fix(atlas): gate final-wave approval on real plan state

Ignore nested plan checkboxes and track parallel final-wave approvals so Atlas only pauses for user approval when the real top-level review wave is complete.

Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)

Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>

src/hooks/atlas/final-wave-plan-state.ts

@@ -0,0 +1,60 @@
+import { existsSync, readFileSync } from "node:fs"
+
+const TODO_HEADING_PATTERN = /^##\s+TODOs\b/i
+const FINAL_VERIFICATION_HEADING_PATTERN = /^##\s+Final Verification Wave\b/i
+const SECOND_LEVEL_HEADING_PATTERN = /^##\s+/
+const UNCHECKED_CHECKBOX_PATTERN = /^\s*[-*]\s*\[\s*\]\s*(.+)$/
+const TODO_TASK_PATTERN = /^\d+\./
+const FINAL_WAVE_TASK_PATTERN = /^F\d+\./i
+
+type PlanSection = "todo" | "final-wave" | "other"
+
+export type FinalWavePlanState = {
+  pendingImplementationTaskCount: number
+  pendingFinalWaveTaskCount: number
+}
+
+export function readFinalWavePlanState(planPath: string): FinalWavePlanState | null {
+  if (!existsSync(planPath)) {
+    return null
+  }
+
+  try {
+    const content = readFileSync(planPath, "utf-8")
+    const lines = content.split(/\r?\n/)
+    let section: PlanSection = "other"
+    let pendingImplementationTaskCount = 0
+    let pendingFinalWaveTaskCount = 0
+
+    for (const line of lines) {
+      if (SECOND_LEVEL_HEADING_PATTERN.test(line)) {
+        section = TODO_HEADING_PATTERN.test(line)
+          ? "todo"
+          : FINAL_VERIFICATION_HEADING_PATTERN.test(line)
+            ? "final-wave"
+            : "other"
+      }
+
+      const uncheckedTaskMatch = line.match(UNCHECKED_CHECKBOX_PATTERN)
+      if (!uncheckedTaskMatch) {
+        continue
+      }
+
+      const taskLabel = uncheckedTaskMatch[1].trim()
+      if (section === "todo" && TODO_TASK_PATTERN.test(taskLabel)) {
+        pendingImplementationTaskCount += 1
+      }
+
+      if (section === "final-wave" && FINAL_WAVE_TASK_PATTERN.test(taskLabel)) {
+        pendingFinalWaveTaskCount += 1
+      }
+    }
+
+    return {
+      pendingImplementationTaskCount,
+      pendingFinalWaveTaskCount,
+    }
+  } catch {
+    return null
+  }
+}