ref #560 doxygen.conf settings change

doxygen.conf

@@ -788,9 +788,9 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ./Deploy \
-                         ./md  \
-                         ./README.md
+INPUT                  = ./md  \
+                         
+                         
 
 
 # This tag can be used to specify the character encoding of the source files
@@ -983,7 +983,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE = README.md
+USE_MDFILE_AS_MAINPAGE = md/README.md
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing