fix(atlas): pause after final verification wave for explicit user approval

src/hooks/atlas/atlas-hook.ts

@@ -21,6 +21,6 @@ export function createAtlasHook(ctx: PluginInput, options?: AtlasHookOptions) {
   return {
     handler: createAtlasEventHandler({ ctx, options, sessions, getState }),
     "tool.execute.before": createToolExecuteBeforeHandler({ ctx, pendingFilePaths }),
-    "tool.execute.after": createToolExecuteAfterHandler({ ctx, pendingFilePaths, autoCommit }),
+    "tool.execute.after": createToolExecuteAfterHandler({ ctx, pendingFilePaths, autoCommit, getState }),
   }
 }

src/hooks/atlas/event-handler.ts

@@ -38,11 +38,15 @@ export function createAtlasEventHandler(input: {
     if (event.type === "message.updated") {
       const info = props?.info as Record<string, unknown> | undefined
       const sessionID = info?.sessionID as string | undefined
+      const role = info?.role as string | undefined
       if (!sessionID) return
 
       const state = sessions.get(sessionID)
       if (state) {
         state.lastEventWasAbortError = false
+        if (role === "user") {
+          state.waitingForFinalWaveApproval = false
+        }
       }
       return
     }

src/hooks/atlas/final-wave-approval-gate.test.ts

@@ -0,0 +1,224 @@
+import { afterEach, beforeEach, describe, expect, mock, test } from "bun:test"
+import { randomUUID } from "node:crypto"
+import { existsSync, mkdirSync, rmSync, writeFileSync } from "node:fs"
+import { tmpdir } from "node:os"
+import { join } from "node:path"
+import { createOpencodeClient } from "@opencode-ai/sdk"
+import type { AssistantMessage, Session } from "@opencode-ai/sdk"
+import type { BoulderState } from "../../features/boulder-state"
+import { clearBoulderState, writeBoulderState } from "../../features/boulder-state"
+
+const TEST_STORAGE_ROOT = join(tmpdir(), `atlas-final-wave-storage-${randomUUID()}`)
+const TEST_MESSAGE_STORAGE = join(TEST_STORAGE_ROOT, "message")
+const TEST_PART_STORAGE = join(TEST_STORAGE_ROOT, "part")
+
+mock.module("../../features/hook-message-injector/constants", () => ({
+  OPENCODE_STORAGE: TEST_STORAGE_ROOT,
+  MESSAGE_STORAGE: TEST_MESSAGE_STORAGE,
+  PART_STORAGE: TEST_PART_STORAGE,
+}))
+
+mock.module("../../shared/opencode-message-dir", () => ({
+  getMessageDir: (sessionID: string) => {
+    const directoryPath = join(TEST_MESSAGE_STORAGE, sessionID)
+    return existsSync(directoryPath) ? directoryPath : null
+  },
+}))
+
+mock.module("../../shared/opencode-storage-detection", () => ({
+  isSqliteBackend: () => false,
+}))
+
+const { createAtlasHook } = await import("./index")
+const { MESSAGE_STORAGE } = await import("../../features/hook-message-injector")
+
+type AtlasHookContext = Parameters<typeof createAtlasHook>[0]
+type PromptMock = ReturnType<typeof mock>
+
+describe("Atlas final verification approval gate", () => {
+  let testDirectory = ""
+
+  function createMockPluginInput(): AtlasHookContext & { _promptMock: PromptMock } {
+    const client = createOpencodeClient({ baseUrl: "http://localhost" })
+    const promptMock = mock((input: unknown) => input)
+
+    Reflect.set(client.session, "prompt", async (input: unknown) => {
+      promptMock(input)
+      return {
+        data: { info: {} as AssistantMessage, parts: [] },
+        request: new Request("http://localhost/session/prompt"),
+        response: new Response(),
+      }
+    })
+
+    Reflect.set(client.session, "promptAsync", async (input: unknown) => {
+      promptMock(input)
+      return {
+        data: undefined,
+        request: new Request("http://localhost/session/prompt_async"),
+        response: new Response(),
+      }
+    })
+
+    Reflect.set(client.session, "get", async () => {
+      return {
+        data: { parentID: "main-session-123" } as Session,
+        request: new Request("http://localhost/session/main-session-123"),
+        response: new Response(),
+      }
+    })
+
+    return {
+      directory: testDirectory,
+      project: {} as AtlasHookContext["project"],
+      worktree: testDirectory,
+      serverUrl: new URL("http://localhost"),
+      $: {} as AtlasHookContext["$"],
+      client,
+      _promptMock: promptMock,
+    }
+  }
+
+  function setupMessageStorage(sessionID: string): void {
+    const messageDirectory = join(MESSAGE_STORAGE, sessionID)
+    if (!existsSync(messageDirectory)) {
+      mkdirSync(messageDirectory, { recursive: true })
+    }
+
+    writeFileSync(
+      join(messageDirectory, "msg_test001.json"),
+      JSON.stringify({
+        agent: "atlas",
+        model: { providerID: "anthropic", modelID: "claude-opus-4-6" },
+      }),
+    )
+  }
+
+  function cleanupMessageStorage(sessionID: string): void {
+    const messageDirectory = join(MESSAGE_STORAGE, sessionID)
+    if (existsSync(messageDirectory)) {
+      rmSync(messageDirectory, { recursive: true, force: true })
+    }
+  }
+
+  beforeEach(() => {
+    testDirectory = join(tmpdir(), `atlas-final-wave-test-${randomUUID()}`)
+    mkdirSync(join(testDirectory, ".sisyphus"), { recursive: true })
+    clearBoulderState(testDirectory)
+  })
+
+  afterEach(() => {
+    clearBoulderState(testDirectory)
+    if (existsSync(testDirectory)) {
+      rmSync(testDirectory, { recursive: true, force: true })
+    }
+  })
+
+  test("waits for explicit user approval after the last final-wave approval arrives", async () => {
+    // given
+    const sessionID = "atlas-final-wave-session"
+    setupMessageStorage(sessionID)
+
+    const planPath = join(testDirectory, "final-wave-plan.md")
+    writeFileSync(
+      planPath,
+      `# Plan
+
+## TODOs
+- [x] 1. Ship the implementation
+
+## Final Verification Wave (MANDATORY - after ALL implementation tasks)
+- [x] F1. **Plan Compliance Audit** - \`oracle\`
+- [x] F2. **Code Quality Review** - \`unspecified-high\`
+- [x] F3. **Real Manual QA** - \`unspecified-high\`
+- [ ] F4. **Scope Fidelity Check** - \`deep\`
+`,
+    )
+
+    const state: BoulderState = {
+      active_plan: planPath,
+      started_at: "2026-01-02T10:00:00Z",
+      session_ids: [sessionID],
+      plan_name: "final-wave-plan",
+      agent: "atlas",
+    }
+    writeBoulderState(testDirectory, state)
+
+    const mockInput = createMockPluginInput()
+    const hook = createAtlasHook(mockInput)
+    const toolOutput = {
+      title: "Sisyphus Task",
+      output: `Tasks [4/4 compliant] | Contamination [CLEAN] | Unaccounted [CLEAN] | VERDICT: APPROVE
+
+<task_metadata>
+session_id: ses_final_wave_review
+</task_metadata>`,
+      metadata: {},
+    }
+
+    // when
+    await hook["tool.execute.after"]({ tool: "task", sessionID }, toolOutput)
+    await hook.handler({ event: { type: "session.idle", properties: { sessionID } } })
+
+    // then
+    expect(toolOutput.output).toContain("FINAL WAVE APPROVAL GATE")
+    expect(toolOutput.output).toContain("explicit user approval")
+    expect(toolOutput.output).not.toContain("STEP 8: PROCEED TO NEXT TASK")
+    expect(mockInput._promptMock).not.toHaveBeenCalled()
+
+    cleanupMessageStorage(sessionID)
+  })
+
+  test("keeps normal auto-continue instructions for non-final tasks", async () => {
+    // given
+    const sessionID = "atlas-non-final-session"
+    setupMessageStorage(sessionID)
+
+    const planPath = join(testDirectory, "implementation-plan.md")
+    writeFileSync(
+      planPath,
+      `# Plan
+
+## TODOs
+- [x] 1. Setup
+- [ ] 2. Implement feature
+
+## Final Verification Wave (MANDATORY - after ALL implementation tasks)
+- [ ] F1. **Plan Compliance Audit** - \`oracle\`
+- [ ] F2. **Code Quality Review** - \`unspecified-high\`
+- [ ] F3. **Real Manual QA** - \`unspecified-high\`
+- [ ] F4. **Scope Fidelity Check** - \`deep\`
+`,
+    )
+
+    const state: BoulderState = {
+      active_plan: planPath,
+      started_at: "2026-01-02T10:00:00Z",
+      session_ids: [sessionID],
+      plan_name: "implementation-plan",
+      agent: "atlas",
+    }
+    writeBoulderState(testDirectory, state)
+
+    const hook = createAtlasHook(createMockPluginInput())
+    const toolOutput = {
+      title: "Sisyphus Task",
+      output: `Implementation finished successfully
+
+<task_metadata>
+session_id: ses_feature_task
+</task_metadata>`,
+      metadata: {},
+    }
+
+    // when
+    await hook["tool.execute.after"]({ tool: "task", sessionID }, toolOutput)
+
+    // then
+    expect(toolOutput.output).toContain("COMPLETION GATE")
+    expect(toolOutput.output).toContain("STEP 8: PROCEED TO NEXT TASK")
+    expect(toolOutput.output).not.toContain("FINAL WAVE APPROVAL GATE")
+
+    cleanupMessageStorage(sessionID)
+  })
+})

src/hooks/atlas/final-wave-approval-gate.ts

@@ -0,0 +1,47 @@
+import { existsSync, readFileSync } from "node:fs"
+
+const APPROVE_VERDICT_PATTERN = /\bVERDICT:\s*APPROVE\b/i
+const FINAL_VERIFICATION_HEADING_PATTERN = /^##\s+Final Verification Wave\b/i
+const UNCHECKED_TASK_PATTERN = /^\s*[-*]\s*\[\s*\]\s*(.+)$/
+const FINAL_WAVE_TASK_PATTERN = /^F\d+\./i
+
+export function shouldPauseForFinalWaveApproval(input: {
+  planPath: string
+  taskOutput: string
+}): boolean {
+  if (!APPROVE_VERDICT_PATTERN.test(input.taskOutput)) {
+    return false
+  }
+
+  if (!existsSync(input.planPath)) {
+    return false
+  }
+
+  try {
+    const content = readFileSync(input.planPath, "utf-8")
+    const lines = content.split(/\r?\n/)
+    let inFinalVerificationWave = false
+    let uncheckedTaskCount = 0
+    let uncheckedFinalWaveTaskCount = 0
+
+    for (const line of lines) {
+      if (/^##\s+/.test(line)) {
+        inFinalVerificationWave = FINAL_VERIFICATION_HEADING_PATTERN.test(line)
+      }
+
+      const uncheckedTaskMatch = line.match(UNCHECKED_TASK_PATTERN)
+      if (!uncheckedTaskMatch) {
+        continue
+      }
+
+      uncheckedTaskCount += 1
+      if (inFinalVerificationWave && FINAL_WAVE_TASK_PATTERN.test(uncheckedTaskMatch[1].trim())) {
+        uncheckedFinalWaveTaskCount += 1
+      }
+    }
+
+    return uncheckedTaskCount === 1 && uncheckedFinalWaveTaskCount === 1
+  } catch {
+    return false
+  }
+}

src/hooks/atlas/idle-event.ts

@@ -1,11 +1,9 @@
 import type { PluginInput } from "@opencode-ai/plugin"
-import { appendSessionId, getPlanProgress, readBoulderState } from "../../features/boulder-state"
-import type { BoulderState, PlanProgress } from "../../features/boulder-state"
-import { subagentSessions } from "../../features/claude-code-session-state"
+import { getPlanProgress, readBoulderState } from "../../features/boulder-state"
 import { log } from "../../shared/logger"
-import { isSessionInBoulderLineage } from "./boulder-session-lineage"
 import { injectBoulderContinuation } from "./boulder-continuation-injector"
 import { HOOK_NAME } from "./hook-name"
+import { resolveActiveBoulderSession } from "./resolve-active-boulder-session"
 import type { AtlasHookOptions, SessionState } from "./types"
 
 const CONTINUATION_COOLDOWN_MS = 5000
@@ -19,54 +17,6 @@ function hasRunningBackgroundTasks(sessionID: string, options?: AtlasHookOptions
     : false
 }
 
-async function resolveActiveBoulderSession(input: {
-  client: PluginInput["client"]
-  directory: string
-  sessionID: string
-}): Promise<{
-  boulderState: BoulderState
-  progress: PlanProgress
-  appendedSession: boolean
-} | null> {
-  const boulderState = readBoulderState(input.directory)
-  if (!boulderState) {
-    return null
-  }
-
-  const progress = getPlanProgress(boulderState.active_plan)
-  if (progress.isComplete) {
-    return { boulderState, progress, appendedSession: false }
-  }
-
-  if (boulderState.session_ids.includes(input.sessionID)) {
-    return { boulderState, progress, appendedSession: false }
-  }
-
-  if (!subagentSessions.has(input.sessionID)) {
-    return null
-  }
-
-  const belongsToActiveBoulder = await isSessionInBoulderLineage({
-    client: input.client,
-    sessionID: input.sessionID,
-    boulderSessionIDs: boulderState.session_ids,
-  })
-  if (!belongsToActiveBoulder) {
-    return null
-  }
-
-  const updatedBoulderState = appendSessionId(input.directory, input.sessionID)
-  if (!updatedBoulderState?.session_ids.includes(input.sessionID)) {
-    return null
-  }
-
-  return {
-    boulderState: updatedBoulderState,
-    progress,
-    appendedSession: true,
-  }
-}
-
 async function injectContinuation(input: {
   ctx: PluginInput
   sessionID: string
@@ -113,6 +63,7 @@ function scheduleRetry(input: {
     sessionState.pendingRetryTimer = undefined
 
     if (sessionState.promptFailureCount >= 2) return
+    if (sessionState.waitingForFinalWaveApproval) return
 
     const currentBoulder = readBoulderState(ctx.directory)
     if (!currentBoulder) return
@@ -173,6 +124,11 @@ export async function handleAtlasSessionIdle(input: {
   const sessionState = getState(sessionID)
   const now = Date.now()
 
+  if (sessionState.waitingForFinalWaveApproval) {
+    log(`[${HOOK_NAME}] Skipped: waiting for explicit final-wave approval`, { sessionID })
+    return
+  }
+
   if (sessionState.lastEventWasAbortError) {
     sessionState.lastEventWasAbortError = false
     log(`[${HOOK_NAME}] Skipped: abort error immediately before idle`, { sessionID })

src/hooks/atlas/resolve-active-boulder-session.ts

@@ -0,0 +1,53 @@
+import type { PluginInput } from "@opencode-ai/plugin"
+import { appendSessionId, getPlanProgress, readBoulderState } from "../../features/boulder-state"
+import type { BoulderState, PlanProgress } from "../../features/boulder-state"
+import { subagentSessions } from "../../features/claude-code-session-state"
+import { isSessionInBoulderLineage } from "./boulder-session-lineage"
+
+export async function resolveActiveBoulderSession(input: {
+  client: PluginInput["client"]
+  directory: string
+  sessionID: string
+}): Promise<{
+  boulderState: BoulderState
+  progress: PlanProgress
+  appendedSession: boolean
+} | null> {
+  const boulderState = readBoulderState(input.directory)
+  if (!boulderState) {
+    return null
+  }
+
+  const progress = getPlanProgress(boulderState.active_plan)
+  if (progress.isComplete) {
+    return { boulderState, progress, appendedSession: false }
+  }
+
+  if (boulderState.session_ids.includes(input.sessionID)) {
+    return { boulderState, progress, appendedSession: false }
+  }
+
+  if (!subagentSessions.has(input.sessionID)) {
+    return null
+  }
+
+  const belongsToActiveBoulder = await isSessionInBoulderLineage({
+    client: input.client,
+    sessionID: input.sessionID,
+    boulderSessionIDs: boulderState.session_ids,
+  })
+  if (!belongsToActiveBoulder) {
+    return null
+  }
+
+  const updatedBoulderState = appendSessionId(input.directory, input.sessionID)
+  if (!updatedBoulderState?.session_ids.includes(input.sessionID)) {
+    return null
+  }
+
+  return {
+    boulderState: updatedBoulderState,
+    progress,
+    appendedSession: true,
+  }
+}

src/hooks/atlas/tool-execute-after.ts

@@ -3,20 +3,28 @@ import { appendSessionId, getPlanProgress, readBoulderState } from "../../featur
 import { log } from "../../shared/logger"
 import { isCallerOrchestrator } from "../../shared/session-utils"
 import { collectGitDiffStats, formatFileChanges } from "../../shared/git-worktree"
+import { shouldPauseForFinalWaveApproval } from "./final-wave-approval-gate"
 import { HOOK_NAME } from "./hook-name"
 import { DIRECT_WORK_REMINDER } from "./system-reminder-templates"
 import { isSisyphusPath } from "./sisyphus-path"
 import { extractSessionIdFromOutput } from "./subagent-session-id"
-import { buildCompletionGate, buildOrchestratorReminder, buildStandaloneVerificationReminder } from "./verification-reminders"
+import {
+  buildCompletionGate,
+  buildFinalWaveApprovalReminder,
+  buildOrchestratorReminder,
+  buildStandaloneVerificationReminder,
+} from "./verification-reminders"
 import { isWriteOrEditToolName } from "./write-edit-tool-policy"
+import type { SessionState } from "./types"
 import type { ToolExecuteAfterInput, ToolExecuteAfterOutput } from "./types"
 
 export function createToolExecuteAfterHandler(input: {
   ctx: PluginInput
   pendingFilePaths: Map<string, string>
   autoCommit: boolean
-  }): (toolInput: ToolExecuteAfterInput, toolOutput: ToolExecuteAfterOutput) => Promise<void> {
-  const { ctx, pendingFilePaths, autoCommit } = input
+  getState: (sessionID: string) => SessionState
+}): (toolInput: ToolExecuteAfterInput, toolOutput: ToolExecuteAfterOutput) => Promise<void> {
+  const { ctx, pendingFilePaths, autoCommit, getState } = input
   return async (toolInput, toolOutput): Promise<void> => {
     // Guard against undefined output (e.g., from /review command - see issue #1035)
     if (!toolOutput) {
@@ -75,10 +83,31 @@ export function createToolExecuteAfterHandler(input: {
 
         // Preserve original subagent response - critical for debugging failed tasks
         const originalResponse = toolOutput.output
+        const shouldPauseForApproval = shouldPauseForFinalWaveApproval({
+          planPath: boulderState.active_plan,
+          taskOutput: originalResponse,
+        })
+
+        if (toolInput.sessionID) {
+          const sessionState = getState(toolInput.sessionID)
+          sessionState.waitingForFinalWaveApproval = shouldPauseForApproval
+
+          if (shouldPauseForApproval && sessionState.pendingRetryTimer) {
+            clearTimeout(sessionState.pendingRetryTimer)
+            sessionState.pendingRetryTimer = undefined
+          }
+        }
+
+        const leadReminder = shouldPauseForApproval
+          ? buildFinalWaveApprovalReminder(boulderState.plan_name, progress, subagentSessionId)
+          : buildCompletionGate(boulderState.plan_name, subagentSessionId)
+        const followupReminder = shouldPauseForApproval
+          ? null
+          : buildOrchestratorReminder(boulderState.plan_name, progress, subagentSessionId, autoCommit, false)
 
         toolOutput.output = `
 <system-reminder>
-${buildCompletionGate(boulderState.plan_name, subagentSessionId)}
+${leadReminder}
 </system-reminder>
 
 ## SUBAGENT WORK COMPLETED
@@ -91,13 +120,16 @@ ${fileChanges}
 
 ${originalResponse}
 
-<system-reminder>
-${buildOrchestratorReminder(boulderState.plan_name, progress, subagentSessionId, autoCommit, false)}
-</system-reminder>`
+${
+  followupReminder === null
+    ? ""
+    : `<system-reminder>\n${followupReminder}\n</system-reminder>`
+}`
         log(`[${HOOK_NAME}] Output transformed for orchestrator mode (boulder)`, {
           plan: boulderState.plan_name,
           progress: `${progress.completed}/${progress.total}`,
           fileCount: gitStats.length,
+          waitingForFinalWaveApproval: shouldPauseForApproval,
         })
       } else {
         toolOutput.output += `\n<system-reminder>\n${buildStandaloneVerificationReminder(subagentSessionId)}\n</system-reminder>`

src/hooks/atlas/types.ts

@@ -31,4 +31,5 @@ export interface SessionState {
   promptFailureCount: number
   lastFailureAt?: number
   pendingRetryTimer?: ReturnType<typeof setTimeout>
+  waitingForFinalWaveApproval?: boolean
 }

src/hooks/atlas/verification-reminders.ts

@@ -108,6 +108,45 @@ ${commitStep}
 **${remaining} tasks remain. Keep bouldering.**`
 }
 
+export function buildFinalWaveApprovalReminder(
+  planName: string,
+  progress: { total: number; completed: number },
+  sessionId: string
+): string {
+  const remaining = progress.total - progress.completed
+
+  return `
+---
+
+**BOULDER STATE:** Plan: \
+\`${planName}\` | ${progress.completed}/${progress.total} done | ${remaining} remaining
+
+---
+
+${buildVerificationReminder(sessionId)}
+
+**FINAL WAVE APPROVAL GATE**
+
+The last Final Verification Wave result just passed.
+This is the ONLY point where approval-style user interaction is required.
+
+1. Read \
+\`.sisyphus/plans/${planName}.md\` again and confirm the remaining unchecked item is the last final-wave task.
+2. Consolidate the F1-F4 verdicts into a short summary for the user.
+3. Tell the user all final reviewers approved.
+4. Ask for explicit user approval before editing the last final-wave checkbox or marking the plan complete.
+5. Wait for the user's explicit approval. Do NOT auto-continue. Do NOT call \
+\`task()\` again unless the user rejects and requests fixes.
+
+If the user rejects or requests changes:
+- delegate the required fix
+- re-run the affected final-wave reviewer
+- present the updated results again
+- wait again for explicit user approval
+
+**DO NOT mark the final-wave checkbox complete until the user explicitly says okay.**`
+}
+
 export function buildStandaloneVerificationReminder(sessionId: string): string {
   return `
 ---