Second pass on fixing up documentation. Still some links not fixed.

Doxyfile

@@ -790,7 +790,7 @@ WARN_LOGFILE           = doxy.log
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = src docs
+INPUT                  = src docs lisp
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -817,6 +817,7 @@ INPUT_ENCODING         = UTF-8
 
 FILE_PATTERNS          = *.c \
                          *.h \
+                         *.lisp \
                          *.markdown \
                          *.md