refactor: consolidate daemon/autonomous into squads run

[kokevidaurre]

Problem

Three execution systems that don't compose:

• daemon.ts (488 lines) — dead code, never registered
• autonomous.ts (796 lines) — cron-based daemon, no intelligence, no cognition
• runAutopilot() in run.ts (~300 lines) — intelligent scoring, but foreground only

Solution

One command, two modes:

• squads run — daemon mode (autonomous, intelligent scheduling, runs forever)
• squads run <target> — single execution (one squad/agent, then exit)

Daemon mode (squads run)

Composes cron routines (from autonomous) + intelligence scoring (from autopilot):

every 60s tick:
  1. Evaluate cron routines from SQUAD.md → spawn matching
  2. Every N minutes (--interval): score all squads → dispatch top-scoring
  3. After each dispatch: grade outcomes, push cognition signals, check PR reviews
  4. Budget/quota gate before any spawn → auto-pause if exceeded

Flags

squads run                            # daemon: runs forever
squads run --once                     # daemon: one cycle, exit
squads run --interval 15 --budget 50  # daemon: custom settings
squads run --stop                     # stop running daemon
squads run --status                   # show daemon status
squads run --pause                    # pause without stopping
squads run engineering                # single: run squad, exit
squads run engineering/code-review    # single: run agent, exit

What to keep from each system

From autonomous.ts: cron evaluation, persistent cooldowns (JSON), detached daemon + PID, pause/resume + auto-pause, agent timeout enforcement, logging

From runAutopilot(): scoreSquads() intelligence, full squad loop dispatch (scanner→lead→worker→verifier), cognition cycle, role-based agent classification, conversation mode, budget tracking, Slack notifications

From daemon.ts: outcome grading (A-F), phantom detection (<30s = skip), PR review feedback loop

File changes

File	Action
daemon.ts	Delete (dead code)
autonomous.ts	Delete (absorbed into run.ts)
run.ts	Refactor: clean runAutopilot() + absorb cron/cooldowns/PID/pause
cli.ts	Remove autonomous + daemon registration
cron.ts, squad-loop.ts, cognition.ts	Keep as-is

Net impact

~1,284 lines deleted (488 + 796), ~200 lines added to run.ts. Net ~1,000 lines cleaner. One system, one mental model. Dispatch always via squads run <target> subprocess — full conversation depth, context injection, cognition signals.