Doxygen docs: Corrected doxyFilter to preserve line numbers

Also corrected many formatting errors in the comments in C and H files

bin/tools/doxyFilter.sed

@@ -11,34 +11,20 @@
 /^License/,/\*\//{
 /^License/,\%http://www.gnu.org/licenses%{
 s?^License.*?\*\/\
-\/\*! @file %filePath%\
+\/\*! \\file %filePath%\
 <b>Original source file</b> <a href="%filePath%">%fileName%</a>\
+\
+\
+\
+\
+\
+\
+\
+\
 ?
 /^    /d
 }
 
-# old FSF address
-/^License/,/MA 0211.-130. USA/{
-s?^License.*?\*\/\
-\/\*! @file %filePath%\
-<b>Original source file</b> <a href="%filePath%">%fileName%</a>\
-?
-/^    /d
-}
-
-# remove entry
-/^Primitive *$/{
-N
-N
-d
-}
-
-# remove entry
-/^Implementation *$/{
-N
-N
-d
-}
 
 # remove entry
 /^Application *$/{
@@ -47,12 +33,6 @@ N
 d
 }
 
-# remove entry
-/^Type *$/{
-N
-N
-d
-}
 
 # remove entry
 /^Global *$/{
@@ -62,96 +42,109 @@ d
 }
 
 
+# Primitive
+#     typename
+# =>
+# \\relates typename
+#
+/^Primitive *$/,/^[^ ]/{
+s/^Primitive *$//
+s/^    /\\relates /
+}
+
+
 # Class
 #     Foam::className
 # =>
-# @class Foam::className
+# \\class Foam::className
 #
 /^Class *$/,/^[^ ]/{
-/^Class/d
-s/^    /@class /
+s/^Class *$//
+s/^    /\\class /
 }
 
 
 # Namespace
 #     namespaceName
 # =>
-# @namespace namespaceName
+# \namespace namespaceName
 #
 /^Namespace *$/,/^[^ ]/{
-/^Namespace/d
-s/^    /@namespace /
+s/^Namespace//
+s/^    /\\namespace /
 }
 
 
 # Typedef
 #     Foam::def
 # =>
-# @class Foam::def
-# This is not strictly correct, but makes it easier to find the typedefs
+# \typedef Foam::def
 /^Typedef *$/,/^[^ ]/{
-/^Typedef/d
-s/^    /@class /
+s/^Typedef//
+s/^    /\\typedef /
 }
 
 
-# add anchor and use @brief
+# add anchor and use \brief
 # the first paragraph will be 'brief' and the others 'detail'
 /^Description *$/,/^[^ ]/{
 /^Description/c\
-<a class="anchor" name="Description"></a>\
-@brief
+<a class="anchor" name="Description"></a> \\brief
 s/^    //
 }
 
 /^Usage *$/,/^[^ ]/{
 /^Usage/c\
-@par Usage
+\\par Usage
 s/^    //
 }
 
 
 /^See *Also *$/,/^[^ ]/{
 /^See *Also/c\
-@see
-s/^    //
-}
-
-/^Author *$/,/^[^ ]/{
-/^Author/c\
-@author
+\\see
 s/^    //
 }
 
 /^Note *$/,/^[^ ]/{
 /^Note/c\
-@note
+\\note
 s/^    //
 }
 
 
 # remove ToDo paragraph to avoid them showing on related pages
-/^To[Dd]o *$/,/^ *$/d
+/^To[Dd]o *$/,/^[^ ]/{
+s/^To[Dd]o *$//
+s/^    .*//
+}
 
 
 /^Warning *$/,/^[^ ]/{
 /^Warning/c\
-@warning
+\\warning
 s/^    //
 }
 
+
 /^Deprecated *$/,/^[^ ]/{
 /^Deprecated/c\
-@deprecated
+\\deprecated
 s/^    //
 }
 
-/SourceFiles/,/^[ ]*$/{
-s?SourceFiles?@par Source files\
-<ul>\
-  <li><a href="%filePath%">%fileName%</a></li>?
-s?^[ ]*$?</ul>\
-?
+
+/^SourceFiles *$/,/^$/{
+s?SourceFiles?\\par Source files\
+<ul><li><a href="%filePath%">%fileName%</a></li>?
+s? *\([a-zA-Z0-9]*\.[a-zA-Z]*\)?  <li><a href="%dirName%/\1">\1</a></li>?
+s?^$?</ul>?
+}
+
+/fileName%<\/a><\/li>$/{
+N
+s?\n$?</ul>?g
+s/<\/li>\n/<\/li> /
 s? *\([a-zA-Z0-9]*\.[a-zA-Z]*\)?  <li><a href="%dirName%/\1">\1</a></li>?
 }