Merge codex/commands into codex/goal-commands

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 It awaits the unpublished setup transaction before returning; `meta` carries cwd/lineage/seed-boundary metadata and `seed` reconstructs a forked child prefix after the session boundary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register the agent under that same id, reconstruct its history, then await setup against a fresh unpublished agent scope before rollback-covered publication.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register the agent under that same id, reconstruct its history, then await setup against a fresh unpublished agent scope before rollback-covered publication.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)