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diff --git a/.doctrees/develop/classlist.doctree b/.doctrees/develop/classlist.doctree
diff --git a/.doctrees/develop/core.doctree b/.doctrees/develop/core.doctree
diff --git a/.doctrees/develop/io.doctree b/.doctrees/develop/io.doctree
diff --git a/.doctrees/develop/molequeue.doctree b/.doctrees/develop/molequeue.doctree
diff --git a/.doctrees/develop/qtgui.doctree b/.doctrees/develop/qtgui.doctree
diff --git a/.doctrees/develop/rendering.doctree b/.doctrees/develop/rendering.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/_sources/develop/classlist.md.txt b/_sources/develop/classlist.md.txt
@@ -1,9 +1,10 @@
 (develop-classlist)=
 
-# Class List
+# API Documentation
 
 ```{toctree}
 :glob: true
+:maxdepth: 1
 
 core
 io

diff --git a/_sources/develop/core.md.txt b/_sources/develop/core.md.txt
@@ -1,6 +1,6 @@
 (develop-core)=
 
-# Core Classes
+# Avogadro::Core
 
 ```{toctree}
 :glob: true

diff --git a/_sources/develop/io.md.txt b/_sources/develop/io.md.txt
@@ -1,6 +1,6 @@
 (develop-io)=
 
-# IO Classes
+# Avogadro::IO
 
 The IO classes handle Avogadro's native file input/output. Beyond these
 classes, an Open Babel plugin loads translation via `obabel` command calls

diff --git a/_sources/develop/molequeue.md.txt b/_sources/develop/molequeue.md.txt
@@ -1,11 +1,17 @@
 (develop-molequeue)=
 
-# MoleQueue Classes
+# Avogadro::MoleQueue
 
 MoleQueue classes handle interaction with the MoleQueue queue system
 for submitting calculations to programs and  opening completed output
 files.
 
+```{tip}
+While MoleQueue is not actively developed, some features of Avogadro
+are still handled by this code, including [RPC](develop-rpc) for
+scripting `avogadroapp` and handling scripts for input generator dialogs.
+```
+
 ```{toctree}
 :glob: true
 

diff --git a/_sources/develop/qtgui.md.txt b/_sources/develop/qtgui.md.txt
@@ -1,9 +1,12 @@
 (develop-qtgui)=
 
-# QtGui Classes
+# Avogadro::QtGui
 
-The QtGui classes handle basic operations with the GUI using Qt widgets and objects.
-Most of the gui is handled through plugins.
+The QtGui classes handle operations with the GUI using Qt widgets
+and objects. Most of the interface is handled through plugins.
+
+These classes provide individual widgets, dialogs, and interaction
+with plugin scripts, etc.
 
 ```{toctree}
 :glob: true

diff --git a/_sources/develop/rendering.md.txt b/_sources/develop/rendering.md.txt
@@ -1,6 +1,10 @@
 (develop-rendering)=
 
-# Rendering Classes
+# Avogadro::Rendering
+
+The rendering classes handle 3D graphics including various GLSL
+shader programs for spheres, cylinders (atoms and bonds),
+protein cartoons, meshes, orbitals, etc.
 
 ```{toctree}
 :glob: true

diff --git a/develop/build.html b/develop/build.html
@@ -438,7 +438,7 @@
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">Building Source Code</a></li>
 <li class="toctree-l1"><a class="reference internal" href="scripts/index.html">Script Plugins</a></li>
 <li class="toctree-l1"><a class="reference internal" href="rpc.html">Avogadro Remote Procedure Call (RPC)</a></li>
-<li class="toctree-l1"><a class="reference internal" href="classlist.html">Class List</a></li>
+<li class="toctree-l1"><a class="reference internal" href="classlist.html">API Documentation</a></li>
 </ul>
 </div>
 </nav></div>

diff --git a/develop/class/class_avogadro_1_1_core_1_1_array.html b/develop/class/class_avogadro_1_1_core_1_1_array.html
@@ -56,7 +56,7 @@
     <link rel="index" title="Index" href="../../genindex.html" />
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     <link rel="next" title="Class Avogadro::Core::ArraySet" href="class_avogadro_1_1_core_1_1_array_set.html" />
-    <link rel="prev" title="Core Classes" href="../core.html" />
+    <link rel="prev" title="Avogadro::Core" href="../core.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
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@@ -438,8 +438,8 @@
 <li class="toctree-l1"><a class="reference internal" href="../build.html">Building Source Code</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../scripts/index.html">Script Plugins</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../rpc.html">Avogadro Remote Procedure Call (RPC)</a></li>
-<li class="toctree-l1 current active has-children"><a class="reference internal" href="../classlist.html">Class List</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
-<li class="toctree-l2 current active has-children"><a class="reference internal" href="../core.html">Core Classes</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
+<li class="toctree-l1 current active has-children"><a class="reference internal" href="../classlist.html">API Documentation</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
+<li class="toctree-l2 current active has-children"><a class="reference internal" href="../core.html">Avogadro::Core</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
 <li class="toctree-l3 current active"><a class="current reference internal" href="#">Class Avogadro::Core::Array</a></li>
 <li class="toctree-l3"><a class="reference internal" href="class_avogadro_1_1_core_1_1_array_set.html">Class Avogadro::Core::ArraySet</a></li>
 <li class="toctree-l3"><a class="reference internal" href="class_avogadro_1_1_core_1_1_array_set_1_1_holder.html">Class Avogadro::Core::ArraySet::Holder</a></li>
@@ -489,10 +489,10 @@
 <li class="toctree-l3"><a class="reference internal" href="class_avogadro_1_1_type_traits_3_01unsigned_01short_01_4.html">Class Avogadro::TypeTraits&lt; unsigned short &gt;</a></li>
 </ul>
 </details></li>
-<li class="toctree-l2"><a class="reference internal" href="../io.html">IO Classes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../molequeue.html">MoleQueue Classes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../qtgui.html">QtGui Classes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../rendering.html">Rendering Classes</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../io.html">Avogadro::IO</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../molequeue.html">Avogadro::MoleQueue</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../qtgui.html">Avogadro::QtGui</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../rendering.html">Avogadro::Rendering</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../vtk.html">VTK Classes</a></li>
 </ul>
 </details></li>
@@ -542,7 +542,7 @@
     <li class="breadcrumb-item"><i class="fa-solid fa-ellipsis"></i></li>
 
 
-    <li class="breadcrumb-item"><a href="../core.html" class="nav-link">Core Classes</a></li>
+    <li class="breadcrumb-item"><a href="../core.html" class="nav-link">Avogadro::Core</a></li>
 
     <li class="breadcrumb-item active" aria-current="page">Class...</li>
   </ul>
@@ -928,7 +928,7 @@ <h1>Class Avogadro::Core::Array<a class="headerlink" href="#class-avogadro-core-
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">Core Classes</p>
+        <p class="prev-next-title">Avogadro::Core</p>
       </div>
     </a>
     <a class="right-next"

diff --git a/develop/class/class_avogadro_1_1_core_1_1_array_set.html b/develop/class/class_avogadro_1_1_core_1_1_array_set.html
@@ -438,8 +438,8 @@
 <li class="toctree-l1"><a class="reference internal" href="../build.html">Building Source Code</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../scripts/index.html">Script Plugins</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../rpc.html">Avogadro Remote Procedure Call (RPC)</a></li>
-<li class="toctree-l1 current active has-children"><a class="reference internal" href="../classlist.html">Class List</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
-<li class="toctree-l2 current active has-children"><a class="reference internal" href="../core.html">Core Classes</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
+<li class="toctree-l1 current active has-children"><a class="reference internal" href="../classlist.html">API Documentation</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
+<li class="toctree-l2 current active has-children"><a class="reference internal" href="../core.html">Avogadro::Core</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
 <li class="toctree-l3"><a class="reference internal" href="class_avogadro_1_1_core_1_1_array.html">Class Avogadro::Core::Array</a></li>
 <li class="toctree-l3 current active"><a class="current reference internal" href="#">Class Avogadro::Core::ArraySet</a></li>
 <li class="toctree-l3"><a class="reference internal" href="class_avogadro_1_1_core_1_1_array_set_1_1_holder.html">Class Avogadro::Core::ArraySet::Holder</a></li>
@@ -489,10 +489,10 @@
 <li class="toctree-l3"><a class="reference internal" href="class_avogadro_1_1_type_traits_3_01unsigned_01short_01_4.html">Class Avogadro::TypeTraits&lt; unsigned short &gt;</a></li>
 </ul>
 </details></li>
-<li class="toctree-l2"><a class="reference internal" href="../io.html">IO Classes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../molequeue.html">MoleQueue Classes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../qtgui.html">QtGui Classes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../rendering.html">Rendering Classes</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../io.html">Avogadro::IO</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../molequeue.html">Avogadro::MoleQueue</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../qtgui.html">Avogadro::QtGui</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../rendering.html">Avogadro::Rendering</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../vtk.html">VTK Classes</a></li>
 </ul>
 </details></li>
@@ -542,7 +542,7 @@
     <li class="breadcrumb-item"><i class="fa-solid fa-ellipsis"></i></li>
 
 
-    <li class="breadcrumb-item"><a href="../core.html" class="nav-link">Core Classes</a></li>
+    <li class="breadcrumb-item"><a href="../core.html" class="nav-link">Avogadro::Core</a></li>
 
     <li class="breadcrumb-item active" aria-current="page">Class...</li>
   </ul>

diff --git a/develop/class/class_avogadro_1_1_core_1_1_array_set_1_1_holder.html b/develop/class/class_avogadro_1_1_core_1_1_array_set_1_1_holder.html
@@ -438,8 +438,8 @@
 <li class="toctree-l1"><a class="reference internal" href="../build.html">Building Source Code</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../scripts/index.html">Script Plugins</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../rpc.html">Avogadro Remote Procedure Call (RPC)</a></li>
-<li class="toctree-l1 current active has-children"><a class="reference internal" href="../classlist.html">Class List</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
-<li class="toctree-l2 current active has-children"><a class="reference internal" href="../core.html">Core Classes</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
+<li class="toctree-l1 current active has-children"><a class="reference internal" href="../classlist.html">API Documentation</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
+<li class="toctree-l2 current active has-children"><a class="reference internal" href="../core.html">Avogadro::Core</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
 <li class="toctree-l3"><a class="reference internal" href="class_avogadro_1_1_core_1_1_array.html">Class Avogadro::Core::Array</a></li>
 <li class="toctree-l3"><a class="reference internal" href="class_avogadro_1_1_core_1_1_array_set.html">Class Avogadro::Core::ArraySet</a></li>
 <li class="toctree-l3 current active"><a class="current reference internal" href="#">Class Avogadro::Core::ArraySet::Holder</a></li>
@@ -489,10 +489,10 @@
 <li class="toctree-l3"><a class="reference internal" href="class_avogadro_1_1_type_traits_3_01unsigned_01short_01_4.html">Class Avogadro::TypeTraits&lt; unsigned short &gt;</a></li>
 </ul>
 </details></li>
-<li class="toctree-l2"><a class="reference internal" href="../io.html">IO Classes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../molequeue.html">MoleQueue Classes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../qtgui.html">QtGui Classes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../rendering.html">Rendering Classes</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../io.html">Avogadro::IO</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../molequeue.html">Avogadro::MoleQueue</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../qtgui.html">Avogadro::QtGui</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../rendering.html">Avogadro::Rendering</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../vtk.html">VTK Classes</a></li>
 </ul>
 </details></li>
@@ -542,7 +542,7 @@
     <li class="breadcrumb-item"><i class="fa-solid fa-ellipsis"></i></li>
 
 
-    <li class="breadcrumb-item"><a href="../core.html" class="nav-link">Core Classes</a></li>
+    <li class="breadcrumb-item"><a href="../core.html" class="nav-link">Avogadro::Core</a></li>
 
     <li class="breadcrumb-item active" aria-current="page">Class...</li>
   </ul>

diff --git a/develop/class/class_avogadro_1_1_core_1_1_array_set_1_1_place_holder.html b/develop/class/class_avogadro_1_1_core_1_1_array_set_1_1_place_holder.html
@@ -438,8 +438,8 @@
 <li class="toctree-l1"><a class="reference internal" href="../build.html">Building Source Code</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../scripts/index.html">Script Plugins</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../rpc.html">Avogadro Remote Procedure Call (RPC)</a></li>
-<li class="toctree-l1 current active has-children"><a class="reference internal" href="../classlist.html">Class List</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
-<li class="toctree-l2 current active has-children"><a class="reference internal" href="../core.html">Core Classes</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
+<li class="toctree-l1 current active has-children"><a class="reference internal" href="../classlist.html">API Documentation</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
+<li class="toctree-l2 current active has-children"><a class="reference internal" href="../core.html">Avogadro::Core</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
 <li class="toctree-l3"><a class="reference internal" href="class_avogadro_1_1_core_1_1_array.html">Class Avogadro::Core::Array</a></li>
 <li class="toctree-l3"><a class="reference internal" href="class_avogadro_1_1_core_1_1_array_set.html">Class Avogadro::Core::ArraySet</a></li>
 <li class="toctree-l3"><a class="reference internal" href="class_avogadro_1_1_core_1_1_array_set_1_1_holder.html">Class Avogadro::Core::ArraySet::Holder</a></li>
@@ -489,10 +489,10 @@
 <li class="toctree-l3"><a class="reference internal" href="class_avogadro_1_1_type_traits_3_01unsigned_01short_01_4.html">Class Avogadro::TypeTraits&lt; unsigned short &gt;</a></li>
 </ul>
 </details></li>
-<li class="toctree-l2"><a class="reference internal" href="../io.html">IO Classes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../molequeue.html">MoleQueue Classes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../qtgui.html">QtGui Classes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../rendering.html">Rendering Classes</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../io.html">Avogadro::IO</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../molequeue.html">Avogadro::MoleQueue</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../qtgui.html">Avogadro::QtGui</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../rendering.html">Avogadro::Rendering</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../vtk.html">VTK Classes</a></li>
 </ul>
 </details></li>
@@ -542,7 +542,7 @@
     <li class="breadcrumb-item"><i class="fa-solid fa-ellipsis"></i></li>
 
 
-    <li class="breadcrumb-item"><a href="../core.html" class="nav-link">Core Classes</a></li>
+    <li class="breadcrumb-item"><a href="../core.html" class="nav-link">Avogadro::Core</a></li>
 
     <li class="breadcrumb-item active" aria-current="page">Class...</li>
   </ul>

diff --git a/develop/class/class_avogadro_1_1_core_1_1_atom.html b/develop/class/class_avogadro_1_1_core_1_1_atom.html
@@ -438,8 +438,8 @@
 <li class="toctree-l1"><a class="reference internal" href="../build.html">Building Source Code</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../scripts/index.html">Script Plugins</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../rpc.html">Avogadro Remote Procedure Call (RPC)</a></li>
-<li class="toctree-l1 current active has-children"><a class="reference internal" href="../classlist.html">Class List</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
-<li class="toctree-l2 current active has-children"><a class="reference internal" href="../core.html">Core Classes</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
+<li class="toctree-l1 current active has-children"><a class="reference internal" href="../classlist.html">API Documentation</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
+<li class="toctree-l2 current active has-children"><a class="reference internal" href="../core.html">Avogadro::Core</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
 <li class="toctree-l3"><a class="reference internal" href="class_avogadro_1_1_core_1_1_array.html">Class Avogadro::Core::Array</a></li>
 <li class="toctree-l3"><a class="reference internal" href="class_avogadro_1_1_core_1_1_array_set.html">Class Avogadro::Core::ArraySet</a></li>
 <li class="toctree-l3"><a class="reference internal" href="class_avogadro_1_1_core_1_1_array_set_1_1_holder.html">Class Avogadro::Core::ArraySet::Holder</a></li>
@@ -489,10 +489,10 @@
 <li class="toctree-l3"><a class="reference internal" href="class_avogadro_1_1_type_traits_3_01unsigned_01short_01_4.html">Class Avogadro::TypeTraits&lt; unsigned short &gt;</a></li>
 </ul>
 </details></li>
-<li class="toctree-l2"><a class="reference internal" href="../io.html">IO Classes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../molequeue.html">MoleQueue Classes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../qtgui.html">QtGui Classes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../rendering.html">Rendering Classes</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../io.html">Avogadro::IO</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../molequeue.html">Avogadro::MoleQueue</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../qtgui.html">Avogadro::QtGui</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../rendering.html">Avogadro::Rendering</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../vtk.html">VTK Classes</a></li>
 </ul>
 </details></li>
@@ -542,7 +542,7 @@
     <li class="breadcrumb-item"><i class="fa-solid fa-ellipsis"></i></li>
 
 
-    <li class="breadcrumb-item"><a href="../core.html" class="nav-link">Core Classes</a></li>
+    <li class="breadcrumb-item"><a href="../core.html" class="nav-link">Avogadro::Core</a></li>
 
     <li class="breadcrumb-item active" aria-current="page">Class...</li>
   </ul>