fileHandler: Added flush method

This method waits until all the threads have completed IO operations and
then clears any cached information about the files on disk. This
replaces the deactivation of threading by means of zeroing the buffer
size when writing and reading of a file happen in sequence. It also
allows paraFoam to update the list of available times.

Patch contributed by Mattijs Janssens
Resolves bug report https://bugs.openfoam.org/view.php?id=2962