vsctl: fix timeout

- run_command's timeout argument is named 'timeout_msec', but
  all callers seem to pass the value in second.  so rename
  the argument to 'timeout_sec'.

- gevent.Timeout takes a timeout value in second.
  remove a conversion, which seems wrong even if the argument was in ms.

Signed-off-by: YAMAMOTO Takashi <yamamoto@valinux.co.jp>
Signed-off-by: FUJITA Tomonori <fujita.tomonori@lab.ntt.co.jp>