refactor(agent): retire unused boot runner and duplicate context fixture

The startup review found an exported runBootPhases orchestration/disposal abstraction whose only repository callers are its own tests. startEliza drives BootContext.enterPhase directly. Keeping the unused abstraction and its fixture doubles adds a second unexercised startup architecture. Searches covered source, scripts, templates, docs and workflows; runtime/index.ts publicly re-exports it, so this deliberately retires runBootPhases and BootPhase while preserving the active BootContext, policy and plan API.

Also consolidate the fake-filesystem canary edit into the existing real-disk rewrite/read flow, preserving old-content exclusion and changed-hash assertions. Retain missing/empty file, explicit manifest and primary prompt composition boundaries.

Acceptance: affected startup/context/port tests, agent typecheck/lint, root verify; verify a realistic stale-content fault is rejected by the real-disk flow and restore production bytes. No new harness or live model behavior change. Device/UI/live model evidence is N/A for unused API retirement and deterministic fixture cleanup.

The same startup review also replaces the hook override declaration-count assertion with actual dynamic hook invocation and observed runtime effect. This preserves the existing override contract without adding a new case or harness.

Unused boot runner retired — becd2c667d (#31688)

Four files,121 net lines removed. Retired exported runBootPhases/BootPhase after whole-repository caller search; active BootContext observers/phase rules remain covered. Removed fake canary edit in favor of the real disk round trip with exact hashes, and replaced hook override declaration count with actual dynamic invocation.24 focused tests,agent types/lint and full root verify pass (377 tasks plus later audits). Stale-read production fault detected,restored byte for byte. BOOT-REVIEW.md contains scope and compatibility limits; IOS-TRANSPORT-REVIEW.md maps next larger overlap. Clean tree,all processes terminal,no peer contacts.