Update dependencies.io handbook page for version 3

Updates some of the information to match the current state of its use. And adds some sections on running the tool locally.

Fixes: gitlab-org/distribution/team-tasks#552 (closed)

Why is this change being made?

The information was outdated, and referenced the previous dependencies.io. version.

Does this MR meet the acceptance criteria?

Conformity

• Added description to this MR explaining the reasons for the proposed change, per say-why-not-just-what