vchoi_fork

[svn-r6496] Purpose:
    Refactoring of Flush Logic

Description:
    The Flushing logic passed in multiple flags to indicate what type of
    flush it was: closing, invalidate, alloc only. This made extending
    the function of the flush logic to handle other flags annoying.

Solution:
    I changed it to be just one bitmasked flag to indicate what type of
    flushing to do. I also added the CLEAR_ONLY flag, which will be used
    in the FPHDF5 stuff.

Platforms tested:
    h5committest doesn't work for me (my environment isn't setup on the
    other machines I guess). I tested it manually:

        Linux parallel & C++
        Sol Fortran
        Modi4 parallel & Fortran.