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/ralph-loop-event-handler.ts

@@ -132,6 +132,7 @@ export function createRalphLoopEventHandler(
 					sessionID,
 					prompt: buildContinuationPrompt(newState),
 					directory: options.directory,
+					apiTimeoutMs: options.apiTimeoutMs,
 				})
 			} catch (err) {
 				log(`[${HOOK_NAME}] Failed to inject continuation`, {