Merge codex/goal-domain into codex/goal-tools

packages/core/agent-loop/README.md

@@ -19,7 +19,7 @@ Each agent and its session share one caller-chosen `SessionId`, assumed globally
 `AgentLoop` also implements the `AgentFactory` seam and registers itself via `ctx.agents.setFactory(this)`, so plugins create/resume agents through `ctx.agents` (the interface):
 
 - `ctx.agents.create({ sessionId, meta?, seed?, agentOptions?, setup?, signal? }): Promise<AgentHandle>` — programmatic create under the caller-supplied shared id. It awaits the unpublished setup transaction before returning; `meta` carries cwd/lineage/seed-boundary metadata and `seed` reconstructs a forked child prefix after the session boundary validates and snapshots the durable values. `signal` applies only until this promise settles. The resolved [`AgentHandle`](../agent/README.md) owns exact teardown.
-- `ctx.agents.resume({ resumeSessionId, agentOptions?, setup?, signal? }): Promise<AgentHandle>` — load a persisted session via `ctx.sessionPersistence` ([session persistence](../../../docs/rfc/implemented/architecture/2026-06-14-session-persistence.md)), register the agent under that same id, reconstruct its history, then await setup against a fresh unpublished agent scope before rollback-covered publication. Turn numbering and derived history continue from the loaded log. Requires a session-persistence backend (NOT hard-injected — non-persistent demos still work; `resume` rejects with a clear error when persistence is absent). `signal` is creation-only. Returns an `AgentHandle`.
+- `ctx.agents.resume({ resumeSessionId, agentOptions?, setup?, signal? }): Promise<AgentHandle>` — load a persisted session via `ctx.sessionPersistence` ([session persistence](../../../.agents/notes/implemented/architecture/2026-06-14-session-persistence.md)), register the agent under that same id, reconstruct its history, then await setup against a fresh unpublished agent scope before rollback-covered publication. Turn numbering and derived history continue from the loaded log. Requires a session-persistence backend (NOT hard-injected — non-persistent demos still work; `resume` rejects with a clear error when persistence is absent). `signal` is creation-only. Returns an `AgentHandle`.
 
 The config-driven `ctx.agentLoop.create()` path keeps its agent owned by the loop fiber (it discards the handle). For a programmatic agent, the handle holder is the only consumer-facing teardown capability; AgentLoop provider unload is the independent structural teardown edge, not another handle exposed to application code.
 
@@ -114,7 +114,7 @@ Append-only; each synthetic result follows the reusable request prefix and does
 
 ## Known Limitations and Deferred Work
 
-- **Classification is unary** — calls whose safety depends on comparing siblings or resources must remain exclusive ([rationale](../../../docs/rfc/implemented/feature/2026-07-10-parallel-tool-call-execution.md)).
+- **Classification is unary** — calls whose safety depends on comparing siblings or resources must remain exclusive ([rationale](../../../.agents/notes/implemented/feature/2026-07-10-parallel-tool-call-execution.md)).
 - **Config labels are fresh by default** — omitting `sessionId` creates a fresh `${id}-session-<uuid>` on every startup; exact resume-or-create behavior requires an explicit stable `sessionId`, while `resumeSessionId` requires existing persisted history.
 - **Config agents have no per-agent persona field or setup hook** — they use the deployment persona; scoped persona/tool composition is available only through the programmatic `ctx.agents.create()` / `resume()` factory options.
 - **No built-in turn budget** — the default continuation is `continue` whenever a step had tool calls or steering; bounding a runaway turn requires an `agent/turn-continuation` force-stop plugin.

packages/core/agent-loop/src/loop.ts

@@ -1,7 +1,7 @@
 /**
  * Drives one agent across queued durable turns. Turn failures are contained so
  * later work can run; the session log, not this driver, owns conversation state.
- * See docs/rfc/implemented/architecture/2026-06-18-agent-lifecycle-and-ownership-seams.md.
+ * See .agents/notes/implemented/architecture/2026-06-18-agent-lifecycle-and-ownership-seams.md.
  * @module dsh-agent-loop/loop
  */
 

packages/core/agent-loop/tests/coverage-edges.spec.ts

@@ -235,7 +235,7 @@ describe('disposed vs aborted branching', () => {
   })
 })
 
-describe('structured tool error propagation (the runtime-validation RFC, part 2)', () => {
+describe('structured tool error propagation (the runtime-validation Agent Note, part 2)', () => {
   it('forwards a tool HarnessError onto the tool/result session event', async () => {
     const { HarnessError } = await import('@deepseek-ai/dsh-llm')
     // First model turn calls the tool; second turn (after the tool result is

packages/core/agent-loop/tests/properties.spec.ts

@@ -1,6 +1,6 @@
 /**
  * Property-based tests for the agent loop's inbox/turn scheduling (the
- * property-testing RFC). Deterministic by construction: schedules are driven
+ * property-testing Agent Note). Deterministic by construction: schedules are driven
  * through the `agent/status` settle signal (no wall-clock sleeps), so a flake
  * is a finding, not timing noise.
  *

packages/core/agent-loop/tests/request-cache.e2e.ts

@@ -14,7 +14,7 @@ import * as LlmDeepSeek from '@deepseek-ai/dsh-llm-deepseek'
  * multi-step tool turn (plus a follow-up turn) against the live DeepSeek API must report
  * `cacheReadTokens > 0` on every request after the first — the adapter maps the provider's
  * `prompt_cache_hit_tokens`, and the per-step usage recorded on `assistant/message` events is
- * the production observable for cache behavior (the reconstructability RFC's measurement
+ * the production observable for cache behavior (the reconstructability Agent Note's measurement
  * layer: prefix stability is corollary #1). Mocks establish append-extension;
  * this key-gated test establishes a real provider cache hit.
  */

packages/core/agent-loop/tests/resume.spec.ts

@@ -75,7 +75,7 @@ function throwUnknown(value: unknown): never {
   throw value
 }
 
-describe('the session-persistence RFC: AgentLoop factory create/resume', () => {
+describe('the session-persistence Agent Note: AgentLoop factory create/resume', () => {
   it('normalizes a non-Error resume publication failure for rollback and rethrows it', async () => {
     const sessionId = SessionId('unknown-resume-failure-s')
     const root = await persistSession(sessionId)

packages/core/agent/README.md

@@ -26,7 +26,7 @@ The scoped-registration surface: `Agent.ctx` is the agent's scope context (`dsh-
 - `ctx.agents.withInitiator(agent, operation)` — run with one exact Agent and preserve the operation's exact synchronous value or Promise.
 - `ctx.agents.withoutInitiator(operation)` — hide an inherited initiator for unrelated process-local work.
 
-The scope carries the `Agent` itself and is process-local. Ambient presence is neither liveness proof nor authorization; explicit Agent fields remain authoritative at service, worker, process, persistence, and wire boundaries. Teardown rejects new boundaries, lets injected dependents and returned-Promise boundaries drain, then disables the underlying `AsyncLocalStorage`; unreturned work remains owned by the subsystem that detached it. If a boundary's inherited async chain starts an owning Cordis fiber's unload, that nested boundary chain is released from the drain so the unload cannot wait on itself; its continuations observe the disposed service after teardown. The [initiator-scope decision](../../../docs/rfc/implemented/architecture/2026-07-15-agent-initiator-scope.md) owns the detailed boundary and teardown contract.
+The scope carries the `Agent` itself and is process-local. Ambient presence is neither liveness proof nor authorization; explicit Agent fields remain authoritative at service, worker, process, persistence, and wire boundaries. Teardown rejects new boundaries, lets injected dependents and returned-Promise boundaries drain, then disables the underlying `AsyncLocalStorage`; unreturned work remains owned by the subsystem that detached it. If a boundary's inherited async chain starts an owning Cordis fiber's unload, that nested boundary chain is released from the drain so the unload cannot wait on itself; its continuations observe the disposed service after teardown. The [initiator-scope decision](../../../.agents/notes/implemented/architecture/2026-07-15-agent-initiator-scope.md) owns the detailed boundary and teardown contract.
 
 #### Factory seam (creation)
 
@@ -34,7 +34,7 @@ Agent *creation* is provided by the plugin implementing `AgentFactory` (`dsh-age
 
 - `ctx.agents.setFactory(factory: AgentFactory): () => void` — register the creation factory (the loop calls this on construction). Throws on a second factory; the slot clears on dispose.
 - `ctx.agents.create(options: CreateAgentOptions): Promise<AgentHandle>` — create a session and agent, await optional setup while unpublished, then publish through final `SessionStore.enter()` and `AgentRegistry.enter()` checks. Concurrent same-ID creation is unsupported: more than one operation may prepare, but only one can enter; every loser rolls its private scope/session/driver back. An optional creation-only `signal` cancels unpublished setup and is detached before the handle is returned; later cancellation uses `handle.dispose()` or `agent.cancel()`. Publication is rollback-covered and every delivered creation edge is paired during rollback. Rejects if no factory is registered.
-- `ctx.agents.resume(options: ResumeAgentOptions): Promise<AgentHandle>` — load a persisted session ([session persistence](../../../docs/rfc/implemented/architecture/2026-06-14-session-persistence.md)), mint a fresh unpublished agent scope, await optional setup, and use the same final-entry publication sequence. Its optional `signal` is likewise creation-only. Rejects if no factory is registered or session persistence is unconfigured.
+- `ctx.agents.resume(options: ResumeAgentOptions): Promise<AgentHandle>` — load a persisted session ([session persistence](../../../.agents/notes/implemented/architecture/2026-06-14-session-persistence.md)), mint a fresh unpublished agent scope, await optional setup, and use the same final-entry publication sequence. Its optional `signal` is likewise creation-only. Rejects if no factory is registered or session persistence is unconfigured.
 
 `AgentHandle = { agent: Agent; dispose(): Promise<void> }`. The disposer is a **consumer capability** — no observer holding the bare registry entry can tear the agent down. The caller fiber and the registered factory provider are structural co-owners: caller unload enforces structured ownership, while factory unload must stop old instances because their scoped dependency surface belongs to that provider. `dispose()` from any owner reaches one memoized quiescence boundary: it stops the loop, `await`s its exit plus every outstanding idle-injection flush (not just the `disposed` status flip), unregisters the agent, removes its session from the store, and finally unwinds its scoped world. This order captures every agent-started `session/flush` before the session is detached and keeps scoped listeners alive through those checkpoints. `ctx.agents.get(id)` still returns a bare `Agent`; the ACP bridge and in-process subagent backends hold consumer handles, while config-created agents are already owned by the loop fiber.
 
@@ -44,7 +44,7 @@ Agent *creation* is provided by the plugin implementing `AgentFactory` (`dsh-age
 
 The lifecycle edges have two important local caveats. `agent/created` runs after scoped setup and after both session and agent registry entries exist. Setup is trusted composition-only code; the immediately following non-vetoing `agent/session-start` notification is the first supported startup injection point. `agent/disposed` always means the exact agent has left the registry. AgentLoop emits it after its driver is quiescent, while ordered teardown may still be detaching the session and unwinding the scope; custom agents registered directly own any stronger driver-ordering contract themselves.
 
-Most interception points are cooperative waterfalls returning seam-specific decisions. `agent/pre-step` and `agent/post-step` are serial checkpoints around a step's durable work, while `agent/request-error` is the failed-model-request recovery waterfall: a retry opens a new numbered step after the failed step closes. `agent/turn-stop` is the terminal serial fold: it runs after ordinary continuation and steering folding, and a returned stop remains in force through turn close and flush so later steering cannot create an extra step or turn. Ordinary queued prompts remain intact. The full rationale for scoped dispatch and terminal settlement is in the [agent-scope runtime-design RFC](../../../docs/rfc/implemented/architecture/2026-07-12-agent-scope-runtime-design.md#three-execution-boundaries-are-deliberately-one-way).
+Most interception points are cooperative waterfalls returning seam-specific decisions. `agent/pre-step` and `agent/post-step` are serial checkpoints around a step's durable work, while `agent/request-error` is the failed-model-request recovery waterfall: a retry opens a new numbered step after the failed step closes. `agent/turn-stop` is the terminal serial fold: it runs after ordinary continuation and steering folding, and a returned stop remains in force through turn close and flush so later steering cannot create an extra step or turn. Ordinary queued prompts remain intact. The full rationale for scoped dispatch and terminal settlement is in the [agent-scope runtime-design Agent Note](../../../.agents/notes/implemented/architecture/2026-07-12-agent-scope-runtime-design.md#three-execution-boundaries-are-deliberately-one-way).
 
 `PromptDecision.additionalContexts` is an array so every injected context keeps its own source, envelope, and metadata. A `ContinuationDecision` reason is narrower: it becomes a `steering/message`, not a `context/message`, and therefore carries only content and source.
 
@@ -56,7 +56,7 @@ The handle every plugin programs against:
 
 - `agent.send(content, options?)` — queue a message; starts a turn when idle. Content and resolved source become one detached, deeply frozen lossless-JSON record before `agent/queued` and enqueue; invalid data throws synchronously, and caller or notification-listener in-place mutation cannot change the log or model input (`agent/prompt-submit` still rewrites by returning replacement content).
 - `agent.steer(content, options?)` — steer a running turn (inject between steps); uses the same owned acceptance boundary and behaves like `send` when idle
-- `agent.inject(content, options?)` — accept detached in-session context without running the model; the next request sees its `context/message`. `options.envelope` defaults to the canonical `<context>` framing and may be `'raw'` when the caller owns a complete familiar frame; `options.meta` persists opaque JSON state without rendering it. While a turn is open it joins that turn, deferring FIFO while the current tool batch executes and draining before turn close if execution is interrupted; while idle it is wrapped in a one-shot `injection` turn and durability checkpoint ([the turn-enclosure invariant](../../../docs/rfc/implemented/architecture/2026-06-15-turn-enclosure-invariant.md)).
+- `agent.inject(content, options?)` — accept detached in-session context without running the model; the next request sees its `context/message`. `options.envelope` defaults to the canonical `<context>` framing and may be `'raw'` when the caller owns a complete familiar frame; `options.meta` persists opaque JSON state without rendering it. While a turn is open it joins that turn, deferring FIFO while the current tool batch executes and draining before turn close if execution is interrupted; while idle it is wrapped in a one-shot `injection` turn and durability checkpoint ([the turn-enclosure invariant](../../../.agents/notes/implemented/architecture/2026-06-15-turn-enclosure-invariant.md)).
 - `agent.cancel(reason?)` — cancel ALL pending work: clears the queued + steering FIFOs, aborts the in-flight step, and drops a turn about to start (the pre-step window) so a queued-but-not-started prompt never runs. A UI/ACP `session/cancel` maps to this. The single public stop primitive. Idle with nothing pending → a safe no-op.
 - `agent.whenIdle()` — resolve once the agent reaches quiescence after settling out of `running` (idle → immediately; disposed → awaits the loop exit). A non-owner's quiescence-observation hook: it observes the work settling WITHOUT tearing the agent down. Teardown is separate — a lifecycle owner stops and unregisters via `AgentHandle.dispose()`, which awaits the loop exit directly.
 - `agent.session`, `agent.status`, `agent.options`, `agent.id`
@@ -103,6 +103,6 @@ Prefix-stable while an agent's scoped registrations are unchanged. Setup or relo
 - **Ambient identity may outlive liveness** — consumers still check `agent.status`, cancellation, and the owning capability contract before lifecycle-sensitive work.
 - **Inter-agent channels beyond delegation** — shared state, streaming child output, and background/poll semantics remain outside the current synchronous `ctx.subagents` seam.
 - **`agent/session-start` cannot gate startup** — it remains a synchronous, veto-less notification; async composition that must finish before publication belongs in the factory's `setup(agentCtx)` transaction instead.
-- **No public step-only abort** — `cancel()` clears ALL pending work (queued + steering + in-flight); an abort that preserves queued prompts returns only with a named consumer ([stop-surface RFC](../../../docs/rfc/implemented/simplification/2026-06-20-public-agent-stop-surface.md)).
+- **No public step-only abort** — `cancel()` clears ALL pending work (queued + steering + in-flight); an abort that preserves queued prompts returns only with a named consumer ([stop-surface Agent Note](../../../.agents/notes/implemented/simplification/2026-06-20-public-agent-stop-surface.md)).
 - **`HookContext` carries exactly one `MessageSource`** — contributions from several plugins merged onto one tool call collapse under one source; mixed provenance is unrepresentable.
 - **`SessionStartSource` reserves `'clear'`/`'compact'` with no emitter yet** — only `'startup'`/`'resume'` occur until the driving subsystems land (`TODO(compaction)`).

packages/core/scope/README.md

@@ -15,7 +15,7 @@ Scoped registration primitive. `createScope(ctx, key)` creates a tagged Cordis c
 
 ## Design contract
 
-The registration context determines both visibility and ownership, preventing a registration from being visible in one scope but disposed with another. Scopes route trusted same-process plugins; they are not sandboxes or authority boundaries. See the [agent-scope RFC](../../../docs/rfc/implemented/architecture/2026-07-08-agent-scope-contexts.md#security-and-authority-are-explicit-non-goals) for rationale and security non-goals.
+The registration context determines both visibility and ownership, preventing a registration from being visible in one scope but disposed with another. Scopes route trusted same-process plugins; they are not sandboxes or authority boundaries. See the [agent-scope Agent Note](../../../.agents/notes/implemented/architecture/2026-07-08-agent-scope-contexts.md#security-and-authority-are-explicit-non-goals) for rationale and security non-goals.
 
 Handing out a scoped context hands out the minting plugin's service-resolution surface (resolution walks the minting fiber's dependency chain, not the holder's) — mint it from the plugin whose dependencies the scoped registrations need to resolve.
 

packages/core/session/README.md

@@ -22,7 +22,7 @@ Use the split lifecycle only when teardown must be ordered with another resource
 - `enter(session)` performs the collision check, publishes without announcing, and returns an entry-bound idempotent detach. Concurrent same-id preparations are allowed, but only one entry succeeds; a stale detach cannot remove its replacement.
 - `announce(session)` emits the single creation edge and rejects repeat or reentrant announcements. Detach during that dispatch is deferred and later emits the paired disposal edge; an unannounced entry emits neither lifecycle edge.
 
-`dsh-agent-loop` uses this split so final loop flush precedes session detach; see the [ownership RFC](../../../docs/rfc/implemented/architecture/2026-06-18-agent-lifecycle-and-ownership-seams.md).
+`dsh-agent-loop` uses this split so final loop flush precedes session detach; see the [ownership Agent Note](../../../.agents/notes/implemented/architecture/2026-06-18-agent-lifecycle-and-ownership-seams.md).
 
 ### Live service events
 
@@ -54,7 +54,7 @@ Durable values need one accepted representation, not a check followed by a secon
 
 ### Request-header reconstruction (`request-header.ts`)
 
-`request/header` records a full canonical snapshot of the non-history request envelope with reason `initial`, `resume`, or `change`. `foldRequestHeader()` selects the latest snapshot; legacy delta events and the removed `fallback` reason are rejected. `messagePrefix` remains separate from derived history. See the [reconstructable-requests RFC](../../../docs/rfc/implemented/architecture/2026-07-05-reconstructable-requests.md).
+`request/header` records a full canonical snapshot of the non-history request envelope with reason `initial`, `resume`, or `change`. `foldRequestHeader()` selects the latest snapshot; legacy delta events and the removed `fallback` reason are rejected. `messagePrefix` remains separate from derived history. See the [reconstructable-requests Agent Note](../../../.agents/notes/implemented/architecture/2026-07-05-reconstructable-requests.md).
 
 `context/message` defaults to the canonical tagged context projection. A producer may set `envelope: 'raw'` when its `content` already contains the complete model-facing frame, and may attach JSON `meta` for replayable plugin state; metadata remains durable but is excluded from `deriveMessages()`.
 
@@ -128,6 +128,6 @@ Logging causes no invalidation, and exact reconstruction preserves request-prefi
 ## Known Limitations and Deferred Work
 
 - **Session branching/tree** (pi-style entry tree) — deferred unless needed beyond boundary-based `fork()`.
-- **`fork()` cuts only at closed-turn boundaries of live sessions** — the boundary must be a `turn/end` event and the source must be in the store; forking a persisted-but-unloaded session is excluded from the [fork API](../../../docs/rfc/implemented/feature/2026-06-30-session-store-fork-api.md).
+- **`fork()` cuts only at closed-turn boundaries of live sessions** — the boundary must be a `turn/end` event and the source must be in the store; forking a persisted-but-unloaded session is excluded from the [fork API](../../../.agents/notes/implemented/feature/2026-06-30-session-store-fork-api.md).
 - **`SESSION_FORMAT_VERSION` stays pinned at `0`** — pre-release, no compatibility implied: a backend rejects any other version, and no migration path exists until the first release ([policy](../../../AGENTS.md)).
 - **`TurnEndReasonMap` omits the ACP-named `refusal` / `max_turn_requests` variants** — producer-gated: they land when an adapter or the loop first emits them.

packages/core/session/src/index.ts

@@ -496,7 +496,7 @@ export class Session {
    * The per-node pure function {@link deriveMessages} folds over the surface;
    * an external reconstructor (or the dev invariant) folds the same function
    * over a log prefix's surface to rebuild the exact messages any request was
-   * built from (the reconstructability RFC). The returned message wrapper is
+   * built from (the reconstructability Agent Note). The returned message wrapper is
    * fresh; its content reuses the logged event's already deep-frozen durable
    * data, so changing the wrapper cannot rewrite the log and changing content
    * throws.

packages/core/session/tests/properties.spec.ts

@@ -1,5 +1,5 @@
 /**
- * Property-based tests for the Session event log (the property-testing RFC).
+ * Property-based tests for the Session event log (the property-testing Agent Note).
  *
  * Generates arbitrary event logs and asserts the derivation invariants the
  * agent loop and replay depend on: deriveMessages is deterministic and

packages/core/system-prompt/README.md

@@ -7,7 +7,7 @@ System prompt assembly registry. Plugins contribute ordered sections, tool schem
 | Key | Default | Meaning |
 |---|---|---|
 | `persona` | `''` | The global deployment-persona default: the ONE config-authored prompt fragment, rendered as the order-0 `deployment:persona` section unless an agent-scoped contribution shadows it. A template — complete `{{…}}` groups are interpreted strictly against the registered variables (the shipped loop registers `{{model}}`/`{{cwd}}`), with no escape syntax for literal braces yet. Empty ⇒ the section is dropped at render. |
-| `toolOrder` | — | Explicit model-facing tool order, as a list of `ToolSchema.name`s with one `'<unlisted-tools>'` rest entry (`TOOL_ORDER_REST`): listed tools take their listed position, unlisted tools land at the rest entry in lexicographic name order. Absent ⇒ plain lexicographic name order. Applied to the collected tools BEFORE the `system-prompt/assemble` waterfall — like the sections' `order` sort, it canonicalizes what the registry contributed (registration order is a plugin-load artifact), and a waterfall listener that mutates the list owns the determinism of what it emits. Misconfiguration fails loud: a list without exactly one rest entry, or with duplicates, throws at load; a listed name with no registered tool rejects every `assemble()`; a tool provider returning the reserved rest-entry name also rejects. Under the shipped loop the turn fails before any model request. Why a central list and not per-plugin weights: [Explicit model-facing tool order](../../../docs/rfc/implemented/feature/2026-07-06-explicit-tool-order.md). |
+| `toolOrder` | — | Explicit model-facing tool order, as a list of `ToolSchema.name`s with one `'<unlisted-tools>'` rest entry (`TOOL_ORDER_REST`): listed tools take their listed position, unlisted tools land at the rest entry in lexicographic name order. Absent ⇒ plain lexicographic name order. Applied to the collected tools BEFORE the `system-prompt/assemble` waterfall — like the sections' `order` sort, it canonicalizes what the registry contributed (registration order is a plugin-load artifact), and a waterfall listener that mutates the list owns the determinism of what it emits. Misconfiguration fails loud: a list without exactly one rest entry, or with duplicates, throws at load; a listed name with no registered tool rejects every `assemble()`; a tool provider returning the reserved rest-entry name also rejects. Under the shipped loop the turn fails before any model request. Why a central list and not per-plugin weights: [Explicit model-facing tool order](../../../.agents/notes/implemented/feature/2026-07-06-explicit-tool-order.md). |
 
 ## Service: `SystemPrompt` (ctx key: `systemPrompt`)
 
@@ -38,7 +38,7 @@ Merge-extensible: plugins can declare extra fields on `PromptAssembly` and `Asse
 - Tool schema providers: `ToolRegistry` registers itself as a tool provider automatically.
 - The [`system-prompt/assemble` waterfall](#live-events): cooperatively mutate or replace the assembly per caller.
 
-Design rationale: [the prompt-variables RFC](../../../docs/rfc/implemented/architecture/2026-07-05-prompt-variables-and-tool-guidance-ownership.md).
+Design rationale: [the prompt-variables Agent Note](../../../.agents/notes/implemented/architecture/2026-07-05-prompt-variables-and-tool-guidance-ownership.md).
 
 ## Model Experience
 

packages/core/tools/README.md

@@ -16,9 +16,9 @@ tools:
 ### Public API
 
 - `ctx.tools.register(definition: ToolDefinition): () => void` Register a trusted typed same-process definition. The layer is the calling context's scope: a plain plugin context registers globally; an agent's `agent.ctx` registers for that agent alone, shadowing a same-named global tool there. Duplicate names within one layer throw; non-native modes also reject the reserved `run_code` transport name. `timeoutMs`, when present, must be positive and finite. Disposed with the calling fiber.
-- `ctx.tools.restrict(filter)` applies an agent-scoped allow/deny mask to global tools and throws from a plain context. The filter is snapshotted at registration; multiple masks intersect and scope-local tools merge afterwards. Deny masks admit later unnamed globals, while allow masks exclude later names. Unknown, local, or reserved names and empty filters reject. This is live visibility composition, not an authority boundary; see the [scope security non-goal](../../../docs/rfc/implemented/architecture/2026-07-08-agent-scope-contexts.md#security-and-authority-are-explicit-non-goals).
+- `ctx.tools.restrict(filter)` applies an agent-scoped allow/deny mask to global tools and throws from a plain context. The filter is snapshotted at registration; multiple masks intersect and scope-local tools merge afterwards. Deny masks admit later unnamed globals, while allow masks exclude later names. Unknown, local, or reserved names and empty filters reject. This is live visibility composition, not an authority boundary; see the [scope security non-goal](../../../.agents/notes/implemented/architecture/2026-07-08-agent-scope-contexts.md#security-and-authority-are-explicit-non-goals).
 - `ctx.tools.get(name: string, scope?: ScopeKey): ToolDefinition | undefined` Resolution as one scope sees it (shadowing applied; a restricted-away global reads as absent) — presenters pass the calling agent so the card matches what executed.
-- `ctx.tools.schemas(scope?: ScopeKey): ToolSchema[]` Schemas of everything the scope can see (without the `execute` functions). The shipped tools' schemas are catalogued in [docs/tool-catalog.md](../../../docs/tool-catalog.md), generated by booting each tool plugin and harvesting this method (see [the tool-schema-catalog RFC](../../../docs/rfc/implemented/process/2026-07-02-tool-schema-catalog.md)).
+- `ctx.tools.schemas(scope?: ScopeKey): ToolSchema[]` Schemas of everything the scope can see (without the `execute` functions). The shipped tools' schemas are catalogued in [docs/tool-catalog.md](../../../docs/tool-catalog.md), generated by booting each tool plugin and harvesting this method (see [the tool-schema-catalog Agent Note](../../../.agents/notes/implemented/process/2026-07-02-tool-schema-catalog.md)).
 - `ctx.tools.guard(guard: ToolGuard): () => void` Register a monotonic synchronous execution guard after `tools/pre-execute`: returning a reason denies the call, while `undefined` leaves it unchanged. A plain-context guard applies globally; an `agent.ctx` guard applies only to that agent. Later waterfall listeners cannot turn a guard denial back into permission. Disposed with the calling fiber.
 - `ctx.tools.execute(exec)` losslessly snapshots and freezes arguments, assigns an opaque token, runs the complete policy/dispatch/result pipeline, then independently snapshots the authoritative outcome before final observation. Invalid arguments use the same result path without reaching policy or the body; around wrappers may replace only `signal`.
 - `ctx.tools.executionMode(exec)` returns `parallel` only when the visible definition's `isConcurrencySafe(exec.arguments)` classifier returns exactly `true`; unknown, hidden, undeclared, invalid, or throwing classifications are exclusive.
@@ -88,7 +88,7 @@ See `defineTool`, `validateArgs`, `ToolArgsError`, `SchemaSpec`, `InferArgs`, an
 
 Optional `timeoutMs` must be positive and finite; it is policy metadata, not model-visible schema.
 
-Optional `isConcurrencySafe(args)` receives typed, softly validated arguments. Exact `true` permits concurrent dispatch/body execution; invalid input and all other outcomes remain exclusive. Opted-in bodies do not mutate parent-owned state, and shared-state races must commute or fail closed. The [parallel tool-call RFC](../../../docs/rfc/implemented/feature/2026-07-10-parallel-tool-call-execution.md) owns the full safety contract.
+Optional `isConcurrencySafe(args)` receives typed, softly validated arguments. Exact `true` permits concurrent dispatch/body execution; invalid input and all other outcomes remain exclusive. Opted-in bodies do not mutate parent-owned state, and shared-state races must commute or fail closed. The [parallel tool-call Agent Note](../../../.agents/notes/implemented/feature/2026-07-10-parallel-tool-call-execution.md) owns the full safety contract.
 
 ### Structured-output schema subset
 
@@ -101,11 +101,11 @@ Tools optionally own pure `presentCall()` and `presentResult()` render intents,
 - Call views are `{ card: 'generic', title, kind?, rawInput?, content?, locations? }`, `{ card: 'terminal', title, description?, cwd? }`, or `{ card: 'diff', title, diffs, locations? }`.
 - Result views are `{ card: 'generic', title?, content? }`, `{ card: 'terminal', title?, output?, exitCode?, signal? }`, or `{ card: 'diff', title?, diffs }`.
 
-Returning `undefined` selects generic fallback. Presenters depend only on their arguments because UIs call them during live streaming and log replay. Result presentation may read JSON-serializable `result.meta`, which persists with the result; `defineTool` soft-validates older logged arguments and falls back instead of crashing replay. `dsh-tool-bash` and `dsh-tool-fs` are the reference implementations; the [render-intent RFC](../../../docs/rfc/implemented/architecture/2026-07-02-tool-render-intent-union.md) owns the rationale.
+Returning `undefined` selects generic fallback. Presenters depend only on their arguments because UIs call them during live streaming and log replay. Result presentation may read JSON-serializable `result.meta`, which persists with the result; `defineTool` soft-validates older logged arguments and falls back instead of crashing replay. `dsh-tool-bash` and `dsh-tool-fs` are the reference implementations; the [render-intent Agent Note](../../../.agents/notes/implemented/architecture/2026-07-02-tool-render-intent-union.md) owns the rationale.
 
 ### Code Mode
 
-Under `code` or `both`, the registry exposes the reserved `run_code` transport and a deterministic TypeScript SDK for the current scope; only program output re-enters model context. Each JSON-normalized binding re-enters the complete tool pipeline sequentially with logged correlation to the outer call. Denials reject that binding, ordinary side effects are not rolled back, and sub-call `additionalContexts` are deferred through the parent result to preserve call/result adjacency. Run settlement aborts and drains outstanding bindings; failures surface as `CodeRunFailedError`. See the [Code Mode RFC](../../../docs/rfc/implemented/feature/2026-06-15-code-mode.md) and [code-runtime seam](../../code-runtime/README.md). Try `pnpm run demo:code-mode`.
+Under `code` or `both`, the registry exposes the reserved `run_code` transport and a deterministic TypeScript SDK for the current scope; only program output re-enters model context. Each JSON-normalized binding re-enters the complete tool pipeline sequentially with logged correlation to the outer call. Denials reject that binding, ordinary side effects are not rolled back, and sub-call `additionalContexts` are deferred through the parent result to preserve call/result adjacency. Run settlement aborts and drains outstanding bindings; failures surface as `CodeRunFailedError`. See the [Code Mode Agent Note](../../../.agents/notes/implemented/feature/2026-06-15-code-mode.md) and [code-runtime seam](../../code-runtime/README.md). Try `pnpm run demo:code-mode`.
 
 - **The SDK section** (`tools:sdk`, order 150): a lazy prompt section regenerating, at each assembly, a `declare const tools: {...}` TypeScript declaration of the calling scope's visible end capabilities (exotic names via quoted keys), plus fixed usage instructions. Deterministic — lexicographic tool order, byte-identical text for an unchanged tool set (prefix-cache-friendly). The codegen (`jsonSchemaToTs`, exported) is total: constructs outside the `defineTool` subset degrade to `unknown`, never throw.
 - **The dispatch bridge** (`run_code`'s execute): every binding call is JSON-normalized before dispatch (a value that does not survive — `BigInt`, circulars — rejects that one call, so the dispatched form and logged form are the same JSON value by construction), serialized through a per-run queue (even `Promise.all` executes underlying calls one at a time in submission order), given the outer execution's opaque token as `parent`, and run through the complete pre-execute → guards → execute → post-execute → result pipeline. A denial reaches the program as a binding rejection, and each sub-call is logged as a `tool/code-dispatch` session event with deterministic id `<parent>:code:<n>`; `deriveMessages()` does not surface that event. Token correlation lets commit-style observers defer an inner success until the final `run_code` result without exposing the live outer execution; ordinary tool side effects are not rolled back. Every sub-call `additionalContexts` entry is deferred through the outer `ToolRunContext` in dispatch order; the loop appends those contexts only after the parent `run_code` result, preserving adjacency and retaining each source/envelope/meta even when the program later fails.
@@ -113,7 +113,7 @@ Under `code` or `both`, the registry exposes the reserved `run_code` transport a
 
 ### Parallel execution
 
-The agent loop groups consecutive `parallel` calls into a bounded rolling pool and treats each `exclusive` call as an ordering barrier. Only dispatch/body overlaps; policy, durable results, and context retain model order. Code Mode bindings remain serial. The [parallel tool-call RFC](../../../docs/rfc/implemented/feature/2026-07-10-parallel-tool-call-execution.md) owns the shipped declarations and rationale.
+The agent loop groups consecutive `parallel` calls into a bounded rolling pool and treats each `exclusive` call as an ordering barrier. Only dispatch/body overlaps; policy, durable results, and context retain model order. Code Mode bindings remain serial. The [parallel tool-call Agent Note](../../../.agents/notes/implemented/feature/2026-07-10-parallel-tool-call-execution.md) owns the shipped declarations and rationale.
 
 ## Model Experience
 
@@ -177,9 +177,9 @@ Append-only; newly visible content follows the reusable request prefix and does
 ## Known Limitations and Deferred Work
 
 - **Concurrency policy is not an event seam** — `executionMode()` reads the resolved tool definition directly; plugins can only declare a classifier on definitions they own.
-- **`tools/pre-execute` deliberately cannot rewrite `exec.arguments`** — logged and rendered args would desync from what ran; the rewrite design is [a proposed RFC](../../../docs/rfc/proposed/feature/2026-06-30-pre-tool-input-rewrite.md).
+- **`tools/pre-execute` deliberately cannot rewrite `exec.arguments`** — logged and rendered args would desync from what ran; the rewrite design is [a proposed Agent Note](../../../.agents/notes/proposed/feature/2026-06-30-pre-tool-input-rewrite.md).
 - **`defineTool`'s schema DSL is a deliberate subset** — string/number/boolean/object/array with string-only `enum`; `validateArgs` tolerates extra keys and preserves `default` as a model-visible JSON Schema annotation without applying it during validation; dynamic Cordis mounts may supply defaults even though first-party definitions do not, while raw-registered JSON-Schema tools validate their own input.
 - **`timeoutMs` on a definition is declarative only** — the registry never enforces deadlines; enforcement requires the `@deepseek-ai/dsh-timeout-policy` wrapper.
 - **Code Mode is TypeScript-only and the presentation mode is service-wide** — `mode: code`/`both` rejects prompt assembly unless `ctx.codeRuntime.language === 'typescript'`; scoped restrictions/shadows still choose each agent's visible bindings, but one tool cannot be native-only while another is code-only.
 - **Code Mode bindings return text only** — non-text content blocks in a sub-call result collapse to `[<type> content]` placeholders.
-- **`run_code` state is fresh per run** — a persistent REPL-style kernel is rejected for the MVP (cross-call state would be invisible to the log); see [the Code Mode RFC](../../../docs/rfc/implemented/feature/2026-06-15-code-mode.md).
+- **`run_code` state is fresh per run** — a persistent REPL-style kernel is rejected for the MVP (cross-call state would be invisible to the log); see [the Code Mode Agent Note](../../../.agents/notes/implemented/feature/2026-06-15-code-mode.md).

packages/core/tools/src/index.ts

@@ -139,7 +139,7 @@ export interface ToolDefinition extends ToolSchema {
    * Opted-in executions must not mutate parent-owned state. Shared state must
    * tolerate concurrent dispatch; recorder races are permitted only when they
    * commute or fail closed. See the
-   * [parallel-tool-call RFC](../../../../docs/rfc/implemented/feature/2026-07-10-parallel-tool-call-execution.md)
+   * [parallel-tool-call Agent Note](../../../../.agents/notes/implemented/feature/2026-07-10-parallel-tool-call-execution.md)
    * for the full contract.
    * @param args - parsed arguments; `defineTool` validates before calling.
    * @returns Whether this call may join a parallel group.

packages/core/tools/src/ts-types.ts

@@ -75,7 +75,7 @@ export function jsonSchemaToTs(schema: unknown, indent = 0): string {
   }
 }
 
-/** The fixed model-facing usage contract rendered above the declarations (see the Code Mode RFC's "What the model sees"). */
+/** The fixed model-facing usage contract rendered above the declarations (see the Code Mode Agent Note's "What the model sees"). */
 const SDK_INSTRUCTIONS = `## Writing code for run_code
 
 Pass \`run_code\` the body of an async TypeScript function (erasable syntax only — no \`enum\` or namespaces; type annotations are advisory, the code runs type-stripped). Inside the program:

packages/core/tools/tests/code-mode.spec.ts

@@ -13,7 +13,7 @@ import { Session, SessionId } from '@deepseek-ai/dsh-session'
 import type { SessionEventMap } from '@deepseek-ai/dsh-session'
 
 /**
- * Code Mode unit tier (per the RFC's plan): provider contribution per mode,
+ * Code Mode unit tier (per the Agent Note's plan): provider contribution per mode,
  * misconfiguration rejections, the run_code dispatch bridge (serialization,
  * abort, JSON normalization, error mapping, events, quiescence), and HMR
  * safety — all against an in-repo fake runtime, exactly the

packages/core/tools/tests/properties.spec.ts

@@ -1,8 +1,8 @@
 /**
- * Property-based tests for the tool-schema DSL (the property-testing RFC), including
+ * Property-based tests for the tool-schema DSL (the property-testing Agent Note), including
  * the the property-testing ↔ runtime-validation composition composition: generated args that satisfy a SchemaSpec must
  * pass validateArgs, and targeted corruptions must be rejected. This closes the
- * validator/InferArgs drift risk noted in the arg-validation RFC.
+ * validator/InferArgs drift risk noted in the arg-validation Agent Note.
  */
 
 import { describe, expect, it } from 'vitest'

packages/core/tools/tests/tools.spec.ts

@@ -1174,7 +1174,7 @@ describe('ToolRegistry.get', () => {
   })
 })
 
-describe('validateArgs (the runtime-validation RFC, part 1)', () => {
+describe('validateArgs (the runtime-validation Agent Note, part 1)', () => {
   it('returns [] for valid args and is total over malformed input', () => {
     const spec = {
       path: { type: 'string', required: true },
@@ -1274,7 +1274,7 @@ describe('validateArgs (the runtime-validation RFC, part 1)', () => {
   })
 })
 
-describe('defineTool validation (the runtime-validation RFC, part 1)', () => {
+describe('defineTool validation (the runtime-validation Agent Note, part 1)', () => {
   it('returns an isError result with the violations when the model sends bad args', async () => {
     const ctx = await setup()
     ctx.tools.register(defineTool({