vinyl: log reads that take too long

If read of a single statement from vinyl takes more than the value of
box.cfg.too_long_threshold, the request will be logged:

  512/1: select([1], EQ) => REPLACE([100001, 1], lsn=200006) took too long: 0.626 sec

This is useful for debugging.

While we are at it, let's also remove 'timeout' from the vinyl engine
constructor arguments and set it with box_set_vinyl_timeout() on box
initialization instead, similarly to vinyl_max_tuple_size.

Closes #2871