Merge origin/master: scope-aware fusion of the tools/execute seam, session-prefix, and tool-cordis

Master brought 50 commits (the tool-cordis group, dsh-code-runtime + worker,
the tools/execute around-dispatch seam + timeout-policy, repeat-tool-guard,
agent/session-prefix, the ui reorganization). Beyond the ten textual
conflicts, the merge reconciles master's new seams with this branch's
scoped-registration world:

- tools/execute (new waterfall around core dispatch): dispatched with the
  SAME exec.agent carrier as the pre/post waterfalls — an agent.ctx wrapper
  times/retries only its own agent's calls — and its base thunk resolves the
  tool through the caller's visible view (get(exec.name, exec.agent)), so a
  scoped/shadowed tool dispatches and a restricted-away global stays
  UNKNOWN_TOOL. Declared this: Scoped<ToolRegistry> with the scope-filtered
  doc sentence; invariants table + verify-scoped-dispatch pin it (21 events).
- agent/session-prefix (new waterfall, once per loop instance): composed via
  the fused agentEvents dispatcher (scope-filtered like every agent-subject
  event), declared this: Scoped<Agent>, table-pinned. agent/pre-step keeps
  master's new sessionPrefix parameter with this branch's Scoped this.
- timeout-policy reads the budget through the caller's visible view
  (get(exec.name, exec.agent)): a scoped tool's own timeoutMs governs its
  calls; a global name-twin's budget is never misapplied to a shadowing
  per-agent variant.
- tool-cordis: cordis_inspect's tools section lists the CALLING agent's view
  (its description promises "what you can call"); the sandbox tool façade's
  reads resolve through the mount's own scope, mirroring where its register
  lands writes; sandboxRegisterTool's return type carries the exact-disposer
  union honestly. dsh-scope declared as peer+dev with the project reference.
- doc-sync chain unions master's verify-cordis-api with this branch's
  verify-scoped-dispatch; the generated catalogs, event matrix (the
  zero-dispatcher guard passes over master's new events), module graph, and
  the cordis api-catalog are regenerated on the merged surface.

Full gate sequence green on the merged tree: typecheck, lint, per-file 100%
coverage (2668 tests), snapshots (38), doc-sync, module graph, build,
hygiene, demo smoke.

scripts/gen-doc-graphs.ts

@@ -75,6 +75,7 @@ const GROUP_ORDER = [
   'subagent',
   'web',
   'todo',
+  'cordis',
   'hooks',
   'session-persistence',
   'support',
@@ -121,9 +122,18 @@ const SERVICE_ROLES: ServiceRole[] = [
     pkg: 'tools',
     title: 'Tool registry and execution waterfall',
     mode: 'core',
-    consumers: ['agent-loop', 'tool-bash', 'tool-fs', 'tool-subagent', 'tool-todo', 'tool-web', 'acp'],
+    consumers: ['agent-loop', 'tool-ask-user', 'tool-bash', 'tool-cordis', 'tool-fs', 'tool-subagent', 'tool-todo', 'tool-web', 'acp'],
     note: 'Registers tool definitions, exposes schemas to the prompt, and routes calls through tools/pre-execute and tools/post-execute.',
   },
+  {
+    key: 'userInteraction',
+    pkg: 'user-interaction',
+    title: 'Human question/answer seam',
+    mode: 'seam',
+    implementations: ['stdio-agent', 'acp'],
+    consumers: ['tool-ask-user', 'stdio-agent', 'acp'],
+    note: 'UI front doors provide the active human-answer provider; tool-ask-user pauses a tool call on the provider-neutral ask() promise.',
+  },
   {
     key: 'agents',
     pkg: 'agent',
@@ -154,7 +164,7 @@ const SERVICE_ROLES: ServiceRole[] = [
     pkg: 'code-runtime',
     title: 'Code-execution seam',
     mode: 'seam',
-    implementations: [],
+    implementations: ['code-runtime-worker'],
     consumers: [],
     note: 'Runs one model-written program against host-provided async bindings; backends differ by substrate and language (the Code Mode RFC specifies the worker-thread backend and the tool-registry consumer).',
   },
@@ -413,6 +423,14 @@ const APP_EXAMPLES = [
     config: 'examples/coding-agent/cordis.yml',
     summary: 'The coding REPL demo adds the real DeepSeek adapter, filesystem tools, todo_write, compaction, and both subagent transports on top of the stdio app package.',
   },
+  {
+    id: 'cordis',
+    rel: 'examples/cordis-agent/composition.md',
+    title: 'Cordis Agent App Composition',
+    label: 'examples/cordis-agent',
+    config: 'examples/cordis-agent/cordis.yml',
+    summary: 'The self-referential demo puts @deepseek-ai/dsh-tool-cordis on the coding spine, letting the agent inspect its own runtime and mount/unmount plugins into it.',
+  },
   {
     id: 'acp',
     rel: 'examples/acp-agent/composition.md',
@@ -670,7 +688,7 @@ function renderToolPipeline(): string {
   const maintenance = 'curated Mermaid flow; exact tool schemas and event signatures live in generated catalogs'
   return [
     ...generatedHeader('Tool Execution Pipeline'),
-    'This graph shows where policy, hooks, sandboxing, filesystem guards, result rewriting, and UI rendering fit without changing the loop. The key extension points are the `tools/pre-execute` and `tools/post-execute` waterfalls.',
+    'This graph shows where policy, hooks, sandboxing, filesystem guards, result rewriting, and UI rendering fit without changing the loop. The key extension points are the `tools/pre-execute`, `tools/execute`, and `tools/post-execute` waterfalls.',
     '',
     '```mermaid',
     'flowchart TD',
@@ -679,6 +697,7 @@ function renderToolPipeline(): string {
     '  presentCall["UI pending card<br/>presentCall(args)"]',
     `  pre["${mermaidCode('tools/pre-execute')} waterfall<br/>hooks, permission, sandbox"]`,
     '  denied["deny or ask<br/>tool body skipped"]',
+    `  around["${mermaidCode('tools/execute')} waterfall<br/>timeout, retry, metrics (around dispatch)"]`,
     '  toolBody["Registered tool execute() body"]',
     `  fsGate["${mermaidCode('fs/write-intent')} or ${mermaidCode('fs/edit-intent')}<br/>tool-fs mutations only"]`,
     `  owned["Tool-owned session events<br/>${mermaidCode('todo/write')}, ${mermaidCode('fs/observed')}, ${mermaidCode('hook/invoked')}, ${mermaidCode('hook/result')}"]`,
@@ -689,19 +708,21 @@ function renderToolPipeline(): string {
     '  model --> toolCall',
     '  toolCall --> presentCall',
     '  toolCall --> pre',
-    '  pre -->|allow| toolBody',
+    '  pre -->|allow| around',
+    '  around --> toolBody',
     '  pre -->|deny or ask| denied',
     '  denied --> post',
     '  toolBody --> fsGate',
     '  fsGate --> toolBody',
     '  toolBody --> owned',
-    '  toolBody --> post',
+    '  toolBody --> around',
+    '  around --> post',
     '  post --> context',
     '  post --> toolResult',
     '  toolResult --> presentResult',
     '```',
     '',
-    'Filesystem read-before-edit checks live below `tool-fs` on the `fs/*` event gate, while hook bridges and future permission prompts live on the generic tool waterfalls. That split lets the same hooks observe bash, fs, web, todo, and subagent calls without coupling those tools to one policy service.',
+    'Filesystem read-before-edit checks live below `tool-fs` on the `fs/*` event gate; hook bridges and future permission prompts live on the generic pre/post tool waterfalls; and around-dispatch concerns like the tool-call timeout policy (`@deepseek-ai/dsh-timeout-policy`) wrap core dispatch on `tools/execute`. That split lets the same hooks observe bash, fs, web, todo, and subagent calls without coupling those tools to one policy service.',
     '',
     ...maintenanceFooter(maintenance),
   ].join('\n')
@@ -755,6 +776,7 @@ function renderIndex(docs: GraphDoc[]): string {
     'docs/capability-seams.md': 'capability seams and core services',
     'examples/echo-agent/composition.md': 'echo-agent app composition',
     'examples/coding-agent/composition.md': 'coding-agent app composition',
+    'examples/cordis-agent/composition.md': 'cordis-agent app composition',
     'examples/acp-agent/composition.md': 'acp-agent app composition',
     'docs/event-producer-consumer.md': 'event producer/consumer matrix',
     'docs/agent-lifecycle.md': 'agent turn and step lifecycle',
@@ -765,6 +787,7 @@ function renderIndex(docs: GraphDoc[]): string {
     'docs/capability-seams.md': 'hybrid generated',
     'examples/echo-agent/composition.md': 'hybrid generated',
     'examples/coding-agent/composition.md': 'hybrid generated',
+    'examples/cordis-agent/composition.md': 'hybrid generated',
     'examples/acp-agent/composition.md': 'hybrid generated',
     'docs/event-producer-consumer.md': 'hybrid generated',
     'docs/agent-lifecycle.md': 'curated',