finished porting guide documentation, update and fixed some doxygen issues

opener.doxyfile

@@ -542,7 +542,7 @@ RECURSIVE = YES
 # excluded from the INPUT source files. This way you can easily exclude a 
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
 
-EXCLUDE = src\ports
+EXCLUDE = src/ports/platform-pc/.deps src/enet_encap/.deps src/cip/.deps 
 
 # The EXCLUDE_SYMLINKS tag can be used select whether or not files or 
 # directories that are symbolic links (a Unix filesystem feature) are excluded 
@@ -570,7 +570,7 @@ EXCLUDE_SYMBOLS =
 # directories that contain example code fragments that are included (see 
 # the \include command).
 
-EXAMPLE_PATH = ./ 
+EXAMPLE_PATH = ./
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the 
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp