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>