diff --git a/Doxyfile b/Doxyfile
index 206679c1d..0dfdb4843 100644
--- a/Doxyfile
+++ b/Doxyfile
@@ -754,7 +754,11 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  =
+INPUT                  =  server/
+INPUT                  += documentation/
+INPUT                  += clients/gtfpga/s2ss/
+INPUT                  += clients/gtfpga/pcores/
+INPUT                  += clients/opal/models/AsyncIP_sl/s2ss/
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
diff --git a/documentation/Server.md b/documentation/Server.md
index 57a3aa221..72d9edc40 100644
--- a/documentation/Server.md
+++ b/documentation/Server.md
@@ -1,9 +1,7 @@
 # Server {#server}
 
-@defgroup server Server
-
-@subpage Configuration
-@subpage Usage
-@subpage Netem
+@subpage configuration
+@subpage usage
+@subpage netem
 
 @todo Move documentation from Mainpage to Server.
diff --git a/documentation/server/Configuration.md b/documentation/server/Configuration.md
index f53be34f7..2cc2f1584 100644
--- a/documentation/server/Configuration.md
+++ b/documentation/server/Configuration.md
@@ -1,4 +1,4 @@
-# Configuration {#Configuration}
+# Configuration {#configuration}
 
 ## File
 
diff --git a/documentation/server/Netem.md b/documentation/server/Netem.md
index b0b691cca..758e785e3 100644
--- a/documentation/server/Netem.md
+++ b/documentation/server/Netem.md
@@ -1,4 +1,4 @@
-# Network Emulation {#Netem}
+# Network Emulation {#netem}
 
 S2SS supports the emulation of wide-area network characterisics.
 
diff --git a/documentation/server/Usage.md b/documentation/server/Usage.md
index b2ae02025..f27353e23 100644
--- a/documentation/server/Usage.md
+++ b/documentation/server/Usage.md
@@ -1,4 +1,4 @@
-# Usage Instructions {#Usage}
+# Usage Instructions {#usage}
 
 The S2SS server (`server`) expects the path to a configuration file as a single argument.