docs: post-merge sweep after agent-eval (#139)

[SutuSebastian]

Summary

• Merged context: PR feat(agent-eval): probe A/B harness and log parser (PR 9) #139 (agent-eval probe harness) already on main.
• Deleted ten shipped agent-surface plans (Wave 1–2, feat(mcp): server instructions + CODEMAP_MCP_TOOLS allowlist #126–feat(show): field-qualified search (PR 7) #138) per docs-governance lift-and-delete.
• Pruned roadmap [x] backlog lines; consolidated shipped work into agents.md pointers.
• Refreshed user-facing docs: README (17 MCP tools, codemap unlock), glossary, why-codemap, benchmark.md (removed invalid bun src/index.ts benchmark).
• Updated agent templates (10-recipes-context, 00-full, 50-maintenance, templates/agents/README).
• Fixed cross-refs in open plans; delivery tracker rows no longer link deleted plan files.
• Minor CI/packaging comment updates (bundled recipes wording, npm version note).

Test plan

• bun run format:check on touched paths
• Pre-commit hook (lint-staged) green on commit

[changeset-bot]

⚠️ No Changeset found

Latest commit: 256a1dc

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: abd04771-afd8-4503-a0d7-001f2b335122

📥 Commits

Reviewing files that changed from the base of the PR and between a6065ca and 256a1dc.

📒 Files selected for processing (31)

• .github/workflows/ci.yml
• README.md
• docs/architecture.md
• docs/benchmark.md
• docs/glossary.md
• docs/packaging.md
• docs/plans/affected-tests-recipe.md
• docs/plans/agent-eval-harness.md
• docs/plans/agent-surface-and-ops.md
• docs/plans/agent-surface-delivery.md
• docs/plans/agents-init-mcp-wiring.md
• docs/plans/call-path-type-hierarchy-recipes.md
• docs/plans/callback-dispatch-synthesis.md
• docs/plans/cross-project-mcp-root.md
• docs/plans/field-qualified-search.md
• docs/plans/fts-default-on-evaluation.md
• docs/plans/git-hook-auto-sync.md
• docs/plans/index-lock-and-error-log.md
• docs/plans/mcp-server-instructions.md
• docs/plans/mcp-tool-allowlist.md
• docs/plans/mcp-trace-explore-tools.md
• docs/plans/parse-worker-hardening.md
• docs/plans/unresolved-calls-staging.md
• docs/plans/wsl-watch-policy.md
• docs/roadmap.md
• docs/why-codemap.md
• src/application/query-recipes.dist.test.ts
• templates/agent-content/rule/00-full.md
• templates/agent-content/skill/10-recipes-context.md
• templates/agent-content/skill/50-maintenance.md
• templates/agents/README.md

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch docs/post-merge-doc-sweep

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