Merge remote-tracking branch 'origin/master' into codex/agent-session-jsonl-location

# Conflicts:
#	docs/config-catalog.md
#	docs/cordis-catalog/services.md
#	docs/core-data-structures/bash.md
#	docs/module-graph.md
#	docs/rfc/INDEX.md
#	docs/rfc/implemented/architecture/2026-06-30-bash-stdin-env-trusted-plugin-surface.md
#	docs/rfc/implemented/feature/2026-06-30-hook-bridges.md
#	examples/acp-agent/tests/snapshots/advanced-toolchain/session.1.jsonl
#	examples/acp-agent/tests/snapshots/advanced-toolchain/session.2.jsonl
#	examples/acp-agent/tests/snapshots/advanced-toolchain/session.jsonl
#	examples/acp-agent/tests/snapshots/advanced-toolchain/system-prompt.golden.md
#	examples/acp-agent/tests/snapshots/both-mode-turn/session.jsonl
#	examples/acp-agent/tests/snapshots/both-mode-turn/system-prompt.golden.md
#	examples/acp-agent/tests/snapshots/code-mode-turn/system-prompt.golden.md
#	examples/acp-agent/tests/snapshots/skill-load/session.jsonl
#	examples/acp-agent/tests/snapshots/text-turn/session.jsonl
#	examples/sandbox-acp-agent/tests/snapshots/mode-switching/session.jsonl
#	packages/bash/bash-local/README.md
#	packages/bash/bash-local/src/run.ts
#	packages/bash/bash-local/tests/run.spec.ts
#	packages/bash/bash/README.md
#	packages/bash/tool-bash/README.md
#	packages/bash/tool-bash/src/index.ts
#	packages/bash/tool-bash/tests/tools.spec.ts
#	packages/cordis/tool-cordis/src/api-catalog.ts
#	packages/core/agent-core/src/index.ts
#	packages/session-persistence/session-persistence-jsonl/src/index.ts
#	packages/session-persistence/session-persistence-sqlite/src/index.ts
#	packages/session-persistence/session-persistence/README.md
#	packages/session-persistence/session-persistence/src/index.ts
#	packages/ui/acp-agent/README.md
#	packages/ui/stdio-agent/README.md

docs/rfc/implemented/architecture/2026-06-30-bash-stdin-env-trusted-plugin-surface.md

@@ -6,7 +6,7 @@ Status: implemented
 
 The hooks subsystem runs external hook commands the way Claude Code and Codex do: a hook is a shell command that receives its event payload as **JSON on stdin** and reads context from a handful of **environment variables** (`CLAUDE_PROJECT_DIR`, `CLAUDE_PLUGIN_ROOT`, `PLUGIN_ROOT`, …). The harness already has a perfectly good command runner behind the `ctx.bash` capability seam ([dsh-bash](../../../../packages/bash/bash) → [dsh-bash-local](../../../../packages/bash/bash-local)), with process-group kills, output truncation/spill, and a credential scrub. Reusing it for hook execution means a hook bridge does not re-implement subprocess plumbing — but the seam had no way to write stdin or set extra env. This RFC adds those two inputs.
 
-**These fields are NOT a new security boundary.** It is tempting to frame arbitrary-stdin / arbitrary-env as "dangerous, so gate who may use them" — but that framing is wrong, because a model driving the `bash` tool **already** has equivalent power through ordinary shell syntax: `FOO=bar cmd` sets an env var, a heredoc or `printf … | cmd` feeds arbitrary stdin. Adding `env`/`stdin` as seam fields grants the model no capability it lacks. In particular they cannot exfiltrate the harness's ambient credentials: the real control for that is the **credential scrub** in [dsh-bash-local](../../../../packages/bash/bash-local)'s `childEnv()`, which strips `*KEY*`/`*SECRET*`/`*TOKEN*` from `process.env` before the child sees it (see [docs/defensive-patterns.md](../../../defensive-patterns.md) § "Never hand untrusted output the ambient environment or predictable paths"). The scrub works regardless of these fields — a model cannot read a value that is not in the environment, and tool-call arguments are static JSON, never shell-evaluated, so a model cannot write `env: {LEAK: $DEEPSEEK_API_KEY}` and have it expand. So the security question is already answered by the scrub; this RFC is only about giving trusted in-process callers a clean way to pass a JSON payload + `CLAUDE_*` vars without routing them through model-visible shell text.
+`stdin` and `env` do not create a new model capability because ordinary shell syntax already supplies both. Ambient credentials are protected by `dsh-bash-local`'s child-environment scrub, not by hiding these seam fields; model tool arguments are static JSON and do not expand shell variables. The fields therefore serve trusted in-process callers, such as hook bridges, that need to pass structured input and `CLAUDE_*` variables without embedding them in model-visible shell text. See [defensive-patterns.md](../../../defensive-patterns.md) for the ambient-environment rule.
 
 ## Decision
 
@@ -14,18 +14,18 @@ Add `stdin?: string` and `env?: Record<string, string>` to **both** `BashExecReq
 
 Three deliberate choices:
 
-1. **The model-facing `bash` tool does NOT expose `stdin`/`env` as parameters** — not as a security wall, but because bash syntax already covers the model's needs, so duplicating them as tool params would be redundant surface. [dsh-tool-bash](../../../../packages/bash/tool-bash)'s `bash` tool builds its `BashExecRequest` from named schema fields; a model that includes `env`/`stdin` keys has them ignored. Harness-owned variables use the distinct `dshEnv` channel added by the [session environment decision](../feature/2026-07-10-agent-session-identity-and-log-location.md), so ordinary `env` cannot replace them. In-process plugins such as hook bridges construct requests directly and set ordinary `stdin`/`env`; the seam otherwise imposes no access policy.
+1. **The model-facing tool omits `stdin` and `env`.** Shell syntax already covers those needs, so duplicate parameters would add surface without authority separation. The tool builds requests only from declared model arguments, signal, and owner; trusted in-process callers may set the seam fields directly. Harness-owned variables use the separate `dshEnv` channel from the [managed environment decision](../feature/2026-07-10-agent-session-identity-and-log-location.md), so ordinary `env` cannot replace them.
 
 2. **`env` merges AFTER the credential scrub, so an explicit caller entry wins even on a credential-shaped name.** The later managed-namespace decision reserves `DSH_*`: ambient entries are removed, ordinary `env` cannot set them, and trusted `dshEnv` merges last. The complete order is `scrub(process.env, including DSH_*)` → `ENV_OVERRIDES` → ordinary `env` → `dshEnv`.
 
 3. **`stdin`/`env` are required-absent-OK (plain optional) on the resolved spec, NOT required-but-nullable like `owner`.** `owner` is required-but-nullable because a *silently* missing owner yields an unowned, cross-session-readable task — a security footgun that a visible `undefined` guards against. `stdin`/`env` have no such hazard: a missing one means "no stdin / no extra env", which is the safe, ordinary case (every model-driven call). So they stay plain optionals, matching `signal`.
 
-`dsh-bash-local` spawns stdin as a `'pipe'` (writing the supplied bytes, then closing) ONLY when a caller set `stdin`; with none supplied it uses `'ignore'` — fd 0 → `/dev/null` — the exact pre-seam default. This distinction is observable and deliberate: a closed empty pipe and `/dev/null` are NOT the same file type (node's spawn pipe is an `AF_UNIX` socket, so `test -c /dev/stdin` holds for `/dev/null` but not for an empty pipe), so the no-stdin path — every model-driven call — must keep `/dev/null` rather than regress to an always-open pipe. Each branch's `stdio` tuple is a literal, which preserves the typed `spawn` overload that guarantees non-null `stdout`/`stderr`. When stdin IS written, a child that exits without reading makes the write fail EPIPE; that error is swallowed (the command's outcome rides on its exit code/output, not the write) so it never crashes the host or rejects `done`.
+`dsh-bash-local` creates a stdin pipe only when bytes are supplied; otherwise fd 0 remains `/dev/null`, preserving prior behavior. It writes the bytes and closes the pipe. `EPIPE` from a child that exits without reading is ignored because command exit and output determine the result.
 
 ## Alternatives considered
 
-An earlier sketch of this work also proposed making `SENSITIVE_ENV_PATTERN` configurable. Validating against the code, that is **speculative and already subsumed**: `run.ts` documents a configurable whitelist as future work, and the new explicit `env` field — merged after the scrub — already gives a caller full control, including over credential-shaped vars. There is no current caller that needs to *broaden* the ambient scrub (the hazard runs the other way). Adding a config knob now would be a speculative surface with no consumer. If a real workflow ever needs to forward a specific ambient credential, the explicit `env` field is the supported path; a configurable scrub can be reconsidered then.
+**Configurable ambient-secret scrub.** Rejected as speculative. Trusted callers can explicitly provide required values after the scrub without weakening the default ambient protection.
 
 ## Consequences
 
-A hook bridge builds a `BashExecRequest` with the hook's JSON payload as `stdin` and its `CLAUDE_*`/`PLUGIN_ROOT` vars as `env`, and runs it through the same `ctx.bash` everything else uses — no bespoke subprocess code, and the full process-group-kill / truncation / spill machinery for free. The model-facing attack surface is unchanged (the credential scrub, not these fields, is what bounds it), and the `bash` tool's request-building stays the single place that decides which fields a model call carries — guarded by a test that fails if a refactor starts forwarding model input. The vocabulary addition is documented in [docs/core-data-structures/bash.md](../../../core-data-structures/bash.md) (the `type-equiv` request/spec blocks) and the three bash-package READMEs.
+Hook bridges pass JSON payloads and hook-specific variables through the existing bash seam, retaining its process-group, truncation, and spill behavior. The model surface remains unchanged, and the bash tool remains the sole owner of model-call request construction. The vocabulary lives in [the bash data-structure reference](../../../core-data-structures/bash.md).