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/echo-agent/tests/echo.e2e.ts

@@ -37,6 +37,14 @@ const tsxLoader = fileURLToPath(import.meta.resolve('tsx'))
 // a temp cwd OUTSIDE the repo, so point tsx at the repo tsconfig explicitly
 // (repo root is four levels up from examples/echo-agent/tests).
 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
@@ -51,7 +59,7 @@ afterEach(async () => {
 /**
  * Boot echo-agent, write `lines` to its stdin, close stdin, and resolve with
  * the full stdout once the process exits (the stdio UI exits on EOF after the
- * agent settles). Rejects on a non-zero exit or a 30s timeout.
+ * agent settles). Rejects on a non-zero exit or the process deadline.
  */
 async function runEcho(lines: string[]): Promise<{ stdout: string; code: number }> {
   workdir = await mkdtemp(join(tmpdir(), 'echo-smoke-'))
@@ -84,8 +92,8 @@ async function runEcho(lines: string[]): Promise<{ stdout: string; code: number
 
     const timer = setTimeout(() => {
       proc.kill('SIGKILL')
-      reject(new Error(`echo-agent did not exit within 30s. stdout:\n${stdout}\nstderr:\n${stderr}`))
-    }, 30_000)
+      reject(new Error(`echo-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)
@@ -105,19 +113,19 @@ describe('echo-agent keyless smoke (real cordis.yml via the Loader)', () => {
     const { stdout, code } = await runEcho([])
     expect(code).toBe(0)
     expect(stdout).toContain('echo-agent ready.')
-  }, 45_000)
+  }, TEST_TIMEOUT_MS)
 
   it('runs the echo tool round-trip for an "echo …" line', async () => {
     const { stdout } = await runEcho(['echo hello world'])
     // mock-llm.ts emits a tool-call for the echo tool; echo-tool.ts uppercases.
     expect(stdout).toContain('[tool call] echo')
     expect(stdout).toContain('[tool result] ECHO: HELLO WORLD')
-  }, 45_000)
+  }, TEST_TIMEOUT_MS)
 
   it('streams a direct canned reply for a non-echo line', async () => {
     const { stdout } = await runEcho(['just chatting'])
     // The direct-response branch of mock-llm.ts quotes the input back.
     expect(stdout).toContain('just chatting')
     expect(stdout).not.toContain('[tool call]')
-  }, 45_000)
+  }, TEST_TIMEOUT_MS)
 })