fix various doxygen errors

doc/doxygen.conf

@@ -25,7 +25,7 @@ DOXYFILE_ENCODING      = UTF-8
 # The PROJECT_NAME tag is a single word (or a sequence of words surrounded
 # by quotes) that should identify the project.
 
-PROJECT_NAME           = "NS-3 "
+PROJECT_NAME           = "ns-3 "
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number.
 # This could be handy for archiving the generated documentation or
@@ -590,8 +590,7 @@ INPUT_ENCODING         = UTF-8
 # *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
 
 FILE_PATTERNS          = *.h \
-                         *.tcc \
-                         node-list.cc
+                         *.cc
 
 # The RECURSIVE tag can be used to turn specify whether or not subdirectories
 # should be searched for input files as well. Possible values are YES and NO.
@@ -603,11 +602,7 @@ RECURSIVE              = YES
 # excluded from the INPUT source files. This way you can easily exclude a
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
 
-EXCLUDE                = src/olsr/model/olsr-state.h \
-                         src/olsr/model/olsr-repositories.h \
-                         src/core/model/high-precision.h \
-                         src/core/model/high-precision-128.h \
-                         src/core/model/high-precision-double.h
+EXCLUDE                =
 
 # The EXCLUDE_SYMLINKS tag can be used select whether or not files or
 # directories that are symbolic links (a Unix filesystem feature) are excluded
@@ -635,7 +630,39 @@ EXCLUDE_SYMBOLS        =
 # directories that contain example code fragments that are included (see
 # the \include command).
 
-EXAMPLE_PATH           = 
+EXAMPLE_PATH           = src/aodv/examples \
+                         src/bridge/examples \
+                         src/click/examples \
+                         src/config-store/examples \
+                         src/core/examples \
+                         src/csma/examples \
+                         src/csma-layout/examples \
+                         src/dsdv/examples \
+                         src/emu/examples \
+                         src/energy/examples \
+                         src/flow-monitor/examples \
+                         src/internet/examples \
+                         src/lte/examples \
+                         src/mesh/examples \
+                         src/mobility/examples \
+                         src/mpi/examples \
+                         src/netanim/examples \
+                         src/network/examples \
+                         src/nix-vector-routing/examples \
+                         src/olsr/examples \
+                         src/openflow/examples \
+                         src/point-to-point/examples \
+                         src/propagation/examples \
+                         src/spectrum/examples \
+                         src/tap-bridge/examples \
+                         src/template/examples \
+                         src/tools/examples \
+                         src/topology-read/examples \
+                         src/uan/examples \
+                         src/virtual-net-device/examples \
+                         src/visualizer/examples \
+                         src/wifi/examples \
+                         src/wimax/examples
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp