vinyl: do not use space_vtab::commit_alter for preparing new indexes

Currently, space_vtab::commit_alter is called before WAL write so we can
use it for preparing new indexes in vinyl. However, this is going to
change soon, because actually space_vtab::commit_alter should be called
after WAL write, like index_vtab::commit_drop or commit_create. Calling
it before WAL write may result in use-after-free in memtx (see #3289).
Besides, using this function for iterating over space indexes just feels
wrong, as we have index methods invoked by AlterSpaceOp descendants for
this.

So let's move all the operations performed by vinyl_space_commit_alter
somewhere else. Fortunately, it's easy to do without damaging code
readability or efficiency:

 - Update of vy_lsm::pk can be done by vinyl_space_swap_index and
   vinyl_build_secondary_key.

 - vy_lsm->check_is_unique can be computed by vinyl_engine_create_space
   and then set by vinyl_space_swap_index.

 - Call to key_def_update_optionality is implied by key_def_swap, which
   is already called by vinyl_space_swap_index, hence it can be removed.

Needed for #3289