merge: integrate origin/dev into modular-enforcement branch

Resolves all merge conflicts, preserving our split module structure
while integrating all dev changes:
- Custom agent summaries support (parseRegisteredAgentSummaries)
- Background notification queue (enqueueNotificationForParent)
- Atlas shared git-worktree module (collectGitDiffStats, formatFileChanges)
- Ralph-loop withTimeout + DEFAULT_API_TIMEOUT=5000
- Session recovery assistant_prefill_unsupported error type
- Atlas agentOverrides forwarding
- Config handler plan model demotion (buildPlanDemoteConfig)
- Delegate-task agentOverrides, promptSyncWithModelSuggestionRetry, variant
- LSP init timeout + stale init detection
- isPlanFamily function + task-continuation-enforcer hook
- Handoff command

src/hooks/ralph-loop/with-timeout.ts

@@ -0,0 +1,20 @@
+export async function withTimeout<TData>(
+	promise: Promise<TData>,
+	timeoutMs: number,
+): Promise<TData> {
+	let timeoutId: ReturnType<typeof setTimeout> | undefined
+
+	const timeoutPromise = new Promise<never>((_, reject) => {
+		timeoutId = setTimeout(() => {
+			reject(new Error("API timeout"))
+		}, timeoutMs)
+	})
+
+	try {
+		return await Promise.race([promise, timeoutPromise])
+	} finally {
+		if (timeoutId !== undefined) {
+			clearTimeout(timeoutId)
+		}
+	}
+}