Doxygen omits directories without documentation.

Doxyfile

@@ -889,7 +889,23 @@ EXCLUDE_SYMLINKS       = NO
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       =
+EXCLUDE_PATTERNS       = */Communicators/* \
+                         */Config/* \
+                         */Containers/* \
+                         */Debugging/* \
+                         */Devices/* \
+                         */DistributedContainers/* \
+                         */Exceptions/* \
+                         */Experimental/* \
+                         */Functions/* \
+                         */Images/* \
+                         */Matrices/* \
+                         */Meshes/* \
+                         */Operators/* \
+                         */Pointers/* \
+                         */Problems/* \
+                         */Solvers/* 
+
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the

generate-doc

@@ -15,6 +15,7 @@ done
 doxygen
 
 if [[ "$INSTALL" == "yes" ]]; then
-   cp -r Documentation/* ${PREFIX}/share/doc
+   mkdir -p ${PREFIX}/share/doc/tnl
+   cp -r Documentation/* ${PREFIX}/share/doc/tnl
 fi