refactor(packages): merge timeout/ into guard/, rename cordis/ to self-modification/

git mv timeout-policy beside repeat-tool-guard (both are loop-hygiene
policies on the tool-execution pipeline, and the timeout/ group name
collided with util/timeout) and tool-cordis into self-modification/
(naming the role the framework name obscured). Merged/renamed group
README triplets, tsconfig globs, generator sources, hierarchy tables,
catalogs, and the timeout-policy design note's group references
follow. Adds the fifth FIXME marker (dsh-timeout-guard, recorded as a
suggestion to settle at resolution time).

guard + self-modification suites: 197 passed.

packages/self-modification/tool-cordis/tests/integration.spec.ts

@@ -0,0 +1,101 @@
+import { describe, expect, it } from 'vitest'
+import { Context } from 'cordis'
+import { createUserMessage, CallId  } from '@deepseek-ai/dsh-llm'
+import { SessionId } from '@deepseek-ai/dsh-session'
+import type { Agent } from '@deepseek-ai/dsh-agent'
+import AgentLoop from '@deepseek-ai/dsh-agent-loop'
+import { mountAgentLoopTestDependencies } from '@deepseek-ai/dsh-agent-loop-testkit'
+import * as ToolCordis from '../src/index.ts'
+import { MockAdapter, textResponse, toolCallResponse } from '../../../core/agent-loop/tests/mock-adapter.ts'
+import { call, REVERSE_TOOL_CODE, setup, text } from './helpers.ts'
+
+/**
+ * Full-loop integration: a scripted mock model mounts a plugin that registers
+ * a NEW tool, calls that tool on the very next step (tool schemas are
+ * reassembled per step — the real loop proves the self-extension contract),
+ * and unmounts it again. Only the model is mocked; the sandbox, the fiber
+ * tree, and the session log are real.
+ */
+
+async function harness(adapter: MockAdapter): Promise<Context> {
+  const ctx = new Context()
+  await mountAgentLoopTestDependencies(ctx)
+  await ctx.plugin(AgentLoop, { agents: [] })
+  await ctx.plugin(ToolCordis)
+  ctx.llm.registerAdapter(['mock'], adapter)
+  return ctx
+}
+
+function waitForIdle(ctx: Context, agent: Agent): Promise<void> {
+  return new Promise((resolve) => {
+    const dispose = ctx.on('agent/status', ({ agent: subject, status }) => {
+      if (subject === agent && status === 'idle') {
+        dispose()
+        resolve()
+      }
+    })
+  })
+}
+
+describe('cordis tools through the agent loop', () => {
+  it('mounts a tool, calls it on the next step, and unmounts it — all as real tool/call events', async () => {
+    const adapter = new MockAdapter([
+      toolCallResponse('call-1', 'cordis_mount', { code: REVERSE_TOOL_CODE }, 'Extending myself.'),
+      toolCallResponse('call-2', 'reverse_text', { text: 'harness' }),
+      toolCallResponse('call-3', 'cordis_unmount', { id: 'dyn-1' }),
+      textResponse('Done.'),
+    ])
+    const ctx = await harness(adapter)
+    const agent = ctx.agentLoop.create(SessionId('it-cordis'), { provider: 'mock', model: 'mock' })
+
+    agent.followup(createUserMessage({ content: [{ type: 'text', text: 'give yourself reverse_text, use it, clean up' }], source: { kind: 'user' } }))
+    await waitForIdle(ctx, agent)
+
+    const log = agent.session.events
+    const calls = log.filter(event => event.type === 'tool/call').map(event => event.data.name)
+    expect(calls).toEqual(['cordis_mount', 'reverse_text', 'cordis_unmount'])
+
+    const results = log.filter(event => event.type === 'tool/result')
+    expect(results.map(event => event.data.message.content[0].isError)).toEqual([false, false, false])
+    const reversed = results[1]!.data.message.content[0].content
+      .filter(block => block.type === 'text')
+      .map(block => block.text)
+      .join('')
+    expect(reversed).toBe('ssenrah')
+
+    // After the unmount the self-made tool is gone from the registry.
+    expect(ctx.tools.get('reverse_text')).toBeUndefined()
+  })
+
+  it('keeps a temporary Plugin across turns, unmounts it, and does not restore it in a new runtime', async () => {
+    const adapter = new MockAdapter([
+      toolCallResponse('mount-1', 'cordis_mount', { code: 'return { name: \'turn-marker\', apply() {} }' }),
+      toolCallResponse('inspect-1', 'cordis_inspect', { what: 'temporary' }),
+      textResponse('Turn one complete.'),
+      toolCallResponse('inspect-2', 'cordis_inspect', { what: 'temporary' }),
+      toolCallResponse('unmount-1', 'cordis_unmount', { id: 'dyn-1' }),
+      toolCallResponse('inspect-3', 'cordis_inspect', { what: 'temporary' }),
+      textResponse('Turn two complete.'),
+    ])
+    const ctx = await harness(adapter)
+    const agent = ctx.agentLoop.create(SessionId('it-cordis-turn-lifetime'), { provider: 'mock', model: 'mock' })
+
+    agent.followup(createUserMessage({ content: [{ type: 'text', text: 'Mount the marker and inspect it.' }], source: { kind: 'user' } }))
+    await waitForIdle(ctx, agent)
+    agent.followup(createUserMessage({ content: [{ type: 'text', text: 'On this later turn, inspect the marker, unmount it, then inspect again.' }], source: { kind: 'user' } }))
+    await waitForIdle(ctx, agent)
+
+    const resultText = new Map(
+      agent.session.events
+        .filter(event => event.type === 'tool/result')
+        .map(event => [event.data.message.source.callId, event.data.message.content[0].content.filter(block => block.type === 'text').map(block => block.text).join('')]),
+    )
+    expect(resultText.get(CallId('inspect-1'))).toContain('Temporary Plugin dyn-1: turn-marker [running]')
+    expect(resultText.get(CallId('inspect-2'))).toContain('Temporary Plugin dyn-1: turn-marker [running]')
+    expect(resultText.get(CallId('unmount-1'))).toBe('Temporary Plugin dyn-1 was unmounted and removed.')
+    expect(resultText.get(CallId('inspect-3'))).toContain('No temporary Plugins are running.')
+
+    const restarted = await setup()
+    expect(text(await call(restarted, 'cordis_inspect', { what: 'temporary' }))).toContain('No temporary Plugins are running.')
+  })
+})