diff --git a/user-doc/Doxyfile b/user-doc/Doxyfile
index b9919b5e3f7fa7592e00d4e82344eebfc4b584a2..62abc0717ea61a0b100e4f611b1b469c2ab189a8 100644
--- a/user-doc/Doxyfile
+++ b/user-doc/Doxyfile
@@ -744,6 +744,8 @@ INPUT                  = IntroPP.txt \
                          GlossaryPP.txt \
                          TutorialsPP.txt \
                          ModulesPP.txt \
+                         MiscPP.txt \
+                         ToolsPP.txt \
                          RegexPP.txt \
                          ../CHANGES \
                          tutorials \
@@ -1356,7 +1358,7 @@ DISABLE_INDEX          = NO
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-GENERATE_TREEVIEW      = NO
+GENERATE_TREEVIEW      = YES
 
 # The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
 # doxygen will group on one line in the generated HTML documentation.
diff --git a/user-doc/Glossary.txt b/user-doc/Glossary.txt
index c4c5d42476e6be0c157fd72690d5f282a5a3d4d3..2e9450e240042670c7675da42edb28f2bfd4aa08 100644
--- a/user-doc/Glossary.txt
+++ b/user-doc/Glossary.txt
@@ -1,6 +1,6 @@
 /**
 
-@page glossary Glossary of Actions 
+@page glossary Index of Actions 
 
 The following page contains an alphabetically ordered list of all the Actions and command line tools 
 that are available in PLUMED 2. For lists of Actions classified in accordance with the 
@@ -15,8 +15,4 @@ particular tasks that are being performed see:
 
 @GLOSSARY@
 
-\section dictionary Dictionary 
-
-@DICTIONARY@
-
 */
diff --git a/user-doc/Intro.txt b/user-doc/Intro.txt
index 5154a4ff7579e404b52dd18223dba059cee1f3a2..cf0b0d5c04c8300fc4e9ff27c4ecc440ca6c4ab7 100644
--- a/user-doc/Intro.txt
+++ b/user-doc/Intro.txt
@@ -40,17 +40,6 @@ analsyis tools that come with PLUMED are given in:
 PLUMED can be used in one of two ways.  It can be incorporated into any one of the MD codes listed on the
 \ref Installation page and used to analyse or bias a molecular dynamics run on the fly.  Alternatively, one
 can use it as a standalone tool for postprocessing the results from molecular dynamics or enhanced sampling calculations.
-To use PLUMED in this second way you will issue a command something like:
-
-\verbatim
-plumed <toolname> <list of input flags for that tool>
-\endverbatim
-
-The following is a list of the various standalone tools that PLUMED contains.
-
-@TOOLS@
-
-For all these tools and to use PLUMED as a plugin in an MD calculation you will need an input file.
 
 
 */
diff --git a/user-doc/Misc.txt b/user-doc/Misc.txt
new file mode 100644
index 0000000000000000000000000000000000000000..598e617d69d2f0e084b6925031951b3b1294e25f
--- /dev/null
+++ b/user-doc/Misc.txt
@@ -0,0 +1,8 @@
+/**
+
+\page misc Miscellaneus
+
+@DICTIONARY@
+
+
+*/
diff --git a/user-doc/PlumedLayout.xml b/user-doc/PlumedLayout.xml
index 49d7ddcc650111ad6fe36edd0233985c3676ef89..ccc60e87bcb69cb0feb91a955776be0f4f03f160 100644
--- a/user-doc/PlumedLayout.xml
+++ b/user-doc/PlumedLayout.xml
@@ -2,15 +2,21 @@
   <!-- Navigation index tabs for HTML output -->
   <navindex>
     <tab type="mainpage" visible="yes" title=""/>
-    <tab type="user" visible="no" url="mymodules.html" title="Modules"/>
     <tab type="user" visible="yes" url="_installation.html" title="Installation"/>
-    <tab type="user" visible="yes" url="tutorials.html" title="Tutorials"/>
-    <tab type="user" visible="yes" url="_group.html" title="Groups and Atoms"/>
-    <tab type="user" visible="yes" url="_colvar.html" title="Collective Variables"/>
-    <tab type="user" visible="yes" url="_function.html" title="Functions"/>
+    <tab type="usergroup" title="Basics">
+      <tab type="user" visible="yes" url="_syntax.html" title="Input File"/>
+      <tab type="user" visible="yes" url="_group.html" title="Groups and Atoms"/>
+    </tab>
+    <tab type="usergroup" title="Collective variables">
+      <tab type="user" visible="yes" url="_colvar.html" title="Collective Variables"/>
+      <tab type="user" visible="yes" url="_function.html" title="Functions"/>
+    </tab>
     <tab type="user" visible="yes" url="_analysis.html" title="Analysis"/>
     <tab type="user" visible="yes" url="_bias.html" title="Bias"/>
-    <tab type="user" visible="yes" url="glossary.html" title="Glossary"/>
+    <tab type="user" visible="yes" url="tools.html" title="Tools"/>
+    <tab type="user" visible="yes" url="misc.html" title="Misc"/>
+    <tab type="user" visible="yes" url="tutorials.html" title="Tutorials"/>
+    <tab type="user" visible="yes" url="glossary.html" title="Index"/>
     <tab type="pages" visible="no" title="" intro=""/>
     <tab type="modules" visible="yes" title="" intro=""/>
     <tab type="namespaces" visible="yes" title="">
diff --git a/user-doc/Tools.txt b/user-doc/Tools.txt
new file mode 100644
index 0000000000000000000000000000000000000000..81b7a916194567a52778a5d314148bad96f5d02f
--- /dev/null
+++ b/user-doc/Tools.txt
@@ -0,0 +1,17 @@
+/**
+
+\page tools Command Line Tools
+
+To use PLUMED in this second way you will issue a command something like:
+
+\verbatim
+plumed <toolname> <list of input flags for that tool>
+\endverbatim
+
+The following is a list of the various standalone tools that PLUMED contains.
+
+@TOOLS@
+
+For all these tools and to use PLUMED as a plugin in an MD calculation you will need an input file.
+
+*/
diff --git a/user-doc/extract b/user-doc/extract
index 7d221b5bfa883a81e6c9c5d32044df7d70b9f61a..570d9bab8ff86b35ac4cc9d32d7e9230437535df 100755
--- a/user-doc/extract
+++ b/user-doc/extract
@@ -213,7 +213,7 @@ do
    fi
 done
 
-for file in Bias Syntax Colvar Functions Group Installation Intro Analysis Glossary Tutorials Modules Regex
+for file in Bias Syntax Colvar Functions Group Installation Intro Analysis Glossary Tutorials Modules Regex  Misc Tools
 do
 
 cat $file.txt |