Merge origin/master into skill system branch

Resolve documentation split, tool presentation, and generated catalog changes from master while preserving the skill system integration.

examples/echo-agent/composition.md

@@ -0,0 +1,40 @@
+<!-- Generated by scripts/gen-doc-graphs.ts - do not edit by hand.
+     Run `pnpm run gen-doc-graphs` to regenerate. -->
+
+# Echo Agent App Composition
+
+The echo demo swaps in a local mock LLM and teaching echo tool, then loads the stdio app package for the shared spine and terminal front door.
+
+```mermaid
+flowchart LR
+  cfg["examples/echo-agent<br/>cordis.yml"]
+  plugin_echo_hmr["hmr<br/>@cordisjs/plugin-hmr"]
+  cfg --> plugin_echo_hmr
+  plugin_echo_mock_llm["mock-llm<br/>./src/mock-llm.ts"]
+  cfg --> plugin_echo_mock_llm
+  plugin_echo_echo_tool["echo-tool<br/>./src/echo-tool.ts"]
+  cfg --> plugin_echo_echo_tool
+  plugin_echo_bash["bash<br/>@deepseek-ai/dsh-bash-local"]
+  cfg --> plugin_echo_bash
+  plugin_echo_stdio_agent["stdio-agent<br/>@deepseek-ai/dsh-stdio-agent"]
+  cfg --> plugin_echo_stdio_agent
+  plugin_echo_stdio_agent --> bundle_agent_core["@deepseek-ai/dsh-agent-core"]
+  plugin_echo_stdio_agent --> bundle_jsonl["@deepseek-ai/dsh-session-persistence-jsonl"]
+  plugin_echo_stdio_agent --> frontdoor_stdio["readline UI<br/>console logger<br/>pre-created main agent"]
+  bundle_agent_core --> spine_llm["ctx.llm"]
+  bundle_agent_core --> spine_sessions["ctx.sessions"]
+  bundle_agent_core --> spine_tools["ctx.tools + tool-bash"]
+  bundle_agent_core --> spine_loop["ctx.agents + ctx.agentLoop"]
+```
+
+| Plugin id | Package / module |
+| --- | --- |
+| `hmr` | `@cordisjs/plugin-hmr` |
+| `mock-llm` | `./src/mock-llm.ts` |
+| `echo-tool` | `./src/echo-tool.ts` |
+| `bash` | `@deepseek-ai/dsh-bash-local` |
+| `stdio-agent` | `@deepseek-ai/dsh-stdio-agent` |
+
+Source config: [`examples/echo-agent/cordis.yml`](cordis.yml).
+
+Maintenance mode: hybrid: the leaf plugin list is parsed from its `cordis.yml`; app package expansion is curated from package source.

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

@@ -13,11 +13,12 @@ import { afterEach, describe, expect, it } from 'vitest'
  *
  * This is the guard the per-file unit suite structurally cannot be: it drives
  * the `@deepseek-ai/dsh-stdio-agent` app plugin, the `@deepseek-ai/dsh-agent-core`
- * bundle it loads, the extracted `@deepseek-ai/dsh-ui-stdio` plugin, AND the
- * example-local `mock-llm.ts` / `echo-tool.ts` through their REAL load path, so
- * a broken plugin export shape (a stray `export default` that `unwrapExports`
- * would collapse, dropping `inject`/`Config`) fails here even though hand-mounted
- * unit tests stay green (see docs/postmortem/0001). It needs no API key — the
+ * bundle it loads, the app's in-package readline UI module, AND the
+ * example-local `mock-llm.ts` / `echo-tool.ts` through their REAL load path
+ * (see docs/postmortem/0001). The app itself carries no `inject`, so a stray
+ * `export default` would boot rather than crash here — the export SHAPE is
+ * pinned by the explicit unwrap assertion in the stdio-agent unit suite; this
+ * smoke proves the composed tree actually runs. It needs no API key — the
  * `mock-echo` adapter never touches the network — so it runs in the default e2e
  * gate.
  *