For any action which is multi-step (requires updating more than 1 DB
key), use transaction to make update atomic.
Also pack big chunks of updates (importing packages for importing and
mirror updates) into single transaction to improve aptly performance and
get some isolation.
Note that still layers up (Collections) provide some level of isolation,
so this is going to shine with the future PRs to remove collection
locks.
Spin-off of #459
