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

examples/acp-agent/code-mode.cordis.yml

@@ -1,12 +1,8 @@
-# Code Mode overlay: the live acp-agent tree (./cordis.yml) with two
-# load-time patches — the app entry's config gains `tools: { mode: code }`
-# (the registry offers exactly one wire tool, run_code, plus the generated
-# TypeScript SDK prompt section) and the worker-thread code runtime joins the
-# tree as `ctx.codeRuntime`. The dsh-acp-agent bin boots this file for
-# `pnpm run demo:code-mode acp` and when the snapshot harness records the
-# code-mode scenarios; DSH_SNAPSHOT=replay swaps it for the sibling
-# code-mode.cordis.snapshot.yml. A config patch REPLACES the entry's whole
-# config, so the base entry's fields are restated verbatim.
+# Code Mode adds `ctx.codeRuntime` and changes the registry to one wire tool,
+# `run_code`, plus its generated TypeScript SDK prompt. The app bin selects this
+# overlay for `demo:code-mode acp` and snapshot recording, and selects the sibling
+# replay overlay for `DSH_SNAPSHOT=replay`. A config patch replaces the whole app
+# config, so unchanged base fields are restated below.
 - id: base
   name: '@cordisjs/plugin-include'
   config: