feat(context): adopt two-tier agent context and 4-store documentation layout

[nilbot]

Summary

This PR establishes the Two-Tier Agent Context Architecture and 4-Store Documentation Layout in dotfiles and defines the LLM-in-the-Loop Migration Architecture for fleet repositories.

Key Changes

1. Two-Tier Agent Context:

   • Inverts root symlinks: AGENTS.md is now the canonical router regular file, and CLAUDE.md is a relative symlink (CLAUDE.md -> AGENTS.md), satisfying safeio.ReadRegular O_NOFOLLOW semantics.
   • Creates .agents/AGENTS.md holding repository-specific engineering guidelines, testing requirements, workflow restrictions, and the CLI Interface Documentation Invariant.
   • Solves the indirection hop via an explicit Bootstrap Protocol in root AGENTS.md.

2. 4-Store Documentation Architecture:

   • Creates docs/plans/ for step-by-step implementation plans.
   • Relocates all active 2026-08-28 implementation plans from docs/journal/ and docs/archive/plans/ into docs/plans/ with the standard -plan.md naming convention.
   • Enforces strict immutability for pre-2026-08-20 historical records in docs/archive/.
   • Updates index files (docs/design/README.md, docs/journal/README.md, docs/plans/README.md).

3. Bundled Skills Delivery:

   • Provisions recording-what-you-learn into .agents/skills/recording-what-you-learn/SKILL.md, exposed to harnesses via existing .claude/skills and .codex/skills symlinks.

4. Scaffold Package & Tests:

   • Updates DefaultAgentsMD and DoctorInstruction in agents/internal/scaffold/scaffold.go to include docs/plans/ and 2-bullet doctor instruction.
   • Updates corresponding unit tests in scaffold_test.go.

5. Design Specification:

   • Authors comprehensive design specification in docs/design/2026-08-29-two-tier-context-and-llm-migration-architecture.md.

Verification

• go test -count=1 ./... in agents/: PASS (all test suites passing)
• agents doctor: PASS (all wiring and scaffold checks report ok)
• Markdown link crawler: 0 broken relative links across all 66 markdown files