Use xvgrclose() for files opened with xvgropen()

Use xvgrclose() for files opened with xvgropen()

Most callers used gmx_ffclose(), but there were also several that just
didn't close the file at all, or used plain fclose().  Not using
gmx_fio_fclose() left internal data structures inconsistent, which could
have an effect in unit test binaries that could execute some code more
than once (in particular, if the checkpoint code was triggered, as it
then got confused about the improperly closed files).

For consistency, changed gmx_fio_fclose() to xvgrclose(), except in
places where there were paths on which the file was not opened with
xvgropen().  Fixed some logic issues with opening/closing files in
different branches.

Change-Id: Iefda6880b06391b73423156888aee1d436e38199