docs: add tool_groups, limits, flake_check to CLAUDE.md file map

CLAUDE.md

@@ -81,7 +81,7 @@ hive-c0re/         host daemon + sibling operator CLI (lib + 2 bins)
                          fans out one Message per active target,
                          re-arms recurring rows, deletes fired one-shots
   src/events_vacuum.rs  host-side hourly sweep of every agent's
-                         /state/hyperhive-events.sqlite
+                         /harness/hyperhive-events.sqlite
   src/crash_watch.rs    poll every 10s; fire HelperEvent::ContainerCrash
                          when a previously-running container disappears
                          without an operator-initiated transient (or a
@@ -130,6 +130,17 @@ hive-c0re/         host daemon + sibling operator CLI (lib + 2 bins)
                          read). Reconciled by `meta::sync_agents`;
                          operator/manager edits land via the
                          eventual write API.
+  src/tool_groups.rs    per-agent tool-group config — reads/writes
+                         `/var/lib/hyperhive/meta/tool-groups.json`;
+                         `set_groups` + `groups_for` + `remove_agent`.
+                         Wired into `render_flake` for `HIVE_TOOL_GROUPS`
+                         injection; operator write via dashboard action.
+  src/limits.rs         wire-protocol size limits (inline body cap,
+                         reminder spill threshold) shared across agent
+                         + manager sockets. Single source of truth.
+  src/flake_check.rs    pre-apply `flake.lock` validation — rejects
+                         proposals missing `inputs.<X>.follows` wiring
+                         (duplicate `original` node check).
   src/forge.rs          optional Forgejo wiring: per-agent users +
                          tokens, the `agent-configs` org (`push_config`),
                          and meta read access; mirrors each applied repo
@@ -177,14 +188,14 @@ hive-ag3nt/        in-container harness crate; produces ONE `hive`
                          /api/compact, /api/model, /events/history,
                          /screen, /screen/ws)
   src/turn_stats.rs     per-turn analytics sink (one sqlite row per
-                         turn at /state/hyperhive-turn-stats.sqlite);
+                         turn at /harness/hyperhive-turn-stats.sqlite);
                          schema + best-effort writer
   src/stats.rs          read-side aggregations over turn-stats.sqlite
                          backing the /stats page (bucketed Snapshot:
                          turns / duration / tokens / model mix)
   src/events.rs         LiveEvent + broadcast Bus + sqlite-backed history
-                         (/state/hyperhive-events.sqlite) + TurnState +
-                         model selection (persisted at /state/hyperhive-model)
+                         (/harness/hyperhive-events.sqlite) + TurnState +
+                         model selection (persisted at /harness/hyperhive-model)
   src/turn.rs           claude --print + stream-json pump; --compact retry;
                          proactive compaction + auto session-reset
   src/mcp.rs            embedded MCP server (rmcp): AgentServer + ManagerServer
@@ -383,3 +394,5 @@ The docs below own the details — this section just points at them.
   window:** → [`docs/turn-loop.md`](docs/turn-loop.md).
 - **Two-step spawn, approval flow, flake.lock validation:** →
   [`docs/approvals.md`](docs/approvals.md).
+
+

docs/conventions.md

@@ -285,6 +285,7 @@ binary flavor.
 | `messaging` | `send`, `recv`, `ask`, `answer` |
 | `meta` | `set_status`, `get_agent_meta` |
 | `inbox` | `get_loose_ends`, `cancel_loose_end`, `remind`, `request_next_turn` |
+| `execution` | `bash_run`, `bash_status` |
 | `lifecycle` | `kill`, `start`, `restart`, `update` *(privileged)* |
 | `approvals` | `request_init_config`, `request_apply_commit`, `request_update_meta_inputs` *(privileged)* |
 | `scheduling` | `request_schedule_prompt`, `fire_schedule_now`, `cancel_schedule`, `edit_schedule`, `list_schedules` *(privileged)* |
@@ -307,7 +308,7 @@ the new `HIVE_TOOL_GROUPS` env var. Agents with no entry get no var.
 **Runtime resolution** — at session start the harness reads `HIVE_TOOL_GROUPS`
 (a comma-separated list of snake_case group names injected by the meta renderer
 from `tool-groups.json`). Unrecognised tokens are logged and skipped. Falls back
-to `ToolGroup::AGENT_DEFAULT` (`messaging`, `meta`, `inbox`) or
+to `ToolGroup::AGENT_DEFAULT` (`messaging`, `meta`, `inbox`, `execution`) or
 `ToolGroup::MANAGER_DEFAULT` (all groups) when the var is absent or empty.
 
 **Updating the surface** — when a new `#[tool]` fn is added to `AgentServer`

docs/persistence.md

@@ -64,17 +64,17 @@ Retention:
   `cancelled_at_unix`, then `reap_cancelled` drops the row on
   the next worker pass.
 
-### `/state/hyperhive-events.sqlite` (per agent)
+### `/harness/hyperhive-events.sqlite` (per agent)
 
-Lives inside each container's bind-mounted `/state/` dir (host
-path: `/var/lib/hyperhive/agents/<name>/state/hyperhive-events.sqlite`).
+Lives inside each container's bind-mounted `/harness/` dir (host
+path: `/var/lib/hyperhive/agents/<name>/harness/hyperhive-events.sqlite`).
 One table:
 
 - `events(id, ts, kind, payload_json)` — every `LiveEvent` the
   harness emits during turn loop execution.
 
 The harness writes; the host vacuums. `hive-c0re::events_vacuum`
-runs hourly and sweeps every existing agent state dir, deleting
+runs hourly and sweeps every existing agent harness dir, deleting
 rows older than 7 days. Age-only — no row cap — so a chatty turn
 doesn't lose history sooner than a quiet one; disk pressure on a
 sustained burst is the cheaper problem to have. Centralising
@@ -82,12 +82,12 @@ retention on the host means a misbehaving harness can't disable
 its own vacuum and agents don't need any cleanup wiring of their
 own.
 
-Path overridable via `HYPERHIVE_EVENTS_DB` (for dev / no-`/state`
+Path overridable via `HYPERHIVE_EVENTS_DB` (for dev / no-`/harness`
 setups). On open failure the `Bus` falls back to no-store mode
 rather than crashing the harness — events still broadcast over SSE,
 just nothing persisted.
 
-### `/state/hyperhive-turn-stats.sqlite` (per agent)
+### `/harness/hyperhive-turn-stats.sqlite` (per agent)
 
 Per-turn analytics sink. One row per claude turn captures
 identity (`model`, `wake_from`, `result_kind`), timing
@@ -149,7 +149,7 @@ Writes are best-effort: `append_stdout` / `append_stderr` / `finish`
 log a warning on sqlite error and let the build continue. A failed
 log row never blocks a rebuild.
 
-### `/state/hyperhive-model` (per agent)
+### `/harness/hyperhive-model` (per agent)
 
 Single-line text file holding the claude model name currently
 selected for this agent (default `haiku` when absent). Written by
@@ -169,11 +169,21 @@ Under `/var/lib/hyperhive/agents/<name>/`:
   `/agents` tree bind.
 - `claude/` — claude OAuth credentials, bind-mounted RW to
   `/home/<name>/.claude` inside the container.
-- `state/` — durable notes, the events.sqlite db, and the
-  turn-stats sqlite db. Bind-mounted to `/agents/<name>/state`
-  inside the container (uniform for sub-agents + manager).
-  The `$HYPERHIVE_STATE_DIR` env var exposes the same path to
-  in-container scripts.
+- `state/` — durable notes and `hyperhive-harness.json`. Bind-mounted
+  to `/agents/<name>/state` inside the container (uniform for
+  sub-agents + manager). The `$HYPERHIVE_STATE_DIR` env var exposes
+  the same path to in-container scripts.
+- `harness/` — harness-internal ephemeral state; not intended for
+  agent consumption. Bind-mounted to `/agents/<name>/harness`
+  inside the container (`$HYPERHIVE_HARNESS_DIR`). Contents:
+  - `bash-tasks/` — task JSON + stdout/stderr files for
+    background `bash_run` jobs. JSON files are
+    `<id>.json` (status + tails), `<id>.out` / `<id>.err`
+    (full captured output). Task files persist until container
+    purge.
+  - `hyperhive-events.sqlite` — turn-loop event log.
+  - `hyperhive-turn-stats.sqlite` — per-turn timing stats.
+  - `hyperhive-model` — single-line model name override file.
 
 Under `/var/lib/hyperhive/applied/<name>/` — the hive-c0re-only
 applied repo. Tracks `flake.nix` (module-only boilerplate; never
@@ -207,7 +217,7 @@ step would re-fire).
 - `PURG3` (opt-in via the dashboard button or
   `hive-c0re destroy --purge <name>`) — DESTR0Y plus wipes
   `/var/lib/hyperhive/{agents,applied}/<name>/`. Config history,
-  claude creds, /state/ notes, and the events db are all gone.
+  claude creds, /state/ notes, and the harness dir are all gone.
   No undo.
 
 The manager is non-destroyable from both paths (declarative
@@ -314,3 +324,4 @@ trigger from the `.path` watcher becomes a no-op. Setting it to
 `false` lets re-fires actually re-execute. The trade-off is the
 service unit shows `inactive (dead)` between fires — visible in
 `journalctl` but harmless; the `.path` unit drives the lifecycle.
+

docs/turn-loop.md

@@ -148,7 +148,7 @@ default is set by `hyperhive.model` in the agent's `agent.nix`
 (NixOS option; propagates via `HIVE_DEFAULT_MODEL` env var; falls
 back to `"haiku"` if unset). The operator can flip it at runtime
 with `/model <name>` in the web terminal — the next turn picks it
-up. The choice is persisted to `/state/hyperhive-model` so it
+up. The choice is persisted to `/harness/hyperhive-model` so it
 survives restart; override path: `HYPERHIVE_MODEL_FILE` env var
 for tests.
 
@@ -369,6 +369,20 @@ it as a stdio child via `--mcp-config`. The hyperhive socket name is
   continue without waiting for an external message. The next turn starts
   with `from: "self"` and `body: "continue"`. No-op if new inbox
   messages arrive before this turn ends. No args.
+- `bash_run(cmd, timeout_secs?)` — submit a shell command for
+  background execution (`sh -c <cmd>`). Returns a task ID immediately;
+  the command runs asynchronously in a harness-managed tokio task. Stdout
+  and stderr stream to `harness/bash-tasks/<id>.{out,err}`. When the
+  task completes (or times out, or the process errors), the harness wakes
+  the agent with a summary body — handle on a future turn. Default
+  timeout 180s; pass `timeout_secs` to override. Requires the
+  `execution` tool group.
+- `bash_status(id)` — poll the status of a task submitted with
+  `bash_run`. Returns status (`pending`/`running`/`done`/`timed_out`/
+  `interrupted`), exit code, run duration, and the last 4 KiB of stdout
+  and stderr (full output in the `.out`/`.err` files). Tasks marked
+  `interrupted` had their process killed by a harness restart; a best-
+  effort wake was still sent so the agent is not silently blocked.
 
 ### Waking the agent from inside the container
 
@@ -573,3 +587,4 @@ The harness reads `/etc/hyperhive/bash-allow.json` and replaces
 Commands outside the pattern list require confirmation — which in
 `--print` mode means they will not run. An empty list (default) keeps
 the current wholesale `Bash` entry.
+