More cleanup on headers/source for doxygen

- it also found things like size_t instead of size_type in fileName class

applications/utilities/mesh/conversion/plot3dToFoam/plot3dToFoam.C

@@ -28,7 +28,8 @@ Description
     Work in progress! Handles ascii multiblock (and optionally singleBlock)
     format.
     By default expects blanking. Use -noBlank if none.
-    Use -2D <thickness> if 2D.
+    Use -2D @a thickness if 2D.
+
     Niklas Nordin has experienced a problem with lefthandedness of the blocks.
     The code should detect this automatically - see hexBlock::readPoints but
     if this goes wrong just set the blockHandedness_ variable to 'right'