docs: update for recent commits (rate limiting, reply threading, screen, auto-reset, two-step spawn, ctx chip)

docs/persistence.md

@@ -9,7 +9,9 @@ Where state lives, what survives what, and how it's bounded.
 Three tables, all in one file:
 
 - `messages` — every inter-agent / operator-bound message.
-  `sender / recipient / body / sent_at / delivered_at`.
+  `sender / recipient / body / sent_at / delivered_at / acked_at /
+  in_reply_to`. `in_reply_to` links a reply to its parent row id;
+  the dashboard and per-agent inbox render these as threaded rows.
 - `approvals` — the queue. `agent / kind (apply_commit | spawn) /
   commit_ref / requested_at / status / resolved_at / note`.
 - `operator_questions` — `ask` / `answer` queue (despite the
@@ -72,6 +74,18 @@ No host-side vacuum yet — tracked as forge issue
 [#10](http://localhost:3000/hyperhive/hyperhive/issues/10)
 (target retention ~90 days, age-only sweep like events_vacuum).
 
+### `/state/hyperhive-rate-limited` (per agent)
+
+Sentinel file written by `Bus::emit_status("rate_limited")` when the
+harness detects a 429 / rate-limit response from the Claude API, and
+removed when the retry sleep expires (any subsequent status emit
+clears it). The file's presence is checked by hive-c0re's
+`container_view::is_rate_limited` on each `build_all` sweep (~10s) to
+populate `ContainerView.rate_limited` for the dashboard. Survives a
+harness restart (the Bus reads it back at boot and restores the flag),
+so the badge remains accurate if hive-c0re restarts while the harness
+is mid-sleep.
+
 ### `/state/hyperhive-model` (per agent)
 
 Single-line text file holding the claude model name currently