chore(layering): drop unused agent-knowledge peerDep + correct the layering diagram

[drewstone]

What

Makes agent-runtime's layering truly one-way.

• Remove the unused @tangle-network/agent-knowledge peerDependency (and its peerDependenciesMeta entry) from package.json, plus the matching pnpm-lock.yaml entries.
• Correct the CLAUDE.md repo-layering diagram to the real dependency shape.

Why

agent-runtime's src imports @tangle-network/agent-knowledge zero times — it deliberately avoids it to prevent a dependency cycle. Domain stores/tools enter by injection via createMcpServer({ feedbackStore }) (see src/mcp/feedback-store.ts: "The substrate cannot import @tangle-network/agent-knowledge … consumers wire their own adapter").

The declared peerDep had nothing importing it. The real, correct direction is agent-knowledge → agent-runtime: agent-knowledge/src/profiles/researcher.ts imports @tangle-network/agent-runtime/loops.

The old diagram drew the two packages as siblings both sitting on agent-eval, which is wrong — agent-knowledge sits above agent-runtime. Corrected, and added the rule: the runtime stays domain-clean by taking domain stores/tools as injected adapters, never importing a domain package. The existing "agent-eval MUST NOT import from agent-runtime" rule is left intact.

Verification (all green)

Gate	Result
CI=true pnpm install --frozen-lockfile	exit 0, lockfile up to date
pnpm run build	exit 0
pnpm run typecheck	exit 0 (src + examples)
pnpm run lint	exit 0 (339 files, no fixes)
pnpm test	117 files, 1131 passed / 2 skipped
pnpm run docs:check	0 errors; freshness OK — 3 substrate peers present + accurate

Removing an unused peerDep breaks nothing; the lockfile delta only drops the agent-knowledge resolution.

[tangletools]

✅ Auto-approved PR — 4e71ed4e

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_{tangletools · auto-approval · reason: blanket_auto_approve · 2026-06-24T20:25:27Z}