Fix the broken Doxyfile so people can generate what little code base documentation we have :-)

Copy the Doxyfile to orte so people can generate just that documentation. Adjust the properties on that directory so it ignores the resulting doxygen output tree.

This should go over to the release branch(es)

This commit was SVN r9625.

Doxyfile

@@ -380,7 +380,7 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  = include opal orte ompi
+INPUT                  = opal orte ompi
 
 # If the value of the INPUT tag contains directories, you can use the
 # FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
@@ -401,7 +401,7 @@ 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                = opal/event
+EXCLUDE                = opal/event ompi/mca/io/romio
 
 # The EXCLUDE_SYMLINKS tag can be used select whether or not files or
 # directories that are symbolic links (a Unix filesystem feature) are