitem text="Editing Alignments" target="edit" />
@@ -169,12 +166,17 @@
                        <tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
                </tocitem>
                <tocitem text="Command Line" target="commandline" expand="false">
-                       <tocitem text="Command Line Arguments" target="clarguments" />
-    <tocitem text="Memory Settings" target="memory" expand="false"/>
-    <tocitem text="Jalview Launch Files" target="jvlfiles" expand="false"/>
-    </tocitem>
+                       <tocitem text="Command Line: introduction and reference" target="clarguments" />
+                       <tocitem text="Command Line: basic usage" target="clarguments-basic" />
+                       <tocitem text="Command Line: advanced usage" target="clarguments-advanced" />
+                       <tocitem text="Command Line: argument files" target="clarguments-argfiles" />
+                       <tocitem text="Command Line: reference" target="clarguments-reference" />
+                       <tocitem text="Command Line: old command line arguments" target="clarguments-old" />
+               </tocitem>
+               <tocitem text="Memory Settings" target="memory" expand="false"/>
+               <tocitem text="Jalview Launch Files" target="jvlfiles" expand="false"/>
                <tocitem text="Privacy" target="privacy" />
-       </tocitem>
+    </tocitem>
        <tocitem text="Useful information" expand="true">
                <tocitem text="Amino Acid Table" target="aminoAcids" />
                <tocitem text="Amino Acid Properties" target="aaProperties" />