Merge remote-tracking branch 'origin/master' into codex/project-instruction-files

# Conflicts:
#	AGENTS.md
#	docs/config-catalog.md
#	docs/cordis-catalog/events.md
#	docs/cordis-catalog/services.md
#	docs/core-data-structures/core.md
#	docs/event-producer-consumer.md
#	docs/persistence-catalog.md
#	docs/rfc/implemented/architecture/2026-07-05-reconstructable-requests.md
#	docs/rfc/implemented/feature/2026-06-15-code-mode.md
#	docs/rfc/implemented/feature/2026-06-30-hook-bridges.md
#	docs/rfc/implemented/feature/2026-06-30-interception-seams.md
#	docs/rfc/implemented/feature/2026-07-08-repeat-tool-guard.md
#	docs/rfc/proposed/simplification/2026-07-04-prune-dead-core-spine-surface.md
#	examples/AGENTS.md
#	examples/acp-agent/cordis.yml
#	examples/acp-agent/tests/acp.snapshot.ts
#	examples/echo-agent/cordis.yml
#	examples/sandbox-acp-agent/cordis.yml
#	packages/cordis/tool-cordis/src/api-catalog.ts
#	packages/core/agent-core/README.md
#	packages/core/agent-core/src/index.ts
#	packages/core/agent-loop/README.md
#	packages/core/agent-loop/src/loop.ts
#	packages/core/agent-loop/tests/interception.spec.ts
#	packages/core/agent/src/types.ts
#	packages/core/tools/README.md
#	packages/core/tools/src/code-mode.ts
#	packages/core/tools/src/index.ts
#	packages/fs/fs-local/src/index.ts
#	packages/fs/fs/README.md
#	packages/fs/fs/src/index.ts
#	packages/guard/repeat-tool-guard/README.md
#	packages/guard/repeat-tool-guard/src/index.ts
#	packages/hooks/hooks-claude/src/index.ts
#	packages/hooks/hooks-codex/src/index.ts
#	packages/ui/acp-agent/src/index.ts

docs/tool-execution-pipeline.md

@@ -48,6 +48,6 @@ flowchart TD
   allResults --> context
 ```
 
-Filesystem read-before-edit checks live below `tool-fs` on the `fs/*` event gate; hook bridges and approval-triggering permission policy enter through the generic pre/post tool waterfalls, while `ctx.approval` resolves an `ask` before the monotonic guards; owner policy that must not be reordered uses registered guards; and around-dispatch concerns like the tool-call timeout policy (`@deepseek-ai/dsh-timeout-policy`) wrap core dispatch on `tools/execute`. The synchronous `tools/result` notification observes the immutable final outcome after every transform, lossless-JSON validation, and outer error normalization. That split lets the same hooks observe bash, fs, web, todo, skill, and subagent calls without coupling those tools to one policy service. Code Mode rides the whole pipeline twice over: `run_code` is the reserved registry-owned transport whose body enters the pipeline, and each tool call its program makes re-enters `ctx.tools.execute()` — serialized one at a time, carrying the outer execution's opaque token for correlation, and logged as a `tool/code-dispatch` session event, with a deny surfacing to the program as a binding rejection (a sub-call's `additionalContext` is deliberately dropped — no safe outlet mid-run preserves call/result adjacency).
+Filesystem read-before-edit checks stay below `tool-fs` on `fs/*` events. Generic pre/post waterfalls host hooks and approval policy; `ctx.approval` resolves asks before monotonic guards, and owner policy that must not be reordered remains a registered guard. Around-dispatch concerns such as timeouts wrap `tools/execute`, while `tools/result` observes the immutable outcome after transforms, lossless-JSON validation, and outer error normalization. This lets hooks span tool families without coupling the tools to one policy service. Code Mode sends both the reserved `run_code` transport and its serialized sub-calls through the pipeline; sub-calls carry the parent token, log `tool/code-dispatch`, surface denials as binding rejections, and omit `additionalContext` to preserve call/result adjacency.
 
 Maintenance mode: curated Mermaid flow; exact tool schemas and event signatures live in generated catalogs.