Merge remote-tracking branch 'origin/master' into codex/rfc-subagent-background-tasks

# Conflicts:
#	docs/architecture.md
#	docs/config-catalog.md
#	docs/cordis-catalog/events.md
#	docs/cordis-catalog/services.md
#	docs/event-producer-consumer.md
#	docs/module-graph.md
#	docs/tool-catalog.md
#	packages/bash/tool-bash/tests/integration.spec.ts
#	packages/bash/tool-bash/tests/tools.spec.ts
#	packages/core/agent-core/tests/agent-core.spec.ts
#	packages/core/agent-loop/README.md
#	packages/core/agent-loop/src/index.ts
#	packages/core/agent/README.md
#	packages/core/agent/src/index.ts
#	packages/core/agent/tests/agent.spec.ts
#	packages/subagent/subagent/README.md
#	packages/subagent/subagent/src/index.ts
#	packages/subagent/tool-subagent/README.md
#	packages/subagent/tool-subagent/src/index.ts
#	pnpm-lock.yaml
#	scripts/doc-budgets.manifest.json

examples/coding-agent/README.md

@@ -33,7 +33,7 @@ The id is wired through `cordis.yml` (`resumeSessionId: !!js process.env.RESUME_
 
 ## Code Mode
 
-[`code-mode.cordis.yml`](code-mode.cordis.yml) is this same tree flipped to [Code Mode](../../docs/rfc/implemented/feature/2026-06-15-code-mode.md): an include overlay over `./cordis.yml` whose two patches insert the worker-thread code runtime (`@deepseek-ai/dsh-code-runtime-worker`, registering `ctx.codeRuntime`) and set `tools: { mode: code }` on the app. The model is then offered exactly ONE wire tool — `run_code` — plus a generated TypeScript SDK section declaring every other registered tool; it composes them by writing a program, each program tool call bridges back through the ordinary `tools/pre-execute`/`post-execute` pipeline one at a time and is logged as a `tool/code-dispatch` session event, and ONLY what the program prints or returns re-enters its context. (Flip the mode to `both` to offer native calls AND `run_code` side by side.)
+[`code-mode.cordis.yml`](code-mode.cordis.yml) is this same tree flipped to [Code Mode](../../docs/rfc/implemented/feature/2026-06-15-code-mode.md): an include overlay over `./cordis.yml` whose two patches insert the worker-thread code runtime (`@deepseek-ai/dsh-code-runtime-worker`, registering `ctx.codeRuntime`) and set `tools: { mode: code }` on the app. The registry contributes exactly one reserved wire transport — `run_code` — plus a generated TypeScript SDK section declaring the visible end-capability tools. The model composes those capabilities by writing a program; each program call carries an immutable link to its enclosing transport, bridges back through pre-policy, monotonic guards, around dispatch, post-policy, and final-result observation one at a time, and is logged as a `tool/code-dispatch` session event. Only what the program prints or returns re-enters model context. (Flip the mode to `both` to offer native calls and `run_code` side by side.)
 
 ```sh
 pnpm run demo:code-mode        # this overlay under the REPL (default UI)

examples/coding-agent/tests/code-mode-keyless-smoke.e2e.ts

@@ -26,6 +26,14 @@ const tsxLoader = fileURLToPath(import.meta.resolve('tsx'))
 // `paths` map; tsx searches UP from cwd, and we spawn from a temp dir outside
 // the repo, so point it at the repo tsconfig.
 const repoTsconfig = fileURLToPath(new URL('../../../tsconfig.json', import.meta.url))
+// The real-API workflow runs up to 14 e2e files at once. Cold tsx/Loader
+// startup can therefore outlive a tight smoke-test deadline before the child
+// emits any output; 30s still detects a wedged process without confusing
+// bounded CI contention with a lifecycle failure.
+const PROCESS_TIMEOUT_MS = 30_000
+// Leave enough room for the process-owned timeout to report captured output
+// before Vitest aborts the test itself.
+const TEST_TIMEOUT_MS = PROCESS_TIMEOUT_MS + 15_000
 
 let child: ChildProcessWithoutNullStreams | undefined
 let workdir: string | undefined
@@ -67,8 +75,8 @@ async function bootAndEof(): Promise<{ stdout: string; code: number }> {
 
     const timer = setTimeout(() => {
       proc.kill('SIGKILL')
-      reject(new Error(`code-mode overlay did not exit within 30s. stdout:\n${stdout}\nstderr:\n${stderr}`))
-    }, 30_000)
+      reject(new Error(`code-mode overlay did not exit within ${PROCESS_TIMEOUT_MS / 1_000}s. stdout:\n${stdout}\nstderr:\n${stderr}`))
+    }, PROCESS_TIMEOUT_MS)
 
     proc.on('exit', (code) => {
       clearTimeout(timer)
@@ -87,5 +95,5 @@ describe('code-mode overlay keyless smoke (real code-mode.cordis.yml via the Loa
     const { stdout, code } = await bootAndEof()
     expect(code).toBe(0)
     expect(stdout).toContain('code-mode agent ready.')
-  }, 45_000)
+  }, TEST_TIMEOUT_MS)
 })

examples/coding-agent/tests/keyless-smoke.e2e.ts

@@ -35,6 +35,14 @@ const tsxLoader = fileURLToPath(import.meta.resolve('tsx'))
 // `paths` map; tsx searches UP from cwd, and we spawn from a temp dir outside
 // the repo, so point it at the repo tsconfig (root is four levels up).
 const repoTsconfig = fileURLToPath(new URL('../../../tsconfig.json', import.meta.url))
+// The real-API workflow runs up to 14 e2e files at once. Cold tsx/Loader
+// startup can therefore outlive a tight smoke-test deadline before the child
+// emits any output; 30s still detects a wedged process without confusing
+// bounded CI contention with a lifecycle failure.
+const PROCESS_TIMEOUT_MS = 30_000
+// Leave enough room for the process-owned timeout to report captured output
+// before Vitest aborts the test itself.
+const TEST_TIMEOUT_MS = PROCESS_TIMEOUT_MS + 15_000
 
 let child: ChildProcessWithoutNullStreams | undefined
 let workdir: string | undefined
@@ -78,8 +86,8 @@ async function bootAndEof(): Promise<{ stdout: string; code: number }> {
 
     const timer = setTimeout(() => {
       proc.kill('SIGKILL')
-      reject(new Error(`coding-agent did not exit within 30s. stdout:\n${stdout}\nstderr:\n${stderr}`))
-    }, 30_000)
+      reject(new Error(`coding-agent did not exit within ${PROCESS_TIMEOUT_MS / 1_000}s. stdout:\n${stdout}\nstderr:\n${stderr}`))
+    }, PROCESS_TIMEOUT_MS)
 
     proc.on('exit', (code) => {
       clearTimeout(timer)
@@ -98,5 +106,5 @@ describe('coding-agent keyless smoke (real cordis.yml via the Loader)', () => {
     const { stdout, code } = await bootAndEof()
     expect(code).toBe(0)
     expect(stdout).toContain('agent REPL ready.')
-  }, 45_000)
+  }, TEST_TIMEOUT_MS)
 })

examples/coding-agent/tests/resume.e2e.ts

@@ -39,11 +39,11 @@ describe.skipIf(!process.env.DEEPSEEK_API_KEY)('resume: continue a persisted ses
     // dispose the whole context (simulating process exit) so only the JSONL
     // log on disk survives.
     ctx = await codingHarness(process.cwd(), { persona: SYSTEM_PROMPT, persistenceRoot: root })
-    const first = ctx.agents.create({
+    const first = (await ctx.agents.create({
       agentId: AgentId('resume-1'),
       sessionId: SESSION_ID,
       agentOptions: { model: 'deepseek-v4-flash' },
-    }).agent as ReactLoopAgent
+    })).agent as ReactLoopAgent
     first.send([{ type: 'text', text: `Remember this code for later: ${SECRET}. Just acknowledge it.` }])
     await waitForIdle(ctx, first)
     await ctx.fiber.dispose()