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/continuation-prompt-injector.ts

@@ -2,6 +2,7 @@ import type { PluginInput } from "@opencode-ai/plugin"
 import { log } from "../../shared/logger"
 import { findNearestMessageWithFields } from "../../features/hook-message-injector"
 import { getMessageDir } from "./message-storage-directory"
+import { withTimeout } from "./with-timeout"
 
 type MessageInfo = {
 	agent?: string
@@ -12,15 +13,18 @@ type MessageInfo = {
 
 export async function injectContinuationPrompt(
 	ctx: PluginInput,
-	options: { sessionID: string; prompt: string; directory: string },
+	options: { sessionID: string; prompt: string; directory: string; apiTimeoutMs: number },
 ): Promise<void> {
 	let agent: string | undefined
 	let model: { providerID: string; modelID: string } | undefined
 
 	try {
-		const messagesResp = await ctx.client.session.messages({
-			path: { id: options.sessionID },
-		})
+		const messagesResp = await withTimeout(
+			ctx.client.session.messages({
+				path: { id: options.sessionID },
+			}),
+			options.apiTimeoutMs,
+		)
 		const messages = (messagesResp.data ?? []) as Array<{ info?: MessageInfo }>
 		for (let i = messages.length - 1; i >= 0; i--) {
 			const info = messages[i]?.info