Merge origin/master (agent-scope runtime #224, session-query, run-gates CI harness)

Conflict resolution beyond line merges: the ACP bridge's mode/set
re-notify moved inside master's new containment finally (a throwing
presenter must not desync the picker), and session/new keeps the modes
advertisement beside master's plain object return. dsh-mode's boundary
flush moved off the session/event feed onto the loop's interception
seams (agent/prompt-submit / agent/turn-continuation): master's scoped
dispatch made post-commit session observers observe-only — an append
from one re-enters the publishing append — while the two waterfalls
fire outside any log emit and bracket the same boundaries; mode.spec's
boundary helper now dispatches those seams via agentEvents, and the
containment tests stub only the mode/set append. Catalogs, doc graphs,
and the module graph regenerated.

docs/tool-catalog.md

@@ -16,7 +16,7 @@ This table connects model-visible tool names to the plugin package and service s
 | Tool package | Model-visible names | Requires | Writes / affects | Shipped aliases | Deployment note |
 | --- | --- | --- | --- | --- | --- |
 | `@deepseek-ai/dsh-tool-ask-user` | `ask_user_question` | `ctx.tools`, `ctx.userInteraction` | `tool/call`, `tool/result after a UI/provider answers the question` | - | ask_user_question pauses the tool call until the active UI provider returns a human answer. |
-| `@deepseek-ai/dsh-tools` | `run_code` | `ctx.tools`, `ctx.codeRuntime (execution time)`, `ctx.systemPrompt` | `tool/call`, `one tool/code-dispatch per bridged sub-call`, `tool/result` | - | Registered by the tool registry itself under `mode: code` / `mode: both` (see the Code Mode RFC). Under `code` it is the ONLY wire tool; the other registered tools are declared to the model as a generated TypeScript SDK prompt section instead, and a program calls them through port-bridged bindings that dispatch through the ordinary tools/pre-execute → tools/post-execute pipeline, one at a time. |
+| `@deepseek-ai/dsh-tools` | `run_code` | `ctx.tools`, `ctx.codeRuntime (execution time)`, `ctx.systemPrompt` | `tool/call`, `one tool/code-dispatch per bridged sub-call`, `tool/result` | - | Owned by the tool registry as a reserved transport outside filterable capability layers under `mode: code` / `mode: both` (see the Code Mode RFC). Under `code` it is the registry's only wire contribution; the other visible capabilities are declared in a generated TypeScript SDK section, and a program calls them through serialized bindings that re-enter the complete guarded tool pipeline and link each nested execution to this outer result. |
 | `@deepseek-ai/dsh-mode` | `exit_plan_mode` | `ctx.tools`, `ctx.systemPrompt`, `ctx.userInteraction (execution time, opportunistic)` | `tool/call`, `mode/set back to default on an approved review`, `tool/result` | - | exit_plan_mode presents the plan for the user's review over the user-interaction seam (approve / keep planning with feedback); approval flips the logged session mode back to default at the step boundary (same-batch calls stay plan-gated). The assemble filter shows it only while the folded mode is plan. |
 | `@deepseek-ai/dsh-tool-bash` | `bash`, `bash_kill`, `bash_output` | `ctx.tools`, `ctx.bash` | `tool/call`, `tool/result`, `context/message via agent.inject() for background completion notices` | - | The bash/bash_output/bash_kill tools are model-facing consumers of the bash executor seam. |
 | `@deepseek-ai/dsh-tool-cordis` | `cordis_inspect`, `cordis_mount`, `cordis_unmount` | `ctx.tools` | `tool/call`, `tool/result`, `live plugin-tree mutations (mount/unmount)` | - | Ships in examples/cordis-agent only (a deliberate opt-in — mounted code gets the real ctx, see docs/rfc/implemented/feature/2026-07-08-self-referential-cordis-toolset.md). Plugins the model mounts may register ADDITIONAL model-visible tools at runtime; the request-header ToolsDelta logs those tool-set changes. |
@@ -120,7 +120,7 @@ Execute a TypeScript program against the available tools. Write the BODY of an a
 
 Source: [`packages/core/tools/src/code-mode.ts`](../packages/core/tools/src/code-mode.ts)
 
-Registered by the tool registry itself under `mode: code` / `mode: both` (see the Code Mode RFC). Under `code` it is the ONLY wire tool; the other registered tools are declared to the model as a generated TypeScript SDK prompt section instead, and a program calls them through port-bridged bindings that dispatch through the ordinary tools/pre-execute → tools/post-execute pipeline, one at a time.
+Owned by the tool registry as a reserved transport outside filterable capability layers under `mode: code` / `mode: both` (see the Code Mode RFC). Under `code` it is the registry's only wire contribution; the other visible capabilities are declared in a generated TypeScript SDK section, and a program calls them through serialized bindings that re-enter the complete guarded tool pipeline and link each nested execution to this outer result.
 
 ## `@deepseek-ai/dsh-mode`