hive-c0re: fail on an unparseable permission file, write it atomically

tool_groups::read and capabilities::read returned an empty map when
their file existed but didn't parse. Every set_*/remove_agent is a
read-modify-write, and write() rewrote the file in place, so a crash or
ENOSPC mid-write left a truncated file, and the next write (e.g. the
manager-spawn seed of ruth's tool groups) replaced it with a map holding
only one agent. The scheduling and approval gates then denied every
other agent, recoverable only from meta git history.

- Both registries now read through agent_config::read_map: a missing
  file is still the empty map, any other read failure or a parse
  failure is an io::Error. set_groups / set_caps / remove_agent fail
  without writing.
- Writes go through agent_config::write_map: temp file in the same
  directory, fsync, rename, fsync the directory. hive-c0re had no
  shared atomic-write helper (the existing tmp+rename sites are inline
  and don't fsync).
- Callers of read / groups_for / has_cap now handle the error:
  * dashboard GET /api/tool-groups, /api/capabilities,
    /api/permissions/stale return 500 instead of an empty table;
  * the SSE permission snapshots are skipped with a warn;
  * render_flake returns Result, so sync_agents fails instead of
    rendering every agent without its tool groups / capabilities;
  * set_nspawn_flags propagates has_cap's error;
  * the socket tool-group gates deny with the read error as message;
  * seed_manager_tool_groups logs and does not seed.
- capabilities::write had no callers left once set_caps writes through
  write_map, and is removed.

Closes #4719

hive-c0re/src/lifecycle/host_config.rs

@@ -339,7 +339,7 @@ async fn set_nspawn_flags(
     // parent field took with it the unconditional grant every
     // agent used to get over its own direct children — so an agent with
     // no capability now sees its own dirs and nothing else.
-    if crate::capabilities::has_cap(agent_name, Capability::ManageRootAgent) {
+    if crate::capabilities::has_cap(agent_name, Capability::ManageRootAgent)? {
         // Skipping self is a no-op, not a narrowing: `agent_notes_dir` is
         // `agent_state_dir/state` and `config_bind_source` is shared, so
         // binding the holder as its own virtual child reproduced the two