box: make final join vclock update only in box.cc

The goal is to make sure that no files except box.cc can change
instance_vclock_storage directly. That leads to all sorts of hacks
which in turn lead to bugs - #9916 is a good example.

Now applier on final join only sends rows into the journal. The
journal then is handled by box.cc where vclock is properly
updated.

Part of #10113

NO_DOC=refactoring
NO_TEST=refactoring
NO_CHANGELOG=refactoring