fix: retire leftovers of the removed $DSH_HOME/config.yaml personal overlay

The profile rework left references to the old entry modes behind. Renames
the user patch-layer API and its spec file (watchPersonalPatches ->
watchUserPatches, personal-config.spec.ts -> user-patches.spec.ts) and
retargets the prose that still named `config.yaml`, `--config`, raw-config
mode, and surface overlays: repository-plugin and mcp-memory READMEs, the
credentials-local anchor into app-boot, vendor manifest items 12-13, the
vendored include/hmr comments, and install.sh.

Restores the boot-failure guard the rework dropped with raw mode: the
built-bin case now boots `--profile web --patch <invalid>` and asserts the
settled diagnostic and exit 1, so the HMR initial-scan deadlock stays
covered; its orphaned raw fixture is renamed and the unused one deleted.
The superseded personal-config Agent Note and its superseding profile note
are now cross-linked.

packages/cordis/repository-plugin/README.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 packages/cordis/repository-plugin/README.md
-README.md: 2555876734ddcab7b0bc0f25780010bef0c97a01
-README.zh.md: 41341f7d7ed92ac071dde274a0328784bc2888d4
+README.md: 33cd763d7dbe21b72f9e604b7b2e313081cf656f
+README.zh.md: 903dfbe601cc76acb0c1e87453dc03ef0321409b

packages/cordis/repository-plugin/README.md

@@ -30,7 +30,7 @@ Place an ordinary package in the repository's `.dsh-plugin` directory:
 
 ## Standalone app configuration
 
-The shipped `dsh` base used by raw-config, Web, and headless modes contains an empty `repository-plugins` row. A Web or headless user enables exact GitHub generations by replacing that row's config in `$DSH_HOME/config.yaml` (default `~/.dsh/config.yaml`); a raw-config deployment patches the same row in its explicit overlay:
+The shipped `dsh-base` bundle every profile starts from contains an empty `repository-plugins` row. A user enables exact GitHub generations by replacing that row's config in a user patch layer — `$DSH_HOME/profiles/<name>/cordis.patch.yml`, or the home-level `$DSH_HOME/cordis.patch.yml` shared by every profile; a `--patch` overlay patches the same row for one run:
 
 ```yaml
 - id: repository-plugins
@@ -43,7 +43,7 @@ The shipped `dsh` base used by raw-config, Web, and headless modes contains an e
 
 Each source must use `github:owner/repository#<ref>`. Omitting `&path:` selects `/.dsh-plugin`; an explicit path is absolute within the repository and must end in `.dsh-plugin`. A commit ref gives the clearest immutable identity, while tags and branches remain accepted exact config values. `cacheDir` may override the default `$DSH_HOME/cache/repository-plugins` cache root.
 
-Web watches `config.yaml` through Cordis HMR. A valid source-list change installs and swaps the complete repository Plugin generation; a failed fetch, prepare, import, or Plugin application keeps the last good tree and broadcasts `hmr/config-update-failed(filename, error)`. Headless reads the file only at startup, and raw-config mode reads only its explicit overlay. An identical source string permanently reuses its prepared cache entry, so selecting changed code requires a ref, path, or other source-config change. App integration rationale: [config-only repository Plugins Agent Note](../../../.agents/notes/implemented/feature/2026-07-30-config-only-repository-plugins.md).
+Long-lived surfaces watch both `cordis.patch.yml` layers through Cordis HMR. A valid source-list change installs and swaps the complete repository Plugin generation; a failed fetch, prepare, import, or Plugin application keeps the last good tree and broadcasts `hmr/config-update-failed(filename, error)`. One-shot runs read the layers only at startup, and a `--patch` overlay is never watched. An identical source string permanently reuses its prepared cache entry, so selecting changed code requires a ref, path, or other source-config change. App integration rationale: [config-only repository Plugins Agent Note](../../../.agents/notes/implemented/feature/2026-07-30-config-only-repository-plugins.md).
 
 ## Preparation
 

packages/cordis/repository-plugin/README.zh.md

@@ -30,7 +30,7 @@
 
 ## 独立应用配置
 
-随附 `dsh` 中供原始配置、Web 与无头模式使用的基础配置包含一个空 `repository-plugins` 配置项。Web 或无头用户可在 `$DSH_HOME/config.yaml`（默认 `~/.dsh/config.yaml`）中替换该配置项的配置，以启用精确指定的 GitHub generation；原始配置部署则在显式 overlay 中 patch 同一配置项：
+每个 profile 都以之为起点的随附 `dsh-base` 组合包包含一个空 `repository-plugins` 配置项。用户可在用户 patch 层中替换该配置项的配置来启用精确指定的 GitHub generation：写入 `$DSH_HOME/profiles/<name>/cordis.patch.yml`，或写入各 profile 共享的 home 级 `$DSH_HOME/cordis.patch.yml`；`--patch` overlay 则只为单次运行 patch 同一配置项：
 
 ```yaml
 - id: repository-plugins
@@ -43,7 +43,7 @@
 
 每个源都必须采用 `github:owner/repository#<ref>`。省略 `&path:` 时选择 `/.dsh-plugin`；显式路径是仓库内的绝对路径，并且必须以 `.dsh-plugin` 结尾。commit ref 提供最清晰的不可变身份；tag 和 branch 仍可作为精确配置值使用。`cacheDir` 可覆盖默认缓存根 `$DSH_HOME/cache/repository-plugins`。
 
-Web 通过 Cordis HMR（热模块替换）监视 `config.yaml`。有效的源列表变更会安装并替换整套 repository Plugin generation；拉取、准备、导入或插件应用失败时，最后一个可用树保持运行，并广播 `hmr/config-update-failed(filename, error)`。无头模式只在启动时读取该文件，原始配置模式只读取其显式 overlay。相同的源字符串会永久复用其已准备缓存条目，因此必须改变 ref、路径或其他源配置，才能选择发生变化的代码。应用集成依据见[仅凭配置接入 repository Plugin 的 Agent Note](../../../.agents/notes/implemented/feature/2026-07-30-config-only-repository-plugins.md)。
+长期运行的 surface 通过 Cordis HMR（热模块替换）监视两个 `cordis.patch.yml` 层。有效的源列表变更会安装并替换整套 repository Plugin generation；拉取、准备、导入或插件应用失败时，最后一个可用树保持运行，并广播 `hmr/config-update-failed(filename, error)`。一次性运行只在启动时读取这些层，`--patch` overlay 则从不被监视。相同的源字符串会永久复用其已准备缓存条目，因此必须改变 ref、路径或其他源配置，才能选择发生变化的代码。应用集成依据见[仅凭配置接入 repository Plugin 的 Agent Note](../../../.agents/notes/implemented/feature/2026-07-30-config-only-repository-plugins.md)。
 
 ## 准备阶段