feat: migrate to pnpm

docs/rfc/007-supply-chain-and-vendor-drift.md

@@ -9,7 +9,7 @@ The vendor manifest (ADR 0001) is enforced at commit time in the *forward* direc
 ## Proposal
 
 1. **Vendor drift check** (nightly CI): clone the upstream repos at the manifest SHAs (shallow), copy the corresponding package sources, and diff against `vendor/*/src`. The job fails unless the diff matches the logged local modifications (kept as a checked-in patch file per modification — the log entries become verifiable artifacts rather than prose).
-2. **Dependency advisories**: osv-scanner (or `yarn npm audit`) job on the lockfile, scheduled + on lockfile-touching PRs.
+2. **Dependency advisories**: osv-scanner (or `pnpm audit`) job on the lockfile, scheduled + on lockfile-touching PRs.
 3. **License inventory**: a script asserting every vendored package carries its LICENSE and that package.json `license` fields match the inventory in vendor/README.md (we mix vendored MIT with our BSD-3) — CI step.
 4. **Renovate** (or a scheduled agent task) proposing npm dependency updates in small PRs that ride the full gate suite; vendored packages are excluded (their updates follow the manifest sync procedure, ideally as a semi-automated agent workflow: fetch upstream, re-apply patches, run gates, open PR with the manifest table updated).
 

docs/rfc/010-acp-agent-client-protocol.md

@@ -45,7 +45,7 @@ Lifecycle and disposal: the connection, listeners, and in-flight permission prom
 3. Internal edit — turn-end reason fidelity (sanctioned: edit internals to fit ACP). Extend `TurnEndReasonMap` in the proper places: (a) declaration-merge a `max-tokens` variant in the owning package (`packages/session/src/types.ts`, alongside `completed|aborted|error|disposed`) — add `max-tokens` because `FinishReasonMap` produces it (DeepSeek maps `length` → `max-tokens`); do not add `refusal`, since no current adapter produces it (unknown DeepSeek finish reasons collapse to `error`), but leave a comment in `TurnEndReasonMap` noting `refusal` should be added when an adapter first emits it (`FinishReasonMap` is merge-extensible); (b) make `agent-loop`'s `loop.ts` populate the reason from the model `finish` chunk — `assembler.finish` lives inside `runStep`, so `runStep` must return it up to `runTurn`, and the rule is "the last step's finish reason wins, but any `max-tokens` in the turn surfaces as `max-tokens`"; (c) no consumer exhaustively switches over `TurnEndReason` today (the invariants plugin switches on `SessionEventType`, and `deriveMessages` ignores `turn/end`), so adding `max-tokens` is a non-breaking extension — but recheck before landing; (d) update [docs/architecture.md](../architecture.md) (the CI-verified loop-lifecycle/event-taxonomy doc) and the affected package READMEs/JSDoc (`dsh-session`, `dsh-agent`, `dsh-agent-loop`) per the repo doc-sync policy. This replaces a fragile "observe the finish chunk in the bridge" hack with a real, documented contract.
 4. Prompt-turn streaming plus load: translate `agent/stream-chunk` and `session/event` into `session/update`; resolve `session/prompt` on settle, mapping the harness `TurnEndReason` to the ACP `StopReason` wire enum (`completed`→`end_turn`, `max-tokens`→`max_tokens`, `aborted`→`cancelled`) — a small total function with a test asserting the exact wire strings, since the SDK rejects an unknown `stopReason`. Concrete correlation, since the loop batches queued messages into one turn and `send()` does not synchronously flip to running: install listeners before `send()`; gate on an observed `agent/turn-start` (confirms work was accepted) then resolve on the next `agent/turn-end`; reject an empty/whitespace prompt up front rather than calling `send()` (no turn would ever start, so the RPC would hang). Implement `session/load` on RFC 009's resume seam.
 5. Permission gate: a single `tools/execute` listener registered with `prepend: true`, owning a `WeakMap<Agent, sessionId>` of bridge-created agents; no-op (`next()`) for unowned/no-agent calls; for owned calls → `session/request_permission` → allow (`next()`) / veto; settle the stored resolver exactly once on outcome, cancel, or connection close.
-6. Example wiring (extract a shared base). `@cordisjs/plugin-include` is itself a plugin entry that resets `ctx.baseUrl` and loads a path, so a child `cordis.yml` can nest-include a shared base; the extraction is safe because every dependent plugin declares `inject` (loader groups initialize via `Promise.all`, so YAML order is NOT the dependency mechanism — never rely on it). Extract the provider/tool core (`llm, sessions, system-prompt, tools, agents, invariants, llm-deepseek, bash-local, tool-bash`) into `examples/base.yml`; have both `coding-agent` and a new `examples/acp-agent/` include it and add their own UI plugin plus logger. Keep `agent-loop` per-example (NOT in the base): `AgentLoop` creates its configured agents in its constructor, and the two examples disagree — `coding-agent` needs a pre-created `main` (its `stdio-chat` calls `ctx.agents.get('main')`), while `acp-agent` must pre-create none (ACP `session/new` creates agents). So `coding-agent` declares `agent-loop` with `agents: [{ id: main, … }]` and `acp-agent` with `agents: []`. `acp-agent` loads `dsh-session-persistence-jsonl` (from RFC 009 — required for `session/load`), omits the stdout logger (see Risks), and adds `yarn demo:acp` plus the Zed `agent_servers` snippet.
+6. Example wiring (extract a shared base). `@cordisjs/plugin-include` is itself a plugin entry that resets `ctx.baseUrl` and loads a path, so a child `cordis.yml` can nest-include a shared base; the extraction is safe because every dependent plugin declares `inject` (loader groups initialize via `Promise.all`, so YAML order is NOT the dependency mechanism — never rely on it). Extract the provider/tool core (`llm, sessions, system-prompt, tools, agents, invariants, llm-deepseek, bash-local, tool-bash`) into `examples/base.yml`; have both `coding-agent` and a new `examples/acp-agent/` include it and add their own UI plugin plus logger. Keep `agent-loop` per-example (NOT in the base): `AgentLoop` creates its configured agents in its constructor, and the two examples disagree — `coding-agent` needs a pre-created `main` (its `stdio-chat` calls `ctx.agents.get('main')`), while `acp-agent` must pre-create none (ACP `session/new` creates agents). So `coding-agent` declares `agent-loop` with `agents: [{ id: main, … }]` and `acp-agent` with `agents: []`. `acp-agent` loads `dsh-session-persistence-jsonl` (from RFC 009 — required for `session/load`), omits the stdout logger (see Risks), and adds `pnpm run demo:acp` plus the Zed `agent_servers` snippet.
 7. Tests (the repo cares a lot here): a property-based test for the protocol shape (precedent: RFC 001 / [ADR 0013](../adr/0013-property-based-testing.md)) — fuzz arbitrary harness event sequences and assert ACP-stream invariants (never a `tool_call_update` before its `tool_call`; exactly one `session/prompt` resolution per prompt; monotonic, well-formed ordering; `stopReason` in the legal set); codec unit tests over an in-memory `Duplex` pair (drive `AgentSideConnection` without a subprocess; assert exact frames for `initialize`, `session/new`, a full prompt turn); the mandatory HMR-safety test (dispose the fiber; assert the connection closed, all `ctx.on` listeners gone, any in-flight `request_permission` settled); failure-path tests (connection closes mid-stream; closes with a permission pending; a notification `send()` rejects but the turn survives; `finish{kind:'error'|'aborted'}`; a `tools/execute` throw with no `tool/result`; a second `session/new` rejected; a `session/prompt` while one is in flight; an empty prompt rejected without hanging; a `session/load` re-derives identical history and replays it); and an e2e (`*.e2e.ts`, self-skips without `DEEPSEEK_API_KEY`) that boots `examples/acp-agent`, connects a `ClientSideConnection`, sends a real prompt, owns and disposes the harness in `afterEach`, and verifies the world (files on disk), not the agent's self-report.
 8. Docs: module/JSDoc plus a package README; extend [the extension cookbook](../cookbook/extension-cookbook.md) with the client-driver pattern. Flip Status to `implemented` on landing; write an ADR only if a decision proves durable, contested, and surprising (candidates: the `tools/execute` permission-ownership rule, the npm-dependency choice) — not auto-required.
 

docs/rfc/012-optional-code-mode.md

@@ -85,7 +85,7 @@ It is insufficient for the **composition / round-trip** half, which is the decis
 2. Scaffold the implementation package `packages/code-runtime-vm/`: the node:vm stub — `safe = false`, a constructor that **throws unless given `{ unsafe: true }`**, transpile/type-erase, async-IIFE wrap, capturing `console`, SDK globals, return-value/logs/error capture, output cap, signal-tied timeout. Tests for output capture, return value, error-as-field, abort, the constructor refusal without `unsafe`, and a README documenting the "not a sandbox, trusted-only" caveat prominently.
 3. Scaffold the consumer plugin `packages/code-mode/`: `jsonSchemaToTs` codegen with namespace/quoted-access + alias handling (unit tests, including non-identifier MCP names and unsupported-shape → `unknown`); the registered lazy `ctx.systemPrompt.section()` carrying the SDK `.d.ts`; the `agent/request` listener (`prepend: true`) collapsing `request.tools` to `[run_code]` after `await next()`; the **unsafe-runtime gate** (refuse to register `run_code` when `ctx.codeRuntime.safe === false` unless `allowUnsafeRuntime` is set); the `run_code` tool with the dispatch bridge (per-run serialization queue, deterministic sub-call ids, before/after abort checks, `CodeRunError` on error results); and the `code/dispatch` event declared here via `SessionEventMap` merge. Declare `inject = ['tools', 'systemPrompt', 'codeRuntime']`.
 4. Tests: HMR-safety (dispose removes the tool, the section, and the listener); a waterfall test that the wire tool list is exactly `[run_code]` (spy adapter, asserting via `agent/request` and optionally `llm/stream`); an integration test that a program calling two tools returns only its printed/returned output (verify the world, not the self-report); a **serialization test** that `Promise.all([...])` over SDK calls does not overlap the underlying `ctx.tools.execute` invocations (a probe tool records enter/exit; assert no interleaving); `deriveMessages()` ignores `code/dispatch`; abort mid-program stops further dispatches; `CodeRunError` surfaces as `isError: true`; and the **unsafe-runtime refusal test** (§3, the VM-guard): with the unsafe flag unset, a non-mock agent's `run_code` is refused; with it set, the program runs.
-5. Wire an example: `examples/coding-agent-code-mode` (or a config flag on the existing example) loading the trio. Running it against the node:vm stub requires both opt-ins (`VmCodeRuntime({ unsafe: true })` and `code-mode`'s `allowUnsafeRuntime`); the example sets them explicitly and comments why, or uses a mock model — a real model never reaches the unsandboxed stub without those deliberate flags. Add a `yarn demo:*` entry.
+5. Wire an example: `examples/coding-agent-code-mode` (or a config flag on the existing example) loading the trio. Running it against the node:vm stub requires both opt-ins (`VmCodeRuntime({ unsafe: true })` and `code-mode`'s `allowUnsafeRuntime`); the example sets them explicitly and comments why, or uses a mock model — a real model never reaches the unsandboxed stub without those deliberate flags. Add a `pnpm run demo:*` entry.
 6. Docs: update [docs/architecture.md](../architecture.md) (a `ctx.codeRuntime` row in the service map, a Code Mode note under the tool pipeline / capability seams sections); add a [cookbook](../cookbook/) note on writing a `CodeRuntime` backend; and **file the follow-up RFC for the hardened execution substrate** (the isolate/sandboxed-process design, the additional-language backends sketched in §1 — AssemblyScript/WASM, Python — with their per-language SDK generators, plus the tool-visibility-tier design skipped here). Append the `| 012 | … | proposed |` row to [the RFC index](README.md).
 
 ## Risks