vinyl: extract quota adjustment from vy_tx and vy_index methods

Currently, quota (and some global stats) are adjusted in
vy_index_commit_upsert(), vy_tx_prepare(), and vy_tx_commit(),
which entails dependency of vy_index and tx_manager on vy_env.
Let's move this code to the upper level, i.e. to vy_prepare()
and vy_commit().

Needed for #1906