agent permissions: one set, tool groups included, set at agent creation

mara on #5170: "dont split caps and perms. its all perms. / dont include
the now empty tool groups / nothing set -> default / also add perms to
agent creation screen".

- hive-sh4re: one `Permission` enum (messaging, meta, inbox, execution,
  web_tools, manage_root_agent) replaces `ToolGroup` and `Capability`;
  `lifecycle`/`forge` are gone. `Permission::default_for` is the default
  for an agent the swarm sets nothing for.
- The record is `{ "permissions": [...] }`. Missing key, unset field or
  no successful read yet = default; `[]` = none; a failed read after a
  good one keeps the last value.
- hive-agent reads its own key every 10s and builds each turn's --tools,
  --allowedTools and MCP config (rewritten before every turn) from it;
  the subagent daemon reads it on each start/continue. Agents get a
  read-only grant on their own key.
- hive-c0re restarts an agent only when its manage_root_agent changes.
  The import now merges meta/capabilities.json and meta/tool-groups.json
  into one list per agent and deletes both; the "import pending, don't
  read" decision is `ImportOutcome::read_allowed`, table-tested.
- swarm-controller: `GET /api/permissions` (names + default) and an
  optional `permissions` on `POST /api/agents`, stored before the job is
  queued. swarm-ui's create-agent form gets a permissions field.
- Deleted: HIVE_TOOL_GROUPS and its forward to the subagent daemon,
  tool_groups.rs, ruth's tool-group seed, the permissions rebuild job
  (PermPayload/WritePermFile/perm_change), the dashboard permissions tab
  and its stale-entries panel.

Part of #5170.

hive-c0re/src/job_queue/exec.rs

@@ -120,7 +120,6 @@ pub(super) async fn run_node(
         // The payload rides the node and is destructured here, so the executor
         // takes it directly instead of re-matching the kind behind a `bail!`
         // that could never fire.
-        NodeKind::WritePermFile { payload, .. } => run_write_perm_file(coord, agent, payload).await,
         NodeKind::EmitRebuilt { ok, .. } => {
             run_emit_rebuilt(coord, agent, coord.job_queue.root_of(id), *ok).await;
             Ok(())
@@ -790,30 +789,6 @@ async fn run_write_dropin(coord: &Arc<Coordinator>, name: &str) -> Result<()> {
     Ok(())
 }
 
-/// Write + commit the perm file(s) (fused under `META_LOCK` so the
-/// working tree is never left dirty), then emit the P3RM1SS10NS-tab
-/// snapshots so the dashboard reflects the new assignment.
-async fn run_write_perm_file(
-    coord: &Arc<Coordinator>,
-    name: &str,
-    payload: &super::model::PermPayload,
-) -> Result<()> {
-    use super::model::PermPayload;
-    // Runs under the deploy window (it declares `Resource::MetaWindow`): a
-    // perm commit landing inside another node's staged prepare→finalize
-    // window would sweep the staged deploy lock into its commit (the
-    // commits are also path-limited in meta.rs — belt and braces).
-    match payload {
-        PermPayload::ToolGroups { groups } => {
-            crate::meta::commit_tool_groups(name, groups)
-                .await
-                .with_context(|| format!("commit tool-groups for {name}"))?;
-            coord.emit_tool_groups_snapshot();
-        }
-    }
-    Ok(())
-}
-
 /// Compute which agents a `nix flake update <inputs>` on the meta
 /// flake affects — the fan-out set for `MetaUpdate` DAGs. Empty
 /// `inputs` or any input under `hyperhive` → every container;