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.

.agents/notes/implemented/simplification/2026-07-29-shared-base-config-overlays.i18n.yaml

@@ -2,5 +2,5 @@
 # side as of the last confirmed-consistent state. Both languages carry equal authority;
 # after editing either side, bring the other along and re-record with:
 #   pnpm run verify-translation-pairing --write .agents/notes/implemented/simplification/2026-07-29-shared-base-config-overlays.md
-2026-07-29-shared-base-config-overlays.md: 9fae9775e0b37acc99ce2eb5fc630e6f4f52bf1d
-2026-07-29-shared-base-config-overlays.zh.md: 20cc3e522c369315a1fafc84778fced0260581d0
+2026-07-29-shared-base-config-overlays.md: b2ca5cc8d3a160dd09550827d5f8148c14048ea4
+2026-07-29-shared-base-config-overlays.zh.md: e14aa87bdd6ed3bd711bb9786220b5baf0566e8e

.agents/notes/implemented/simplification/2026-07-29-shared-base-config-overlays.md

@@ -24,7 +24,7 @@ Precedence is list order, last write winning per row: base, then the surface ove
 
 A patch replaces its target row's whole `config` rather than merging, which shapes the split: a row whose value differs per surface lives in the overlays, never in the base, so no row is patched by three layers at once. Session identity therefore cannot ride a config key at all — it moved to `dsh-agent-loop`'s `CONFIGURED_AGENT_IDENTITIES_KEY`, as the launcher-owned identity record documented.
 
-`examples/tui-agent`, `examples/cordis-agent`, `examples/code-mode`, and `packages/examples/tui-demo` are deleted. The TUI tests move to `apps/cli/tests/`, the cordis-toolset e2e to `packages/cordis/tool-cordis/tests/`, and the supported Code Mode demo remains the ACP overlay at `examples/acp-agent/code-mode.cordis.yml`.
+`examples/tui-agent`, `examples/cordis-agent`, `examples/code-mode`, and `packages/examples/tui-demo` are deleted. The TUI tests move to `apps/cli/tests/`, the cordis-toolset e2e to `packages/self-modification/tool-cordis/tests/`, and the supported Code Mode demo remains the ACP overlay at `examples/acp-agent/code-mode.cordis.yml`.
 
 ## Alternatives considered
 
@@ -48,6 +48,6 @@ A patch whose `id` matches no row stays a no-op rather than an error. That is de
 
 Composition is checked by booting each tree through the real Loader and inspecting settled entries, not by reading YAML; both surfaces settle with zero unloaded rows, and Web starts its `httpServer` with sandboxed Bash and filesystem providers. Code Mode remains covered by the ACP overlay and programmatic TUI snapshots rather than a separate shipped TUI application.
 
-All eight terminal snapshot scenarios replay byte-identically after moving, and the 14-case PTY smoke passes, including two cases that assert a personal overlay reaches an **inserted** row — the behavior the vendored `plugin-include` fix enables ([`vendor/README.md`](../../../../vendor/README.md) local modification 8, covered by `packages/ui/app-boot/tests/config-reload.spec.ts`).
+All eight terminal snapshot scenarios replay byte-identically after moving, and the 14-case PTY smoke passes, including two cases that assert a personal overlay reaches an **inserted** row — the behavior the vendored `plugin-include` fix enables ([`vendor/README.md`](../../../../vendor/README.md) local modification 8, covered by `packages/boot/app-boot/tests/config-reload.spec.ts`).
 
 Flattening surfaced three latent defects, each fixed here: the TUI captured the optional `sessionQuery` service once at construction and so could permanently disable `/resume` when it won the mount race; the shipped session-store root silently reverted to a project-local `./.sessions`; and `--config-replace` was dropped by the resume handoff.

.agents/notes/implemented/simplification/2026-07-29-shared-base-config-overlays.zh.md

@@ -24,7 +24,7 @@ Status: implemented
 
 patch 会整体替换目标配置项的 `config` 而不合并，这决定了拆分方式：取值因 surface 而异的配置项住在 overlay 中，绝不住在 base 里，从而没有任何配置项会被三层同时 patch。因此会话身份根本不能经由配置键传递——它迁移到了 `dsh-agent-loop` 的 `CONFIGURED_AGENT_IDENTITIES_KEY`，正如启动器持有身份的记录所述。
 
-`examples/tui-agent`、`examples/cordis-agent`、`examples/code-mode` 与 `packages/examples/tui-demo` 均被删除。TUI 测试迁往 `apps/cli/tests/`，cordis 工具集的 e2e 迁入 `packages/cordis/tool-cordis/tests/`，受支持的 Code Mode demo 则保留为 `examples/acp-agent/code-mode.cordis.yml` 中的 ACP overlay。
+`examples/tui-agent`、`examples/cordis-agent`、`examples/code-mode` 与 `packages/examples/tui-demo` 均被删除。TUI 测试迁往 `apps/cli/tests/`，cordis 工具集的 e2e 迁入 `packages/self-modification/tool-cordis/tests/`，受支持的 Code Mode demo 则保留为 `examples/acp-agent/code-mode.cordis.yml` 中的 ACP overlay。
 
 ## 备选方案
 
@@ -48,6 +48,6 @@ patch 会整体替换目标配置项的 `config` 而不合并，这决定了拆
 
 组合的正确性通过用真实 Loader 启动每棵树并检查已就绪的条目来核对，而不是靠阅读 YAML：两个界面都能稳定完成且没有未加载项；Web 会以沙箱化 Bash 与文件系统提供方启动 `httpServer`。Code Mode 继续由 ACP overlay 与程序化 TUI 快照覆盖，而不再维护独立交付的 TUI 应用。
 
-全部八个终端快照场景在迁移后逐字节重放一致，14 个用例的 PTY 冒烟测试全部通过，其中两个用例断言个人 overlay 能触达一个 **insert 进来的**配置项——这正是 vendored `plugin-include` 修复所启用的行为（[`vendor/README.md`](../../../../vendor/README.md) 本地修改第 8 条，由 `packages/ui/app-boot/tests/config-reload.spec.ts` 覆盖）。
+全部八个终端快照场景在迁移后逐字节重放一致，14 个用例的 PTY 冒烟测试全部通过，其中两个用例断言个人 overlay 能触达一个 **insert 进来的**配置项——这正是 vendored `plugin-include` 修复所启用的行为（[`vendor/README.md`](../../../../vendor/README.md) 本地修改第 8 条，由 `packages/boot/app-boot/tests/config-reload.spec.ts` 覆盖）。
 
 平铺过程暴露出三处潜伏缺陷，均在此一并修复：TUI 曾在构造时一次性捕获可选的 `sessionQuery` 服务，因此在挂载竞争中胜出时会永久禁用 `/resume`；交付的会话存储根目录曾静默退回项目本地的 `./.sessions`；`--config-replace` 曾在 resume 交接中被丢弃。