Fix: Defer gateway restarts during active agent runs and prevent macOS app config writes in remote mode

- Add active agent run tracking functions (getActiveAgentRunCount, getActiveAgentRunIds)
- Add onAgentRunComplete callback to notify when runs complete
- Modify config-reload to defer restarts when active runs exist
- Queue restart and apply when all runs complete
- Add guard in AppState.swift to prevent config writes in remote mode
- Set gateway.reload.mode to "off" as immediate fix

This prevents the bot from interrupting in-flight messages during
config changes, fixing the "bot typing but never responds" issue.

Root cause: macOS app was writing to gateway config even in remote mode,
triggering file watcher → reload handler → SIGUSR1 → shutdown during messages.

apps/macos/Sources/Moltbot/AppState.swift

@@ -449,6 +449,9 @@ final class AppState {
             ? CommandResolver.parseSSHTarget(remoteTarget)?.host
             : nil
 
+        // Don't write to gateway config in remote mode - gateway manages its own config
+        guard connectionMode == .local else { return }
+
         Task { @MainActor in
             // Keep app-only connection settings local to avoid overwriting remote gateway config.
             var root = MoltbotConfigFile.loadDict()

src/gateway/config-reload.ts

@@ -2,6 +2,7 @@ import chokidar from "chokidar";
 import { type ChannelId, listChannelPlugins } from "../channels/plugins/index.js";
 import { getActivePluginRegistry } from "../plugins/runtime.js";
 import type { MoltbotConfig, ConfigFileSnapshot, GatewayReloadMode } from "../config/config.js";
+import { getActiveAgentRunCount, onAgentRunComplete } from "../infra/agent-events.js";
 
 export type GatewayReloadSettings = {
   mode: GatewayReloadMode;
@@ -264,6 +265,8 @@ export function startGatewayConfigReloader(opts: {
   let running = false;
   let stopped = false;
   let restartQueued = false;
+  let queuedPlan: GatewayReloadPlan | null = null;
+  let queuedConfig: MoltbotConfig | null = null;
 
   const schedule = () => {
     if (stopped) return;
@@ -306,6 +309,16 @@ export function startGatewayConfigReloader(opts: {
       }
       if (settings.mode === "restart") {
         if (!restartQueued) {
+          const activeRunCount = getActiveAgentRunCount();
+          if (activeRunCount > 0) {
+            opts.log.warn(
+              `config change requires gateway restart, but deferring (${activeRunCount} active agent run${activeRunCount === 1 ? "" : "s"})`,
+            );
+            restartQueued = true;
+            queuedPlan = plan;
+            queuedConfig = nextConfig;
+            return;
+          }
           restartQueued = true;
           opts.onRestart(plan, nextConfig);
         }
@@ -321,6 +334,16 @@ export function startGatewayConfigReloader(opts: {
           return;
         }
         if (!restartQueued) {
+          const activeRunCount = getActiveAgentRunCount();
+          if (activeRunCount > 0) {
+            opts.log.warn(
+              `config change requires gateway restart, but deferring (${activeRunCount} active agent run${activeRunCount === 1 ? "" : "s"})`,
+            );
+            restartQueued = true;
+            queuedPlan = plan;
+            queuedConfig = nextConfig;
+            return;
+          }
           restartQueued = true;
           opts.onRestart(plan, nextConfig);
         }
@@ -356,12 +379,26 @@ export function startGatewayConfigReloader(opts: {
     void watcher.close().catch(() => {});
   });
 
+  // Register callback to apply queued restart when all runs complete
+  const unregisterCallback = onAgentRunComplete(() => {
+    if (restartQueued && queuedPlan && queuedConfig && getActiveAgentRunCount() === 0) {
+      opts.log.info("applying queued gateway restart (all agent runs completed)");
+      restartQueued = false;
+      const plan = queuedPlan;
+      const config = queuedConfig;
+      queuedPlan = null;
+      queuedConfig = null;
+      opts.onRestart(plan, config);
+    }
+  });
+
   return {
     stop: async () => {
       stopped = true;
       if (debounceTimer) clearTimeout(debounceTimer);
       debounceTimer = null;
       watcherClosed = true;
+      unregisterCallback();
       await watcher.close().catch(() => {});
     },
   };

src/infra/agent-events.ts

@@ -21,6 +21,7 @@ export type AgentRunContext = {
 const seqByRun = new Map<string, number>();
 const listeners = new Set<(evt: AgentEventPayload) => void>();
 const runContextById = new Map<string, AgentRunContext>();
+const runCompletionCallbacks = new Set<() => void>();
 
 export function registerAgentRunContext(runId: string, context: AgentRunContext) {
   if (!runId) return;
@@ -46,6 +47,27 @@ export function getAgentRunContext(runId: string) {
 
 export function clearAgentRunContext(runId: string) {
   runContextById.delete(runId);
+  // Notify callbacks that a run has completed
+  for (const callback of runCompletionCallbacks) {
+    try {
+      callback();
+    } catch {
+      /* ignore */
+    }
+  }
+}
+
+export function onAgentRunComplete(callback: () => void): () => void {
+  runCompletionCallbacks.add(callback);
+  return () => runCompletionCallbacks.delete(callback);
+}
+
+export function getActiveAgentRunCount(): number {
+  return runContextById.size;
+}
+
+export function getActiveAgentRunIds(): string[] {
+  return Array.from(runContextById.keys());
 }
 
 export function resetAgentRunContextForTest() {