fix: keep stdio targeting on runtime roots

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

@@ -229,7 +229,7 @@ class AgentCreationTransaction {
     this.publishing = true
     try {
       this.detachSession = agent.ctx.sessions.enter(session)
-      this.detachAgent = this.loopCtx.agents.enter(agent)
+      this.detachAgent = this.loopCtx.agents.enter(agent, this.ownerAgent)
 
       agent.ctx.sessions.announce(session)
       this.assertActive()

packages/core/agent-loop/tests/scope-lifecycle.spec.ts

@@ -149,6 +149,24 @@ describe('agent scope lifecycle', () => {
     await ctx.agents.get(SessionId('a1'))?.whenIdle()
   })
 
+  it('records agents created through an agent context as non-root runtime children', async () => {
+    const ctx = await harness()
+    const root = await ctx.agents.create({
+      sessionId: SessionId('runtime-root'),
+      agentOptions: { model: 'mock' },
+    })
+    const child = await root.agent.ctx.agents.create({
+      sessionId: SessionId('runtime-child'),
+      agentOptions: { model: 'mock' },
+    })
+
+    expect(ctx.agents.list()).toEqual([root.agent, child.agent])
+    expect(ctx.agents.roots()).toEqual([root.agent])
+
+    await child.dispose()
+    await root.dispose()
+  })
+
   it('scoped registrations live in the agent world and die with the agent', async () => {
     const ctx = await harness()
     const handle = await ctx.agents.create({ sessionId: SessionId('s1'), agentOptions: { model: 'mock' } })

packages/core/agent/README.md

@@ -11,9 +11,10 @@ Tracks live agents so UI, hook, and orchestrator plugins can find them without i
 The scoped-registration surface: `Agent.ctx` is the agent's scope context (`dsh-scope`, key = the agent) — register tools/sections/variables/listeners through it for that agent alone, all unwound on disposal. `agentEvents(ctx, agent)` is the fused dispatcher for ordinary agent-subject operations (carrier + injected subject in one move); its notification mode invokes every listener and contains both synchronous throws and returned-promise rejections. The registry lifecycle pair reuses one stable routing carrier. `assembleContextFor(agent)` builds the per-agent assembly context (`agent` + `scope` together). `CreateAgentOptions.setup(agentCtx)` and `ResumeAgentOptions.setup(agentCtx)` compose a fresh or resumed agent's scoped world while both objects remain unpublished. Setup is trusted, composition-only same-process code: drive the agent only after creation resolves.
 
 - `ctx.agents.register(agent: Agent): () => void` — record an **already-constructed** agent. Disposed with the calling fiber.
-- Advanced ordered lifecycle: `enter(agent): () => void` performs the authoritative ID collision check and inserts without announcing; `announce(agent)` emits `agent/created` exactly once. A detach requested synchronously by a creation listener is deferred until that dispatch unwinds, and every detach checks the captured entry object, so a stale capability cannot delete a later same-ID replacement. The async factory uses this split; ordinary plugins use `register()`.
+- Advanced ordered lifecycle: `enter(agent, owner): () => void` performs the authoritative ID collision check and inserts without announcing; `owner` explicitly records the live creator-agent relation (or `undefined` for a root), independently of durable session lineage. `announce(agent)` emits `agent/created` exactly once. A detach requested synchronously by a creation listener is deferred until that dispatch unwinds, and every detach checks the captured entry object, so a stale capability cannot delete a later same-ID replacement. The async factory uses this split; ordinary plugins use `register()`.
 - `ctx.agents.get(id: SessionId): Agent | undefined`
 - `ctx.agents.list(): Agent[]`
+- `ctx.agents.roots(): Agent[]` — live agents created without an owning agent context; a resumed lineage-bearing session can still be a runtime root.
 
 #### Factory seam (creation)
 

packages/core/agent/src/index.ts

@@ -178,6 +178,8 @@ const NO_FACTORY_MESSAGE = 'no agent factory registered (load an agent-loop plug
 interface AgentEntry {
   readonly id: SessionId
   readonly agent: Agent
+  /** Runtime creator-agent ownership; independent of durable session lineage. */
+  readonly owner: Agent | undefined
   readonly carrier: Scoped<Agent>
   announced: boolean
   announcing: boolean
@@ -303,7 +305,7 @@ export class AgentRegistry extends Service {
    */
   register(agent: Agent): () => void {
     const dispose = this.ctx.effect(function* (this: AgentRegistry) {
-      yield this.enter(agent)
+      yield this.enter(agent, this.ctx.agent)
       this.announce(agent)
     }.bind(this), 'agents.register()')
     // eslint-disable-next-line @typescript-eslint/no-misused-promises -- synchronous cleanup; direct return preserves disposer identity
@@ -317,12 +319,15 @@ export class AgentRegistry extends Service {
    * returned detach closure into its pre-installed composite teardown before
    * calling {@link announce}. Ordinary callers use {@link register}.
    * @param agent - the prepared, unpublished agent.
+   * @param owner - live agent whose scoped context created this agent, or
+   *   undefined for a top-level runtime root. This is runtime ownership, not
+   *   the resumed session's durable parent lineage.
    * @returns an idempotent closure that removes this exact entry and emits
    *   `agent/disposed` with listener failures contained. When called from a
    *   synchronous `agent/created` listener, removal and disposal wait until
    *   that creation dispatch unwinds.
    */
-  enter(agent: Agent): () => void {
+  enter(agent: Agent, owner: Agent | undefined): () => void {
     const id = agent.id
     const carrier = scopeTarget(agent, agent)
     // This is the authoritative collision boundary. Concurrent create/resume
@@ -331,6 +336,7 @@ export class AgentRegistry extends Service {
     const entry: AgentEntry = {
       id,
       agent,
+      owner,
       carrier,
       announced: false,
       announcing: false,
@@ -438,6 +444,18 @@ export class AgentRegistry extends Service {
   list(): Agent[] {
     return [...this.store.values()].map(entry => entry.agent)
   }
+
+  /**
+   * All live top-level agents in registration order. A top-level agent was
+   * created without an owning agent context; durable session lineage does not
+   * affect this runtime relation, so a resumed fork may still be a root.
+   * @returns a fresh array; mutating it does not affect the registry.
+   */
+  roots(): Agent[] {
+    return [...this.store.values()]
+      .filter(entry => entry.owner === undefined)
+      .map(entry => entry.agent)
+  }
 }
 
 export default AgentRegistry

packages/core/agent/tests/agent.spec.ts

@@ -42,6 +42,7 @@ describe('AgentRegistry', () => {
     const dispose = ctx.agents.register(agent)
     expect(ctx.agents.get(agent.id)).toBe(agent)
     expect(ctx.agents.list()).toEqual([agent])
+    expect(ctx.agents.roots()).toEqual([agent])
     expect(() => ctx.agents.register(stubAgent('a1'))).toThrow(/already registered/)
 
     dispose()
@@ -49,6 +50,23 @@ describe('AgentRegistry', () => {
     expect(lifecycle).toEqual(['created:a1', 'disposed:a1'])
   })
 
+  it('tracks runtime creator ownership separately from registry order', async () => {
+    const ctx = new Context()
+    await ctx.plugin(AgentRegistry)
+    const root = stubAgent('root')
+    const child = stubAgent('child')
+    const detachRoot = ctx.agents.enter(root, undefined)
+    ctx.agents.announce(root)
+    const detachChild = ctx.agents.enter(child, root)
+    ctx.agents.announce(child)
+
+    expect(ctx.agents.list()).toEqual([root, child])
+    expect(ctx.agents.roots()).toEqual([root])
+
+    detachChild()
+    detachRoot()
+  })
+
   it('rolls an entry back and pairs a partially delivered creation when a listener throws', async () => {
     const ctx = new Context()
     await ctx.plugin(AgentRegistry)
@@ -94,7 +112,7 @@ describe('AgentRegistry', () => {
     ctx.on('agent/disposed', agent => void lifecycle.push(`disposed:${agent.id}`))
 
     const first = stubAgent('split')
-    const detachFirst = ctx.agents.enter(first)
+    const detachFirst = ctx.agents.enter(first, undefined)
     expect(lifecycle).toEqual([])
     ctx.agents.announce(first)
     expect(() => { ctx.agents.announce(first) }).toThrow(/already announced/)
@@ -102,7 +120,7 @@ describe('AgentRegistry', () => {
     detachFirst()
 
     const replacement = stubAgent('split')
-    const detachReplacement = ctx.agents.enter(replacement)
+    const detachReplacement = ctx.agents.enter(replacement, undefined)
     detachFirst()
     expect(ctx.agents.get(replacement.id)).toBe(replacement)
     expect(() => { ctx.agents.announce(first) }).toThrow(/not live/)
@@ -122,7 +140,7 @@ describe('AgentRegistry', () => {
     })
     ctx.on('agent/created', () => void order.push(`second:${ctx.agents.get(agent.id) === agent}`))
     ctx.on('agent/disposed', () => void order.push('disposed'))
-    const detach = ctx.agents.enter(agent)
+    const detach = ctx.agents.enter(agent, undefined)
     ctx.agents.announce(agent)
     expect(order).toEqual(['first:true', 'after-detach:true', 'second:true', 'disposed'])
     expect(ctx.agents.get(agent.id)).toBeUndefined()