Clean up and document code.

docs/Doxyfile

@@ -135,7 +135,7 @@ ABBREVIATE_BRIEF       = "The $name class" \
 # description.
 # The default value is: NO.
 
-ALWAYS_DETAILED_SEC    = NO
+ALWAYS_DETAILED_SEC    = YES
 
 # If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
 # inherited members of a class in the documentation of that class as if those
@@ -226,7 +226,7 @@ SEPARATE_MEMBER_PAGES  = NO
 # uses this value to replace tabs by spaces in code fragments.
 # Minimum value: 1, maximum value: 16, default value: 4.
 
-TAB_SIZE               = 4
+TAB_SIZE               = 8
 
 # This tag can be used to specify a number of aliases that act as commands in
 # the documentation. An alias has the form:
@@ -995,7 +995,7 @@ USE_MDFILE_AS_MAINPAGE =
 # also VERBATIM_HEADERS is set to NO.
 # The default value is: NO.
 
-SOURCE_BROWSER         = NO
+SOURCE_BROWSER         = YES
 
 # Setting the INLINE_SOURCES tag to YES will include the body of functions,
 # classes and enums directly into the documentation.
@@ -1014,7 +1014,7 @@ STRIP_CODE_COMMENTS    = YES
 # function all documented functions referencing it will be listed.
 # The default value is: NO.
 
-REFERENCED_BY_RELATION = NO
+REFERENCED_BY_RELATION = YES
 
 # If the REFERENCES_RELATION tag is set to YES then for each documented function
 # all documented entities called/used by that function will be listed.
@@ -1533,7 +1533,7 @@ FORMULA_TRANSPARENT    = YES
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-USE_MATHJAX            = NO
+USE_MATHJAX            = YES
 
 # When MathJax is enabled you can set the default output format to be used for
 # the MathJax output. See the MathJax site (see: