(PUP-2639) Change default timeout to 3 minutes

The 5 second timeout was selected assuming that the major use case would be
around a development workflow in which a user edits manifests on a master and
then immediately runs an agent to see the effect. It turns out that this
caused a lot of problems for a much more common and impactful case of users
updating to directory environments where they ended up with excessive CPU
usage. Nearly any value here is arbitrary except 0 (purely development
workflow) and unlimited (best choice for production systems).

This makes the almost arbitrary decision that a 3 minute timeout will create
less confusion for upgrading users. It means that a development workflow will
require more restarts, however. :(