R1:b99c240aa374

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…