refactor: standardize Codex skill API calls to functions.request_user_input and add functions.update_plan

- Replace bare request_user_input() with functions.request_user_input() across 94 skill files
- Replace AskUserQuestion with request_user_input in 3 team-config.json tool arrays
- Add functions.update_plan progress tracking to 9 multi-phase skills
  (investigate, ship, security-audit, team-designer, review-cycle,
   issue-discover, parallel-dev-cycle, spec-generator, workflow-test-fix-cycle)

Author: catlog22

.codex/skills/analyze-with-file/SKILL.md

@@ -228,7 +228,7 @@ const topic = isRole
 
    ```javascript
    if (executionMode === null) {
-     const modeAnswer = request_user_input({
+     const modeAnswer = functions.request_user_input({
        questions: [{
          question: "Choose brainstorming mode:",
          header: "Mode",
@@ -324,7 +324,7 @@ TOPIC: ${topic}" --tool gemini --mode analysis --rule planning-breakdown-task-st
        features.forEach(f => console.log(`  - [${f.id}] ${f.title}`))
      }
 
-     const answer = request_user_input({
+     const answer = functions.request_user_input({
        questions: [{
          question: "Approve brainstorm framework?",
          header: "Validate",
@@ -339,7 +339,7 @@ TOPIC: ${topic}" --tool gemini --mode analysis --rule planning-breakdown-task-st
      if (answer.Validate === "Cancel") return
      if (answer.Validate === "Modify Roles") {
        // Allow user to adjust via request_user_input
-       const roleAnswer = request_user_input({
+       const roleAnswer = functions.request_user_input({
          questions: [{
            question: "Select roles for analysis:",
            header: "Roles",

.codex/skills/brainstorm-with-file/SKILL.md

@@ -252,7 +252,7 @@ Manifest: ${sessionFolder}/cleanup-manifest.json
 }
 
 // User confirmation
-const selection = request_user_input({
+const selection = functions.request_user_input({
   questions: [
     {
       header: "清理类别",

.codex/skills/brainstorm/SKILL.md

@@ -437,7 +437,7 @@ REQUIREMENT: ${requirement}" --tool gemini --mode analysis --rule planning-break
        waveTasks.forEach(t => console.log(`  - [${t.id}] ${t.title}`))
      }
 
-     const answer = request_user_input({
+     const answer = functions.request_user_input({
        questions: [{
          header: "验证",
          id: "validation",
@@ -820,7 +820,7 @@ ${[...new Set(tasks.flatMap(t => (t.files_modified || '').split(';')).filter(Boo
 
    ```javascript
    if (!AUTO_YES && failed.length > 0) {
-     const answer = request_user_input({
+     const answer = functions.request_user_input({
        questions: [{
          header: "下一步",
          id: "next_step",

.codex/skills/clean/SKILL.md

@@ -81,6 +81,20 @@ Utility subagents callable by the investigator agent during analysis phases:
 
 ## Phase Execution
 
+### Progress Tracking Initialization
+
+Before spawning any agent, initialize progress tracking for all phases:
+
+```
+functions.update_plan([
+  { id: "phase-1", title: "Phase 1: Root Cause Investigation", status: "in_progress" },
+  { id: "phase-2", title: "Phase 2: Pattern Analysis", status: "pending" },
+  { id: "phase-3", title: "Phase 3: Hypothesis Testing", status: "pending" },
+  { id: "phase-4", title: "Phase 4: Implementation", status: "pending" },
+  { id: "phase-5", title: "Phase 5: Verification & Report", status: "pending" }
+])
+```
+
 ### Phase 1: Root Cause Investigation
 
 **Objective**: Spawn the investigator agent and assign the Phase 1 investigation task. Agent reproduces the bug, collects evidence, and runs initial diagnosis.
@@ -127,6 +141,8 @@ const p1Result = wait_agent({ targets: ["investigator"], timeout_ms: 300000 })
 |----------|-------------|
 | p1Result | Phase 1 completion summary with evidence, reproduction, initial diagnosis |
 
+**Progress**: `functions.update_plan([{id: "phase-1", status: "completed"}, {id: "phase-2", status: "in_progress"}])`
+
 ---
 
 ### Phase 2: Pattern Analysis
@@ -169,6 +185,8 @@ const p2Result = wait_agent({ targets: ["investigator"], timeout_ms: 300000 })
 |----------|-------------|
 | p2Result | Pattern analysis section: scope classification, similar occurrences, scope justification |
 
+**Progress**: `functions.update_plan([{id: "phase-2", status: "completed"}, {id: "phase-3", status: "in_progress"}])`
+
 ---
 
 ### Phase 3: Hypothesis Testing
@@ -218,6 +236,8 @@ const p3Result = wait_agent({ targets: ["investigator"], timeout_ms: 480000 })
 
 If BLOCKED: close investigator and surface the diagnostic dump to the user. Do not proceed to Phase 4.
 
+**Progress (on success)**: `functions.update_plan([{id: "phase-3", status: "completed"}, {id: "phase-4", status: "in_progress"}])`
+
 ---
 
 ### Phase 4: Implementation
@@ -261,6 +281,8 @@ const p4Result = wait_agent({ targets: ["investigator"], timeout_ms: 480000 })
 |----------|-------------|
 | p4Result | fix_applied section: files changed, regression test details, reproduction verified |
 
+**Progress**: `functions.update_plan([{id: "phase-4", status: "completed"}, {id: "phase-5", status: "in_progress"}])`
+
 ---
 
 ### Phase 5: Verification & Report
@@ -303,6 +325,8 @@ const p5Result = wait_agent({ targets: ["investigator"], timeout_ms: 300000 })
 |----------|-------------|
 | p5Result | Completion status, test suite results, path to debug report file |
 
+**Progress**: `functions.update_plan([{id: "phase-5", status: "completed"}])`
+
 ---
 
 ## Lifecycle Management

.codex/skills/csv-wave-pipeline/SKILL.md

@@ -102,6 +102,7 @@ Action Selection:
    │   ├─ Short text (< 80 chars) → Create New (Phase 1)
    │   └─ Long descriptive text (≥ 80 chars) → Discover by Prompt (Phase 3)
    └─ Otherwise → request_user_input to select action
+   └─ Initialize progress tracking: functions.update_plan([...phases])
 
 Phase Execution (load one phase):
    ├─ Phase 1: Create New          → phases/01-issue-new.md
@@ -172,7 +173,7 @@ function detectAction(input, flags) {
 
 ```javascript
 // When action cannot be auto-detected
-const answer = request_user_input({
+const answer = functions.request_user_input({
   questions: [{
     header: "Action",
     id: "action",
@@ -201,6 +202,13 @@ const actionMap = {
   "Discover Issues": "discover",
   "Discover by Prompt": "discover-by-prompt"
 };
+
+// Initialize progress tracking (MANDATORY)
+functions.update_plan([
+  { id: "action-select", title: "Action Selection", status: "completed" },
+  { id: "phase-exec", title: `Phase: ${selectedAction}`, status: "in_progress" },
+  { id: "post-phase", title: "Post-Phase: Next Steps", status: "pending" }
+])
 ```
 
 ## Data Flow
@@ -317,11 +325,13 @@ close_agent({ id: agentId })
 
 ## Post-Phase Next Steps
 
+**Progress**: `functions.update_plan([{id: "phase-exec", status: "completed"}, {id: "post-phase", status: "in_progress"}])`
+
 After successful phase execution, recommend next action:
 
 ```javascript
 // After Create New (issue created)
-request_user_input({
+functions.request_user_input({
   questions: [{
     header: "Next Step",
     id: "next_after_create",
@@ -336,7 +346,7 @@ request_user_input({
 // answer.answers.next_after_create.answers[0] → selected label
 
 // After Discover / Discover by Prompt (discoveries generated)
-request_user_input({
+functions.request_user_input({
   questions: [{
     header: "Next Step",
     id: "next_after_discover",
@@ -350,6 +360,9 @@ request_user_input({
 });  // BLOCKS (wait for user response)
 // answer.answers.next_after_discover.answers[0] → selected label
 // If "Quick Plan & Execute (Recommended)" → Read phases/04-quick-execute.md, execute
+
+// Mark workflow complete
+functions.update_plan([{ id: "post-phase", status: "completed" }])
 ```
 
 ## Related Skills & Commands

.codex/skills/investigate/orchestrator.md

@@ -145,7 +145,7 @@ if (clarityScore >= 1 && clarityScore <= 2 && !issueData.affected_components?.le
 ```javascript
 // ONLY ask questions if clarity is low
 if (clarityScore < 2 && (!issueData.context || issueData.context.length < 20)) {
-  const answer = request_user_input({
+  const answer = functions.request_user_input({
     questions: [{
       header: "Clarify",
       id: "clarify",

.codex/skills/issue-discover/SKILL.md

@@ -87,7 +87,7 @@ if (args.perspectives) {
   selectedPerspectives = args.perspectives.split(',').map(p => p.trim());
 } else {
   // Interactive selection via request_user_input
-  const response = request_user_input({
+  const response = functions.request_user_input({
     questions: [{
       header: "Focus",
       id: "focus",
@@ -273,7 +273,7 @@ await updateDiscoveryState(outputDir, {
 ```javascript
 const hasHighPriority = issues.some(i => i.priority === 'critical' || i.priority === 'high');
 
-await request_user_input({
+await functions.request_user_input({
   questions: [{
     header: "Next Step",
     id: "next_step",

.codex/skills/issue-discover/phases/01-issue-new.md

@@ -390,7 +390,7 @@ await updateDiscoveryState(outputDir, {
 });
 
 // Prompt user for next action
-await request_user_input({
+await functions.request_user_input({
   questions: [{
     header: "Next Step",
     id: "next_step",