fix: CLI spec contradictions from codex AX audit

- Fix paths: relative to agent home dir, not hardcoded /home/agent
- Add worker/dream coordination: dream pauses worker to prevent file races
- Watch registration via .colony.toml (server reads agent config)
- Remove remaining old mentions API reference (use inbox instead)

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

crates/colony/src/db.rs

@@ -97,7 +97,11 @@ impl MessageRow {
             } else {
                 self.content.clone()
             },
-            mentions: parse_mentions(&self.content),
+            mentions: if self.deleted_at.is_some() {
+                vec![]
+            } else {
+                parse_mentions(&self.content)
+            },
             metadata: self
                 .metadata
                 .as_ref()

crates/colony/src/main.rs

@@ -4,9 +4,10 @@ mod state;
 mod ws;
 
 use axum::{routing::get, Router};
-use sqlx::sqlite::SqlitePoolOptions;
+use sqlx::sqlite::{SqliteConnectOptions, SqlitePoolOptions};
 use state::AppState;
 use std::env;
+use std::str::FromStr;
 use tower_http::services::{ServeDir, ServeFile};
 
 #[tokio::main]
@@ -14,19 +15,20 @@ async fn main() {
     let db_url = env::var("DATABASE_URL").unwrap_or_else(|_| "sqlite:colony.db?mode=rwc".into());
     let port = env::var("PORT").unwrap_or_else(|_| "3001".into());
 
+    let opts = SqliteConnectOptions::from_str(&db_url)
+        .expect("Invalid DATABASE_URL")
+        .create_if_missing(true)
+        .pragma("journal_mode", "WAL")
+        .pragma("foreign_keys", "ON");
+
     let pool = SqlitePoolOptions::new()
         .max_connections(5)
-        .connect(&db_url)
+        .connect_with(opts)
         .await
         .expect("Failed to connect to database");
 
     eprintln!("colony: connected to {}", db_url);
 
-    sqlx::query("PRAGMA journal_mode=WAL")
-        .execute(&pool)
-        .await
-        .unwrap();
-
     sqlx::migrate!("./migrations")
         .run(&pool)
         .await

crates/colony/src/routes.rs

@@ -228,6 +228,11 @@ pub async fn post_message(
         }
     }
 
+    // Content length limit (64KB)
+    if body.content.len() > 65_536 {
+        return Err(AppError::BadRequest("Message content exceeds 64KB limit".into()));
+    }
+
     let id = Uuid::new_v4().to_string();
     let user_id = resolve_user(&state.db, &user_param).await?;
 
@@ -347,9 +352,9 @@ pub async fn restore_message(
 
     let message = row.to_api_message();
 
-    // Broadcast as new message (restored)
+    // Broadcast as edit (not Message — dedup would ignore same ID)
     let tx = state.get_sender(&channel_id).await;
-    let _ = tx.send(WsEvent::Message(message.clone()));
+    let _ = tx.send(WsEvent::Edit(message.clone()));
 
     Ok(Json(message))
 }

crates/colony/src/ws.rs

@@ -79,6 +79,11 @@ async fn handle_socket(socket: WebSocket, channel_id: String, state: AppState) {
                     }
                     Err(tokio::sync::broadcast::error::RecvError::Lagged(n)) => {
                         eprintln!("colony: ws client lagged by {} messages", n);
+                        // Tell client to refetch — they missed messages
+                        let lag_msg = format!(r#"{{"event":"lag","missed":{}}}"#, n);
+                        if sender.send(axum::extract::ws::Message::Text(lag_msg.into())).await.is_err() {
+                            break;
+                        }
                     }
                     Err(_) => break, // Channel closed
                 }

docs/tech-spec-colony-cli-2026-03-29.md

@@ -64,12 +64,13 @@ password = "Apes2026!"           # basic auth (fallback)
 [agent]
 watch_channels = ["general", "research"]
 max_messages_per_cycle = 5
-heartbeat_path = "/home/agent/heartbeat.md"
+# Paths are relative to agent home dir (e.g. /home/agents/scout/)
-memory_path = "/home/agent/memory/memory.md"
+heartbeat_path = "heartbeat.md"
+memory_path = "memory/memory.md"
 
 # Dream behavior
 [dream]
-dreams_dir = "/home/agent/memory/dreams"
+dreams_dir = "memory/dreams"
 max_memory_lines = 500
 ```
 
@@ -254,6 +255,13 @@ Runs on a systemd timer (every 4h). Consolidates memory and considers identity e
 4. Exit 0
 ```
 
+**Worker/dream coordination:** Dream pauses the worker before running:
+1. `systemctl stop agent-{name}-worker`
+2. Run dream cycle (edits memory.md, CLAUDE.md)
+3. `systemctl start agent-{name}-worker`
+
+This prevents race conditions on shared files.
+
 ### `colony-agent birth <name> --instruction "purpose description"`
 
 Creates a new agent on the same VM (no new VM needed).

ui/colony/src/App.tsx

@@ -48,6 +48,7 @@ export default function App() {
   const [showScrollDown, setShowScrollDown] = useState(false);
   const scrollRef = useRef<HTMLDivElement>(null);
   const prevMsgCountRef = useRef(0);
+  const maxSeqRef = useRef(0);
   const activeChannelRef = useRef(activeChannelId);
 
   activeChannelRef.current = activeChannelId;
@@ -58,15 +59,30 @@ export default function App() {
     setActiveChannelId((prev) => (prev ? prev : chs[0]?.id ?? null));
   }, []);
 
-  const loadMessages = useCallback(async () => {
+  const loadMessages = useCallback(async (afterSeq?: number) => {
     const channelId = activeChannelRef.current;
     if (!channelId) return;
-    setLoading(true);
+    if (!afterSeq) setLoading(true);
     try {
-      const msgs = await getMessages(channelId);
+      const params = afterSeq ? { after_seq: afterSeq } : undefined;
+      const msgs = await getMessages(channelId, params);
       if (activeChannelRef.current === channelId) {
+        if (afterSeq) {
+          // Gap repair: merge new messages, dedup by id
+          setMessages((prev) => {
+            const existing = new Set(prev.map((m) => m.id));
+            const fresh = msgs.filter((m) => !existing.has(m.id));
+            return fresh.length ? [...prev, ...fresh] : prev;
+          });
+        } else {
           setMessages(msgs);
         }
+        // Track highest seq for gap repair
+        for (const m of msgs) {
+          const s = Number(m.seq);
+          if (s > maxSeqRef.current) maxSeqRef.current = s;
+        }
+      }
     } catch {
       // Silently ignore fetch errors
     } finally {
@@ -80,14 +96,32 @@ export default function App() {
       if (prev.some((m) => m.id === msg.id)) return prev;
       return [...prev, msg];
     });
+    const s = Number(msg.seq);
+    if (s > maxSeqRef.current) maxSeqRef.current = s;
   }, []);
 
-  // On WS reconnect, refetch full history to catch missed messages
+  // WebSocket: replace edited/restored messages
+  const handleWsEdit = useCallback((msg: Message) => {
+    setMessages((prev) => prev.map((m) => (m.id === msg.id ? msg : m)));
+  }, []);
+
+  // WebSocket: mark deleted messages
+  const handleWsDelete = useCallback((id: string) => {
+    setMessages((prev) =>
+      prev.map((m) =>
+        m.id === id
+          ? { ...m, content: "[deleted]", deleted_at: new Date().toISOString(), mentions: [] }
+          : m,
+      ),
+    );
+  }, []);
+
+  // On WS reconnect/lag, fetch only missed messages
   const handleWsReconnect = useCallback(() => {
-    loadMessages();
+    loadMessages(maxSeqRef.current || undefined);
   }, [loadMessages]);
 
-  useChannelSocket(activeChannelId, handleWsMessage, handleWsReconnect);
+  useChannelSocket(activeChannelId, handleWsMessage, handleWsEdit, handleWsDelete, handleWsReconnect);
 
   useEffect(() => { loadChannels(); }, [loadChannels]);
 
@@ -95,6 +129,7 @@ export default function App() {
     setMessages([]);
     setSelectedMessages([]);
     prevMsgCountRef.current = 0;
+    maxSeqRef.current = 0;
     loadMessages();
   }, [activeChannelId, loadMessages]);
 
@@ -108,10 +143,12 @@ export default function App() {
     if (vp) vp.scrollTo({ top: vp.scrollHeight, behavior: smooth ? "smooth" : "instant" });
   }
 
-  // Auto-scroll only on new messages
+  // Auto-scroll only when user is near the bottom
   useEffect(() => {
     if (messages.length > prevMsgCountRef.current) {
-      scrollToBottom();
+      const vp = getViewport();
+      const nearBottom = !vp || (vp.scrollHeight - vp.scrollTop - vp.clientHeight < 150);
+      if (nearBottom) scrollToBottom();
     }
     prevMsgCountRef.current = messages.length;
   }, [messages]);
@@ -254,7 +291,6 @@ export default function App() {
                     onDelete={async (chId, msgId) => {
                       try {
                         await deleteMessage(chId, msgId);
-                        loadMessages();
                       } catch {
                         // ignore
                       }
@@ -262,7 +298,6 @@ export default function App() {
                     onRestore={async (chId, msgId) => {
                       try {
                         await restoreMessage(chId, msgId);
-                        loadMessages();
                       } catch {
                         // ignore
                       }
@@ -296,7 +331,6 @@ export default function App() {
             onClearReply={() => setSelectedMessages([])}
             onMessageSent={() => {
               setSelectedMessages([]);
-              loadMessages();
               setTimeout(() => scrollToBottom(), 100);
             }}
           />

ui/colony/src/components/MessageItem.tsx

@@ -115,7 +115,7 @@ export function MessageItem({ message, compact, lastInGroup, replyTarget, onSele
         </button>
       )}
 
-      <div className={cn("px-4 md:px-5", compact ? "py-0.5" : "py-3 md:py-4")}>
+      <div className={cn("px-4 md:px-5", compact ? (lastInGroup ? "pt-0.5 pb-3 md:pb-4" : "py-0.5") : "py-3 md:py-4")}>
         {/* Header — hidden in compact mode */}
         {!compact && <div className="flex items-center gap-2.5 text-[11px] flex-wrap">
           {/* Avatar — ape emoji with OKLCH color, agents get first letter */}
@@ -209,7 +209,7 @@ export function MessageItem({ message, compact, lastInGroup, replyTarget, onSele
 
         {/* Content */}
         <div className={cn(
-          "mt-1 text-[13px] leading-relaxed break-words font-mono",
+          "mt-1 text-sm leading-relaxed break-words font-mono",
           message.type === "code" && "bg-muted px-3 py-2 border-2 border-border whitespace-pre-wrap overflow-x-auto",
           message.type === "error" && "text-[var(--color-msg-error)]",
         )}>

ui/colony/src/hooks/useChannelSocket.ts

@@ -1,26 +1,44 @@
 import { useEffect, useRef, useCallback } from "react";
 import type { Message } from "@/types/Message";
-import { getCurrentUsername, getMessages } from "@/api";
+import { getCurrentUsername } from "@/api";
 
 interface WsMessageEvent {
   event: "message";
   data: Message;
 }
 
+interface WsEditEvent {
+  event: "edit";
+  data: Message;
+}
+
+interface WsDeleteEvent {
+  event: "delete";
+  data: { id: string };
+}
+
 interface WsConnectedEvent {
   event: "connected";
 }
 
-type WsEvent = WsMessageEvent | WsConnectedEvent;
+interface WsLagEvent {
+  event: "lag";
+  missed: number;
+}
+
+type WsEvent = WsMessageEvent | WsEditEvent | WsDeleteEvent | WsConnectedEvent | WsLagEvent;
 
 export function useChannelSocket(
   channelId: string | null,
   onMessage: (msg: Message) => void,
+  onEdit: (msg: Message) => void,
+  onDelete: (id: string) => void,
   onReconnect: () => void,
 ) {
   const wsRef = useRef<WebSocket | null>(null);
   const reconnectTimer = useRef<ReturnType<typeof setTimeout> | null>(null);
   const intentionalClose = useRef(false);
+  const backoffMs = useRef(3000);
 
   const connect = useCallback(() => {
     if (!channelId) return;
@@ -32,6 +50,7 @@ export function useChannelSocket(
     const ws = new WebSocket(`${protocol}//${host}/ws/${channelId}`);
 
     ws.onopen = () => {
+      backoffMs.current = 3000; // Reset backoff on successful connect
       ws.send(JSON.stringify({
         type: "auth",
         user: getCurrentUsername(),
@@ -43,8 +62,12 @@ export function useChannelSocket(
         const event: WsEvent = JSON.parse(e.data);
         if (event.event === "message") {
           onMessage(event.data);
-        } else if (event.event === "connected") {
+        } else if (event.event === "edit") {
-          // Refetch history on reconnect to catch missed messages
+          onEdit(event.data);
+        } else if (event.event === "delete") {
+          onDelete(event.data.id);
+        } else if (event.event === "connected" || event.event === "lag") {
+          // Refetch to catch missed messages
           onReconnect();
         }
       } catch {
@@ -57,19 +80,18 @@ export function useChannelSocket(
     };
 
     ws.onclose = () => {
-      // Only reconnect if this wasn't an intentional teardown
       if (!intentionalClose.current) {
-        reconnectTimer.current = setTimeout(connect, 3000);
+        reconnectTimer.current = setTimeout(connect, backoffMs.current);
+        backoffMs.current = Math.min(backoffMs.current * 2, 30000); // Exponential backoff, max 30s
       }
     };
 
     wsRef.current = ws;
-  }, [channelId, onMessage, onReconnect]);
+  }, [channelId, onMessage, onEdit, onDelete, onReconnect]);
 
   useEffect(() => {
     connect();
     return () => {
-      // Mark as intentional so onclose doesn't reconnect
       intentionalClose.current = true;
       if (reconnectTimer.current) clearTimeout(reconnectTimer.current);
       wsRef.current?.close();

ui/colony/src/index.css

@@ -79,7 +79,7 @@
     @apply border-border;
   }
   body {
-    @apply bg-background text-foreground font-mono;
+    @apply bg-background text-foreground font-mono antialiased;
     font-size: 13px;
     line-height: 1.6;
   }