upgrade: Handle upgrade to v6 when the repository already contains v6 unlocked files...

upgrade: Handle upgrade to v6 when the repository already contains v6 unlocked files whose content is already present.

Closes https://github.com/datalad/datalad/issues/1020

The use of runWriter in scanUnlockedFiles broke due to this change;
it failed with blocked indefinitely in mvar, because the database write
handle was taken while linkFromAnnex needed to also write to it (to update
the inode cache). So, switched to using a separate runWriter for each call
to addAssociatedFileFast. A little less efficient, but not greatly; the
writes should all still be cached.