feat(context): two-tier agent context, deterministic drift inspection, and migration skill

[nilbot]

Summary

This PR implements the Two-Tier Agent Context architecture and Model A hybrid migration workflow as specified in docs/design/2026-08-29-two-tier-context-and-llm-migration-architecture.md and docs/plans/2026-08-31-two-tier-context-and-llm-migration-plan.md.

Highlights

1. Asset Embedding & Full Scaffolding (internal/scaffold):

   • Embeds canonical starter assets via Go standard embed.FS (assets.go).
   • scaffold.Create non-destructively scaffolds Tier 1 router (AGENTS.md / CLAUDE.md), Tier 2 domain context (.agents/AGENTS.md), starter skills, and the 4-store docs/{design,plans,journal,qna}/ hierarchy.
   • scaffold.RefreshInfrastructuralSkills safely synchronizes 100% agents-owned machine skills without touching custom user skills.

2. Deterministic Drift Inspection (internal/drift & agents drift):

   • Pure deterministic dynamic-programming LCS diffing against canonical templates.
   • SHA256 canonical and legacy digest catalog with thread-safe memoization.
   • Adds agents drift [--json] [--repo <path>] [--all] for single-repo and fleet inspection (exitcode.OK for clean, exitcode.Advisory for drift).

3. Granular agents doctor Diagnostics (internal/doctor):

   • Replaces generic scaffold checks with 5 granular diagnostics:
     • scaffold:router: Clean current vs. clean legacy vs. drifted vs. missing.
     • scaffold:symlink: Relative symlink integrity (CLAUDE.md -> AGENTS.md).
     • scaffold:domain: .agents/AGENTS.md presence.
     • scaffold:skill-recording: .agents/skills/recording-what-you-learn/.
     • scaffold:skill-migrating: .agents/skills/migrating-fleet-context/.

4. Refined agents update Wiring & Skill Refresh (cmd_fleet.go):

   • Rewires machine hooks and refreshes migrating-fleet-context across registered repositories.
   • Emits non-mutating advisory notices when context drift is detected.

5. Authoritative migrating-fleet-context Skill (.agents/skills/):

   • Comprehensive 5-phase LLM-in-the-loop migration protocol (Preflight -> Branch Isolation -> Semantic Un-nesting -> Docs Realignment -> Automated Gate).

6. Documentation Invariants:

   • Synchronized README.md, agents/README.md, and built-in help text matching live command dispatch tables.

Verification

• go test -count=1 ./... in agents/: 100% PASS across all 15 packages.
• ./bootstrap check: 8 ok, 0 warn, 0 fail.
• All 7 tasks verified via two-stage subagent reviews (spec review + code review) and final whole-branch review.