Merge remote-tracking branch 'origin/master' into codex/project-instruction-files

# Conflicts:
#	docs/config-catalog.md
#	docs/cordis-catalog/events.md
#	docs/cordis-catalog/services.md
#	docs/core-data-structures/core.md
#	docs/event-producer-consumer.md
#	docs/persistence-catalog.md
#	docs/rfc/implemented/feature/2026-06-15-code-mode.md
#	docs/rfc/implemented/feature/2026-06-30-interception-seams.md
#	docs/rfc/proposed/simplification/2026-07-04-prune-dead-core-spine-surface.md
#	docs/tool-execution-pipeline.md
#	packages/cordis/tool-cordis/src/api-catalog.ts
#	packages/core/agent-core/tests/agent-core.spec.ts
#	packages/core/agent-loop/src/agent.ts
#	packages/core/agent/README.md
#	packages/core/session/src/index.ts
#	packages/core/tools/README.md
#	packages/core/tools/src/index.ts
#	pnpm-lock.yaml
#	scripts/gen-doc-graphs.ts
#	scripts/type-equiv.manifest.json

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/code-mode.e2e.ts

@@ -140,7 +140,7 @@ describe.skipIf(!process.env.DEEPSEEK_API_KEY)('Code Mode: real model writes a p
     await writeFile(join(workdir, 'pkg/AGENTS.md'), `If asked for the Code Mode workspace handshake, reply with exactly ${WORKSPACE_PROBE} and nothing else.\n`)
     await writeFile(join(workdir, 'pkg/deep/task.txt'), 'Touch this file to discover the nested instructions.\n')
     ctx = await workspaceCodeModeHarness()
-    const handle = ctx.agents.create({
+    const handle = await ctx.agents.create({
       agentId: AgentId('e2e-code-mode-workspace'),
       sessionId: SessionId('e2e-code-mode-workspace-session'),
       meta: { cwd: workdir },

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()