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.

scripts/gen-tool-catalog.ts

@@ -141,7 +141,7 @@ const TOOL_PACKAGES: ToolPackage[] = [
     toolsConfig: { mode: 'code' },
     async mount() {},
     note:
-      '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.',
   },
   {
     pkg: '@deepseek-ai/dsh-mode',