The slave dump thread running on the master only checked thd->killed whenever
it reached the end of a binlog file, not between events. This could
unnecessarily delay server shutdown.

This was found by code inspection while tracking down some occasional "forcing
close of thread..." errors in Buildbot. Hopefully this will fix the failures,
but the fix is correct in any case.

Also increase the wait during server shutdown, 2 seconds is a bit tight in
case of heavy I/O stall, and it seems better to delay shutdown a bit than
force-kill threads unnecessarily.

Also fix some races in test cases that restart the mysqld server. The .expect
file should be changed with --append_file, --remove_file + --write_file
creates a short window where mysqld can error out due to .expect file missing.