refs: fix corruption by not correctly syncing packed-refs to disk

refs: fix corruption by not correctly syncing packed-refs to disk

At GitLab we have recently received a report where a repository was left
with a corrupted `packed-refs` file after the node hard-crashed even
though `core.fsync=reference` was set. This is something that in theory
should not happen if we correctly did the atomic-rename dance to:

    1. Write the data into a temporary file.

    2. Synchronize the temporary file to disk.

    3. Rename the temporary file into place.

So if we crash in the middle of writing the `packed-refs` file we should
only ever see either the old or the new state of the file.

And while we do the dance when writing the `packed-refs` file, there is
indeed one gotcha: we use a `FILE *` stream to write the temporary file,
but don't flush it before synchronizing it to disk. As a consequence any
data that is still buffered will not get synchronized and a crash of the
machine may cause corruption.

Fix this bug by flushing the file stream before we fsync.

Signed-off-by: Patrick Steinhardt <ps@pks.im>
Signed-off-by: Junio C Hamano <gitster@pobox.com>