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/tools/lsp/lsp-manager-temp-directory-cleanup.ts

@@ -0,0 +1,29 @@
+type ManagedClientForTempDirectoryCleanup = {
+  refCount: number
+  client: {
+    stop: () => Promise<void>
+  }
+}
+
+export async function cleanupTempDirectoryLspClients(
+  clients: Map<string, ManagedClientForTempDirectoryCleanup>
+): Promise<void> {
+  const keysToRemove: string[] = []
+  for (const [key, managed] of clients.entries()) {
+    const isTempDir = key.startsWith("/tmp/") || key.startsWith("/var/folders/")
+    const isIdle = managed.refCount === 0
+    if (isTempDir && isIdle) {
+      keysToRemove.push(key)
+    }
+  }
+
+  for (const key of keysToRemove) {
+    const managed = clients.get(key)
+    if (managed) {
+      clients.delete(key)
+      try {
+        await managed.client.stop()
+      } catch {}
+    }
+  }
+}