(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. :(