ai-eng update orphans ~300 stale skill files on consumer disks

[soydachi]

Split out of spec-201 (autopilot Phase 5 review). Documented in the CHANGELOG and surfaced by a new doctor WARN; the removal sweep was deliberately not built, because deleting files in consumer repos needs its own spec with backup/rollback.

Defect

spec-201 collapsed four redundant skill trees to two. A consumer upgrading from 0.13.0 keeps the deleted trees on disk:

• 137 .github/skills
• 137 .codex/skills
• 19 .codex/agents
• plus .opencode/skills, templates/.cursor/skills

Both Copilot and Codex natively discover the old and new trees, so they read two divergent copies of every skill, and the stale ones still cross-reference .codex/agents/.

Two independent causes

src/ai_engineering/updater/service.py:759-780 - _detect_orphan_files:

1. Sweeps only disabled providers, so an active copilot/codex install is never visited.
2. Enumerates destinations from the current _SURFACE_TREE_MAPS, which no longer names any retired path - so _provider_tree_orphans cannot reach them even for a disabled provider.

Verified on a simulated 0.13.0 tree: with active=['claude-code','github-copilot','codex'], the sweep flags only .cursor/skills and .opencode/skills (disabled), and never .github/skills, .codex/skills, .codex/agents.

RK-14's stated mitigation (a doctor version check) never shipped.

Acceptance

• A retired-trees constant, versioned so future collapses extend it.
• A removal step wired into the existing backup/rollback machinery in the updater.
• Tests covering an upgrading consumer with each provider combination.
• The new retired-surface-trees-present doctor WARN becomes fixable (--fix) once removal exists.