Set staging::extract's timeout in staging::deploy.

I've opted to have extract's timeout default to the same value as file's,
which changes the theoretical maximum execution time from $timeout + 5 minutes
(exec's default timeout) to 2 * $timeout. To give users more control, there's
a new, optional $extract_timeout parameter that affects only the extract
stage.

I've added the corresponding timeout parameter to staging::extract.