docs: docs/commands.md and docs/running.md still reference deprecated squads autopilot

[agents-squads]

Problem

Three documentation files tell users to run squads autopilot for autonomous dispatch, but the command is deprecated. Running it shows a deprecation notice and routes to squads run internally.

Affected files

File	Incorrect example
docs/commands.md (line 19)	squads autopilot listed under "For Humans" as an active command
docs/running.md (lines 29–31)	squads autopilot --interval 30 --budget 50 shown as canonical autonomous dispatch
README.md (lines 57–59)	Same squads autopilot in the quickstart code block

Correct behavior

# Deprecated — shows deprecation notice:
squads autopilot --interval 30 --budget 50

# Correct:
squads run --org
squads run -i 15 --budget 50
squads run --once --dry-run

Fix

1. Replace squads autopilot examples in all three files with squads run equivalents
2. Remove squads autopilot from the "For Humans" list in docs/commands.md
3. No code change — cli.ts tombstone is correct

Source: docs-eval agent

[kokevidaurre]

Resolved in #892 (pause/resume, merged to develop).