refactor: remove and fold the retired commands

[pacphi]

Why

The command surface comes down to four verbs (design Decision 8).

In scope

setup→init; host pick, off and reset-routes→init; check-connection→status --refresh=live; remove host align and the ak x dashboard and admin aliases; heal hooks→maintain and advice; x mcp, statusline, codex-context and aqe-embedding→init; x reference→sync; x ruflo-mcp→launcher; x daemon-gc→sync; remove x harvest and its live check (G6).

Out of scope

aqe-store and skills (#361).

Acceptance criteria

• Each retired command fails with a pointer to its replacement
• Help lists only the new surface

Dependencies

Blocked by: #357

Blocks: #361, #362, #363, #382, #387

Plan

• Release: 4.0.0-beta.3
• Size: size:M · Workstream: ws:project-scope
• Epic: feat: project-scope P5, sync, status, uninstall and the command folds (epic) #300
• Card: P5-06 in the card inventory
• Sources: Design (docs(plans): project-scoped management design and its prerequisites #289) Commands; Supersession ledger (docs(plans): v4 GA master plan, supersession ledger and v5 registers #290) G2, G6

Verification

• pnpm test