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/unmount-hmr.spec.ts

@@ -0,0 +1,84 @@
+import { afterEach, describe, expect, it, vi } from 'vitest'
+import { Context } from 'cordis'
+import SystemPrompt from '@deepseek-ai/dsh-system-prompt'
+import ToolRegistry from '@deepseek-ai/dsh-tools'
+import * as tool from '../src/index.ts'
+import { call, dummyTool, LISTENER_CODE, REVERSE_TOOL_CODE, setup, text } from './helpers.ts'
+
+/**
+ * Disposal semantics: `cordis_unmount` reaches quiescence before returning,
+ * and disposing the tool-cordis fiber itself (the HMR path) cascades over the
+ * whole dynamic subtree through the ordinary parent→child fiber lifecycle.
+ */
+
+afterEach(() => {
+  vi.restoreAllMocks()
+})
+
+describe('cordis_unmount', () => {
+  it('disposes the mount and its registrations have stopped by the time it returns (quiescence)', async () => {
+    const ctx = await setup()
+    const log = vi.spyOn(console, 'log').mockImplementation(() => {})
+    await call(ctx, 'cordis_mount', { code: LISTENER_CODE })
+
+    ctx.tools.register(dummyTool('trigger_before'))
+    expect(log).toHaveBeenCalledTimes(1)
+
+    const result = await call(ctx, 'cordis_unmount', { id: 'dyn-1' })
+    expect(result.isError).toBe(false)
+    if (result.isError) throw new Error('expected cordis_unmount success')
+    expect(result.value).toEqual({ id: 'dyn-1', pluginName: 'change-logger' })
+    expect(text(result)).toBe('Temporary Plugin dyn-1 was unmounted and removed.')
+
+    // Immediately after the awaited unmount, the listener must be gone — no
+    // grace period, no eventual consistency.
+    ctx.tools.register(dummyTool('trigger_after'))
+    expect(log).toHaveBeenCalledTimes(1)
+    expect(text(await call(ctx, 'cordis_inspect', { what: 'temporary' }))).toContain('No temporary Plugins are running.')
+  })
+
+  it('unregisters a self-made tool on unmount', async () => {
+    const ctx = await setup()
+    await call(ctx, 'cordis_mount', { code: REVERSE_TOOL_CODE })
+    expect(ctx.tools.get('reverse_text')).toBeDefined()
+
+    await call(ctx, 'cordis_unmount', { id: 'dyn-1' })
+    expect(ctx.tools.get('reverse_text')).toBeUndefined()
+  })
+
+  it('rejects an unknown id, and a second unmount of the same id', async () => {
+    const ctx = await setup()
+    const unknown = await call(ctx, 'cordis_unmount', { id: 'dyn-99' })
+    expect(unknown.isError).toBe(true)
+    expect(text(unknown)).toContain('no temporary Plugin with id "dyn-99"')
+
+    await call(ctx, 'cordis_mount', { code: LISTENER_CODE })
+    await call(ctx, 'cordis_unmount', { id: 'dyn-1' })
+    const again = await call(ctx, 'cordis_unmount', { id: 'dyn-1' })
+    expect(again.isError).toBe(true)
+  })
+})
+
+describe('HMR safety', () => {
+  it('disposing the tool-cordis fiber cascades over the dynamic subtree and its registrations', async () => {
+    const ctx = new Context()
+    await ctx.plugin(SystemPrompt)
+    await ctx.plugin(ToolRegistry)
+    const fiber = await ctx.plugin(tool)
+
+    const log = vi.spyOn(console, 'log').mockImplementation(() => {})
+    await call(ctx, 'cordis_mount', { code: LISTENER_CODE })
+    await call(ctx, 'cordis_mount', { code: REVERSE_TOOL_CODE })
+    expect(ctx.tools.get('reverse_text')).toBeDefined()
+
+    await fiber.dispose()
+
+    // The whole subtree is gone: the self-made tool, the cordis tools, and the
+    // mounted listener (no log on a fresh tools/change).
+    expect(ctx.tools.get('reverse_text')).toBeUndefined()
+    expect(ctx.tools.get('cordis_mount')).toBeUndefined()
+    const calls = log.mock.calls.length
+    ctx.tools.register(dummyTool('trigger_post_dispose'))
+    expect(log).toHaveBeenCalledTimes(calls)
+  })
+})