fix some issues with doxygen

Author: microdee

docs/Doxyfile

@@ -401,7 +401,7 @@ AUTOLINK_SUPPORT       = YES
 # using \# or the \link or commands.
 # This tag requires that the tag AUTOLINK_SUPPORT is set to YES.
 
-AUTOLINK_IGNORE_WORDS  =
+AUTOLINK_IGNORE_WORDS  = Nuke
 
 # If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
 # to include (a tag file for) the STL sources as input, then you should set this

docs/Manual/ToolExtensions.md

@@ -1,5 +1,7 @@
 # Tool Extensions {#ToolExtensions}
 
+[TOC]
+
 ## Tool Composition
 
 Whenever the Nuke Tooling API gives you a Tool delegate it is a clean slate, meaning you need to provide it your arguments, environment variables, how one reacts to its output etc. With the intended usage once these parameters are given to the `Tool` delegate it immediately executes the tool it represents.
@@ -22,7 +24,7 @@ MyToolMode
     .WithSemanticLogging()("--arg value"); // excercise for the reader
 ```
 
-## `ToolEx`
+## ToolEx
 
 A reimplementation of Nuke's `Tool` with extended features. All the tool composition features are also available for `ToolEx`.
 

docs/Manual/index.md

@@ -16,9 +16,9 @@ Name comes from Nuka Cola of the Fallout franchise.
 
 Highlighted features:
 
-* Automatically discovered build-plugins
-* Declarative folder-to-folder mapping (Folder composition)
-* Extensions for the `Tool` delegate
+* [Automatically discovered build-plugins](@ref BuildPlugins)
+* [Declarative folder-to-folder mapping (Folder composition)](@ref FolderComposition)
+* [Extensions for the `Tool` delegate](@ref ToolExtensions)
 
 Use the sidebar to read further details about them.