Move -Sy operation into its own transaction

This allows us to remove the sync_only flag, and also do the following
steps in the future :
1) refresh the database (if asked)
2) do other stuff (eg checking if a newer pacman version is available)
3) start the actual transaction

Currently when we detect a newer pacman version, we have to release the
current transaction and start a new one.

Signed-off-by: Chantry Xavier <shiningxc@gmail.com>

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