Deprecate "bin/phd ... --gently" and update documentation

Summary:
Ref T13321. Previously, the behavior was:

• bin/phd stop --gently: Stop all daemons with PID files that belong to the current instance.
• bin/phd stop: Stop all daemons with PID files that belong to the current instance. Complain if there are more processes.
• bin/phd stop --force: Stop all processes that look like daemons, ignoring instances.

The new behavior is:

• bin/phd stop: Stop all processes that look like daemons and belong to the current instance.
• bin/phd stop --force: Stop all processes that look like daemons, period.

Test Plan: Grep / documentation only.

Reviewers: amckinley

Reviewed By: amckinley

Maniphest Tasks: T13321

Differential Revision: https://secure.phabricator.com/D20602