diff --git a/.codex/agents/ccw-loop-b-complete.md b/.codex/agents/ccw-loop-b-complete.md
index bc696770..766e96e3 100644
--- a/.codex/agents/ccw-loop-b-complete.md
+++ b/.codex/agents/ccw-loop-b-complete.md
@@ -41,8 +41,8 @@ PROJECT CONTEXT:
 ## Execution Steps
 
 1. **Read all progress**
-   - Load worker outputs from `.loop/{loopId}.workers/`
-   - Read progress files from `.loop/{loopId}.progress/`
+   - Load worker outputs from `.workflow/.loop/{loopId}.workers/`
+   - Read progress files from `.workflow/.loop/{loopId}.progress/`
    - Consolidate findings
 
 2. **Verify completeness**
diff --git a/.codex/agents/ccw-loop-executor.md b/.codex/agents/ccw-loop-executor.md
index 4b040a52..327498b0 100644
--- a/.codex/agents/ccw-loop-executor.md
+++ b/.codex/agents/ccw-loop-executor.md
@@ -39,7 +39,7 @@ You are a CCW Loop Executor - a stateless iterative development specialist that
 
 ```javascript
 // Read current state
-const state = JSON.parse(Read('.loop/{loopId}.json'))
+const state = JSON.parse(Read('.workflow/.loop/{loopId}.json'))
 
 // Check control signals
 if (state.status === 'paused') {
@@ -110,7 +110,7 @@ NEXT_ACTION_NEEDED: {action_name} | WAITING_INPUT | COMPLETED | PAUSED
 
 ```javascript
 function updateState(loopId, skillStateUpdates) {
-  const state = JSON.parse(Read(`.loop/${loopId}.json`))
+  const state = JSON.parse(Read(`.workflow/.loop/${loopId}.json`))
   state.updated_at = getUtc8ISOString()
   state.skill_state = {
     ...state.skill_state,
@@ -118,7 +118,7 @@ function updateState(loopId, skillStateUpdates) {
     last_action: currentAction,
     completed_actions: [...state.skill_state.completed_actions, currentAction]
   }
-  Write(`.loop/${loopId}.json`, JSON.stringify(state, null, 2))
+  Write(`.workflow/.loop/${loopId}.json`, JSON.stringify(state, null, 2))
 }
 ```
 
@@ -136,7 +136,7 @@ function updateState(loopId, skillStateUpdates) {
 5. Update state with skill_state
 
 **Output**:
-- `.loop/{loopId}.progress/develop.md` (initialized)
+- `.workflow/.loop/{loopId}.progress/develop.md` (initialized)
 - State: skill_state populated with tasks
 
 ### DEVELOP Action
diff --git a/.codex/skills/ccw-loop-b/README.md b/.codex/skills/ccw-loop-b/README.md
index f09e3297..aeb708a4 100644
--- a/.codex/skills/ccw-loop-b/README.md
+++ b/.codex/skills/ccw-loop-b/README.md
@@ -91,7 +91,7 @@ Spawn multiple workers simultaneously, batch wait for results.
 ## Session Structure
 
 ```
-.loop/
+.workflow/.loop/
 +-- {loopId}.json                    # Master state
 +-- {loopId}.workers/                # Worker outputs
 |   +-- init.output.json
@@ -184,7 +184,7 @@ Coordinator adapts to mode:
 
 ### 3. State Management
 
-Unified state at `.loop/{loopId}.json`:
+Unified state at `.workflow/.loop/{loopId}.json`:
 - **API compatible**: Works with CCW API
 - **Extension fields**: Skill-specific data in `skill_state`
 - **Worker outputs**: Structured JSON for each action
diff --git a/.codex/skills/ccw-loop-b/SKILL.md b/.codex/skills/ccw-loop-b/SKILL.md
index 0e19004e..2217b2f2 100644
--- a/.codex/skills/ccw-loop-b/SKILL.md
+++ b/.codex/skills/ccw-loop-b/SKILL.md
@@ -61,7 +61,7 @@ Coordinator -> spawn [develop, debug, validate] in parallel -> wait({ ids: all }
 ## Session Structure
 
 ```
-.loop/
+.workflow/.loop/
 +-- {loopId}.json              # Master state
 +-- {loopId}.workers/          # Worker outputs
 |   +-- develop.output.json
@@ -242,9 +242,9 @@ function buildWorkerPrompt(action, loopId, state) {
 
 - **Loop ID**: ${loopId}
 - **Action**: ${action}
-- **State File**: .loop/${loopId}.json
-- **Output File**: .loop/${loopId}.workers/${action}.output.json
-- **Progress File**: .loop/${loopId}.progress/${action}.md
+- **State File**: .workflow/.loop/${loopId}.json
+- **Output File**: .workflow/.loop/${loopId}.workers/${action}.output.json
+- **Progress File**: .workflow/.loop/${loopId}.progress/${action}.md
 
 ## CURRENT STATE
 
diff --git a/.codex/skills/ccw-loop-b/phases/orchestrator.md b/.codex/skills/ccw-loop-b/phases/orchestrator.md
index c65ce6ee..3cc29752 100644
--- a/.codex/skills/ccw-loop-b/phases/orchestrator.md
+++ b/.codex/skills/ccw-loop-b/phases/orchestrator.md
@@ -14,7 +14,7 @@ Read state -> Select mode -> Spawn workers -> Wait results -> Merge -> Update st
 
 ```javascript
 function readState(loopId) {
-  const stateFile = `.loop/${loopId}.json`
+  const stateFile = `.workflow/.loop/${loopId}.json`
   return fs.existsSync(stateFile)
     ? JSON.parse(Read(stateFile))
     : null
@@ -252,6 +252,6 @@ function parseWorkerResult(output) {
 ## Best Practices
 
 1. **Worker 生命周期**: spawn → wait → close，不保留 worker
-2. **结果持久化**: Worker 输出写入 `.loop/{loopId}.workers/`
+2. **结果持久化**: Worker 输出写入 `.workflow/.loop/{loopId}.workers/`
 3. **状态同步**: 每次 worker 完成后更新 state
 4. **超时处理**: send_input 请求收敛，再超时则跳过
diff --git a/.codex/skills/ccw-loop-b/phases/state-schema.md b/.codex/skills/ccw-loop-b/phases/state-schema.md
index d7581e96..17dbf966 100644
--- a/.codex/skills/ccw-loop-b/phases/state-schema.md
+++ b/.codex/skills/ccw-loop-b/phases/state-schema.md
@@ -56,7 +56,7 @@
 
 ## Worker Output Structure
 
-Each worker writes to `.loop/{loopId}.workers/{action}.output.json`:
+Each worker writes to `.workflow/.loop/{loopId}.workers/{action}.output.json`:
 
 ```json
 {
@@ -81,7 +81,7 @@ Each worker writes to `.loop/{loopId}.workers/{action}.output.json`:
 
 ## Progress File Structure
 
-Human-readable progress in `.loop/{loopId}.progress/{action}.md`:
+Human-readable progress in `.workflow/.loop/{loopId}.progress/{action}.md`:
 
 ```markdown
 # Develop Progress
@@ -165,7 +165,7 @@ When `mode === 'parallel'`:
 ## Directory Structure
 
 ```
-.loop/
+.workflow/.loop/
 +-- loop-b-20260122-abc123.json          # Master state
 +-- loop-b-20260122-abc123.workers/
 |   +-- init.output.json
diff --git a/.codex/skills/ccw-loop/README.md b/.codex/skills/ccw-loop/README.md
index 4af1f973..b3b18863 100644
--- a/.codex/skills/ccw-loop/README.md
+++ b/.codex/skills/ccw-loop/README.md
@@ -68,7 +68,7 @@ Files are in `.codex/skills/ccw-loop/`:
 
 ```
 1. Parse arguments (task or --loop-id)
-2. Create/read state from .loop/{loopId}.json
+2. Create/read state from .workflow/.loop/{loopId}.json
 3. spawn_agent with ccw-loop-executor role
 4. Main loop:
    a. wait() for agent output
@@ -84,7 +84,7 @@ Files are in `.codex/skills/ccw-loop/`:
 ## Session Files
 
 ```
-.loop/
+.workflow/.loop/
 +-- {loopId}.json              # Master state (API + Skill)
 +-- {loopId}.progress/
     +-- develop.md             # Development timeline
@@ -157,7 +157,7 @@ spawn_agent({
 Works with CCW Dashboard Loop Monitor:
 - Dashboard creates loop via API
 - API triggers this skill with `--loop-id`
-- Skill reads/writes `.loop/{loopId}.json`
+- Skill reads/writes `.workflow/.loop/{loopId}.json`
 - Dashboard polls state for real-time updates
 
 ### Control Signals
diff --git a/.codex/skills/ccw-loop/SKILL.md b/.codex/skills/ccw-loop/SKILL.md
index b69fb653..74d0306e 100644
--- a/.codex/skills/ccw-loop/SKILL.md
+++ b/.codex/skills/ccw-loop/SKILL.md
@@ -27,8 +27,8 @@ Stateless iterative development loop using Codex subagent pattern. Supports deve
 +-------------------------------------------------------------+
 |              loop-v2-routes.ts (Control Plane)               |
 |                                                              |
-|  State: .loop/{loopId}.json (MASTER)                         |
-|  Tasks: .loop/{loopId}.tasks.jsonl                           |
+|  State: .workflow/.loop/{loopId}.json (MASTER)                         |
+|  Tasks: .workflow/.loop/{loopId}.tasks.jsonl                           |
 |                                                              |
 |  /start -> Trigger ccw-loop skill with --loop-id             |
 |  /pause -> Set status='paused' (skill checks before action)  |
@@ -42,8 +42,8 @@ Stateless iterative development loop using Codex subagent pattern. Supports deve
 |                                                              |
 |  Codex Pattern: spawn_agent -> wait -> send_input -> close   |
 |                                                              |
-|  Reads/Writes: .loop/{loopId}.json (unified state)           |
-|  Writes: .loop/{loopId}.progress/* (progress files)          |
+|  Reads/Writes: .workflow/.loop/{loopId}.json (unified state)           |
+|  Writes: .workflow/.loop/{loopId}.progress/* (progress files)          |
 |                                                              |
 |  BEFORE each action:                                         |
 |    -> Check status: paused/stopped -> exit gracefully        |
@@ -55,9 +55,9 @@ Stateless iterative development loop using Codex subagent pattern. Supports deve
 
 ## Key Design Principles (Codex Adaptation)
 
-1. **Unified State**: API and Skill share `.loop/{loopId}.json` state file
+1. **Unified State**: API and Skill share `.workflow/.loop/{loopId}.json` state file
 2. **Control Signals**: Skill checks status field before each action (paused/stopped)
-3. **File-Driven**: All progress documented in `.loop/{loopId}.progress/`
+3. **File-Driven**: All progress documented in `.workflow/.loop/{loopId}.progress/`
 4. **Resumable**: Continue any loop with `--loop-id`
 5. **Dual Trigger**: Supports API trigger (`--loop-id`) and direct call (task description)
 6. **Single Agent Deep Interaction**: Use send_input for multi-phase execution instead of multiple agents
@@ -100,7 +100,7 @@ Develop -> Debug -> Validate -> (if issues) -> Develop -> ...
 ## Session Structure (Unified Location)
 
 ```
-.loop/
+.workflow/.loop/
 +-- {loopId}.json              # Master state file (API + Skill shared)
 +-- {loopId}.tasks.jsonl       # Task list (API managed)
 +-- {loopId}.progress/         # Skill progress files
@@ -129,8 +129,8 @@ const loopId = args['--loop-id'] || (() => {
   return `loop-v2-${timestamp}-${random}`
 })()
 
-const loopFile = `.loop/${loopId}.json`
-const progressDir = `.loop/${loopId}.progress`
+const loopFile = `.workflow/.loop/${loopId}.json`
+const progressDir = `.workflow/.loop/${loopId}.progress`
 
 // Create progress directory
 mkdir -p "${progressDir}"
@@ -144,14 +144,14 @@ mkdir -p "${progressDir}"
 // Step 1: Read or create initial state
 let state = null
 if (existingLoopId) {
-  state = JSON.parse(Read(`.loop/${loopId}.json`))
+  state = JSON.parse(Read(`.workflow/.loop/${loopId}.json`))
   if (!state) {
     console.error(`Loop not found: ${loopId}`)
     return
   }
 } else {
   state = createInitialState(loopId, taskDescription)
-  Write(`.loop/${loopId}.json`, JSON.stringify(state, null, 2))
+  Write(`.workflow/.loop/${loopId}.json`, JSON.stringify(state, null, 2))
 }
 
 // Step 2: Create orchestrator agent (single agent handles all phases)
@@ -169,7 +169,7 @@ const agent = spawn_agent({
 ## LOOP CONTEXT
 
 - **Loop ID**: ${loopId}
-- **State File**: .loop/${loopId}.json
+- **State File**: .workflow/.loop/${loopId}.json
 - **Progress Dir**: ${progressDir}
 - **Mode**: ${mode}  // 'interactive' or 'auto'
 
@@ -186,7 +186,7 @@ ${taskDescription}
 You are executing CCW Loop orchestrator. Your job:
 
 1. **Check Control Signals**
-   - Read .loop/${loopId}.json
+   - Read .workflow/.loop/${loopId}.json
    - If status === 'paused' -> Output "PAUSED" and stop
    - If status === 'failed' -> Output "STOPPED" and stop
    - If status === 'running' -> Continue
@@ -200,7 +200,7 @@ You are executing CCW Loop orchestrator. Your job:
 3. **Execute Action**
    - Follow action instructions from ~/.codex/skills/ccw-loop/phases/actions/
    - Update progress files in ${progressDir}/
-   - Update state in .loop/${loopId}.json
+   - Update state in .workflow/.loop/${loopId}.json
 
 4. **Output Format**
    \`\`\`
@@ -283,10 +283,10 @@ Continue with: ${actionResult.next_action}
   }
 
   // Update iteration count in state
-  const currentState = JSON.parse(Read(`.loop/${loopId}.json`))
+  const currentState = JSON.parse(Read(`.workflow/.loop/${loopId}.json`))
   currentState.current_iteration = iteration
   currentState.updated_at = getUtc8ISOString()
-  Write(`.loop/${loopId}.json`, JSON.stringify(currentState, null, 2))
+  Write(`.workflow/.loop/${loopId}.json`, JSON.stringify(currentState, null, 2))
 }
 
 // Step 4: Cleanup
diff --git a/.codex/skills/ccw-loop/phases/actions/action-complete.md b/.codex/skills/ccw-loop/phases/actions/action-complete.md
index df4f9a63..bd15d6e8 100644
--- a/.codex/skills/ccw-loop/phases/actions/action-complete.md
+++ b/.codex/skills/ccw-loop/phases/actions/action-complete.md
@@ -20,7 +20,7 @@ Complete CCW Loop session and generate summary report.
 ### Step 1: Verify Control Signals
 
 ```javascript
-const state = JSON.parse(Read(`.loop/${loopId}.json`))
+const state = JSON.parse(Read(`.workflow/.loop/${loopId}.json`))
 
 if (state.status !== 'running') {
   return {
@@ -174,7 +174,7 @@ state.updated_at = timestamp
 state.skill_state.last_action = 'COMPLETE'
 state.skill_state.summary = stats
 
-Write(`.loop/${loopId}.json`, JSON.stringify(state, null, 2))
+Write(`.workflow/.loop/${loopId}.json`, JSON.stringify(state, null, 2))
 ```
 
 ## Output Format
@@ -190,8 +190,8 @@ ACTION_RESULT:
   }
 
 FILES_UPDATED:
-- .loop/{loopId}.json: Status set to completed
-- .loop/{loopId}.progress/summary.md: Summary report generated
+- .workflow/.loop/{loopId}.json: Status set to completed
+- .workflow/.loop/{loopId}.progress/summary.md: Summary report generated
 
 NEXT_ACTION_NEEDED: COMPLETED
 ```
diff --git a/.codex/skills/ccw-loop/phases/actions/action-debug.md b/.codex/skills/ccw-loop/phases/actions/action-debug.md
index 6102e76a..3f5fbeb0 100644
--- a/.codex/skills/ccw-loop/phases/actions/action-debug.md
+++ b/.codex/skills/ccw-loop/phases/actions/action-debug.md
@@ -233,7 +233,7 @@ if (confirmedHypothesis) {
 
 state.skill_state.last_action = 'DEBUG'
 state.updated_at = timestamp
-Write(`.loop/${loopId}.json`, JSON.stringify(state, null, 2))
+Write(`.workflow/.loop/${loopId}.json`, JSON.stringify(state, null, 2))
 ```
 
 ## Output Format
@@ -249,8 +249,8 @@ ACTION_RESULT:
   }
 
 FILES_UPDATED:
-- .loop/{loopId}.progress/debug.md: Understanding updated
-- .loop/{loopId}.progress/hypotheses.json: Hypotheses updated
+- .workflow/.loop/{loopId}.progress/debug.md: Understanding updated
+- .workflow/.loop/{loopId}.progress/hypotheses.json: Hypotheses updated
 - [Source files]: Instrumentation added
 
 NEXT_ACTION_NEEDED: {DEBUG | VALIDATE | DEVELOP | MENU}
diff --git a/.codex/skills/ccw-loop/phases/actions/action-develop.md b/.codex/skills/ccw-loop/phases/actions/action-develop.md
index 8a7322ea..0b23a3ba 100644
--- a/.codex/skills/ccw-loop/phases/actions/action-develop.md
+++ b/.codex/skills/ccw-loop/phases/actions/action-develop.md
@@ -20,7 +20,7 @@ Execute development task and record progress to develop.md.
 ### Step 1: Verify Control Signals
 
 ```javascript
-const state = JSON.parse(Read(`.loop/${loopId}.json`))
+const state = JSON.parse(Read(`.workflow/.loop/${loopId}.json`))
 
 if (state.status !== 'running') {
   return {
@@ -133,7 +133,7 @@ state.skill_state.last_action = 'DEVELOP'
 state.skill_state.completed_actions.push('DEVELOP')
 state.updated_at = timestamp
 
-Write(`.loop/${loopId}.json`, JSON.stringify(state, null, 2))
+Write(`.workflow/.loop/${loopId}.json`, JSON.stringify(state, null, 2))
 ```
 
 ## Output Format
@@ -149,9 +149,9 @@ ACTION_RESULT:
   }
 
 FILES_UPDATED:
-- .loop/{loopId}.json: Task status updated
-- .loop/{loopId}.progress/develop.md: Progress entry added
-- .loop/{loopId}.progress/changes.log: Change entry added
+- .workflow/.loop/{loopId}.json: Task status updated
+- .workflow/.loop/{loopId}.progress/develop.md: Progress entry added
+- .workflow/.loop/{loopId}.progress/changes.log: Change entry added
 
 NEXT_ACTION_NEEDED: {DEVELOP | DEBUG | VALIDATE | MENU}
 ```
diff --git a/.codex/skills/ccw-loop/phases/actions/action-init.md b/.codex/skills/ccw-loop/phases/actions/action-init.md
index 49bb11dd..c9dec20d 100644
--- a/.codex/skills/ccw-loop/phases/actions/action-init.md
+++ b/.codex/skills/ccw-loop/phases/actions/action-init.md
@@ -19,7 +19,7 @@ Initialize CCW Loop session, create directory structure and initial state.
 ### Step 1: Verify Control Signals
 
 ```javascript
-const state = JSON.parse(Read(`.loop/${loopId}.json`))
+const state = JSON.parse(Read(`.workflow/.loop/${loopId}.json`))
 
 if (state.status !== 'running') {
   return {
@@ -34,7 +34,7 @@ if (state.status !== 'running') {
 ### Step 2: Create Directory Structure
 
 ```javascript
-const progressDir = `.loop/${loopId}.progress`
+const progressDir = `.workflow/.loop/${loopId}.progress`
 
 // Directories created by orchestrator, verify they exist
 // mkdir -p ${progressDir}
@@ -131,7 +131,7 @@ const skillState = {
 
 state.skill_state = skillState
 state.updated_at = getUtc8ISOString()
-Write(`.loop/${loopId}.json`, JSON.stringify(state, null, 2))
+Write(`.workflow/.loop/${loopId}.json`, JSON.stringify(state, null, 2))
 ```
 
 ## Output Format
@@ -143,8 +143,8 @@ ACTION_RESULT:
 - message: Session initialized with {N} development tasks
 
 FILES_UPDATED:
-- .loop/{loopId}.json: skill_state initialized
-- .loop/{loopId}.progress/develop.md: Progress document created
+- .workflow/.loop/{loopId}.json: skill_state initialized
+- .workflow/.loop/{loopId}.progress/develop.md: Progress document created
 
 NEXT_ACTION_NEEDED: {DEVELOP (auto) | MENU (interactive)}
 ```
diff --git a/.codex/skills/ccw-loop/phases/actions/action-menu.md b/.codex/skills/ccw-loop/phases/actions/action-menu.md
index 825791f1..d67e0cbe 100644
--- a/.codex/skills/ccw-loop/phases/actions/action-menu.md
+++ b/.codex/skills/ccw-loop/phases/actions/action-menu.md
@@ -20,7 +20,7 @@ Display interactive action menu for user selection.
 ### Step 1: Verify Control Signals
 
 ```javascript
-const state = JSON.parse(Read(`.loop/${loopId}.json`))
+const state = JSON.parse(Read(`.workflow/.loop/${loopId}.json`))
 
 if (state.status !== 'running') {
   return {
@@ -172,7 +172,7 @@ If user selects "exit":
 // Save current state
 state.status = 'user_exit'
 state.updated_at = getUtc8ISOString()
-Write(`.loop/${loopId}.json`, JSON.stringify(state, null, 2))
+Write(`.workflow/.loop/${loopId}.json`, JSON.stringify(state, null, 2))
 
 return {
   action: 'MENU',
diff --git a/.codex/skills/ccw-loop/phases/actions/action-validate.md b/.codex/skills/ccw-loop/phases/actions/action-validate.md
index fd34dd48..6ebf8109 100644
--- a/.codex/skills/ccw-loop/phases/actions/action-validate.md
+++ b/.codex/skills/ccw-loop/phases/actions/action-validate.md
@@ -21,7 +21,7 @@ Run tests and verify implementation, record results to validate.md.
 ### Step 1: Verify Control Signals
 
 ```javascript
-const state = JSON.parse(Read(`.loop/${loopId}.json`))
+const state = JSON.parse(Read(`.workflow/.loop/${loopId}.json`))
 
 if (state.status !== 'running') {
   return {
@@ -174,7 +174,7 @@ state.skill_state.validate.last_run_at = timestamp
 
 state.skill_state.last_action = 'VALIDATE'
 state.updated_at = timestamp
-Write(`.loop/${loopId}.json`, JSON.stringify(state, null, 2))
+Write(`.workflow/.loop/${loopId}.json`, JSON.stringify(state, null, 2))
 ```
 
 ## Output Format
@@ -191,9 +191,9 @@ ACTION_RESULT:
   }
 
 FILES_UPDATED:
-- .loop/{loopId}.progress/validate.md: Validation report created
-- .loop/{loopId}.progress/test-results.json: Test results saved
-- .loop/{loopId}.progress/coverage.json: Coverage data saved (if available)
+- .workflow/.loop/{loopId}.progress/validate.md: Validation report created
+- .workflow/.loop/{loopId}.progress/test-results.json: Test results saved
+- .workflow/.loop/{loopId}.progress/coverage.json: Coverage data saved (if available)
 
 NEXT_ACTION_NEEDED: {COMPLETE | DEBUG | DEVELOP | MENU}
 ```
diff --git a/.codex/skills/ccw-loop/phases/orchestrator.md b/.codex/skills/ccw-loop/phases/orchestrator.md
index e357a9d3..e5a8d2cf 100644
--- a/.codex/skills/ccw-loop/phases/orchestrator.md
+++ b/.codex/skills/ccw-loop/phases/orchestrator.md
@@ -45,7 +45,7 @@ const getUtc8ISOString = () => new Date(Date.now() + 8 * 60 * 60 * 1000).toISOSt
  * @param loopId - Loop ID (e.g., "loop-v2-20260122-abc123")
  */
 function readLoopState(loopId) {
-  const stateFile = `.loop/${loopId}.json`
+  const stateFile = `.workflow/.loop/${loopId}.json`
 
   if (!fs.existsSync(stateFile)) {
     return null
@@ -63,7 +63,7 @@ function readLoopState(loopId) {
  * Create new loop state (only for direct calls, API triggers have existing state)
  */
 function createLoopState(loopId, taskDescription) {
-  const stateFile = `.loop/${loopId}.json`
+  const stateFile = `.workflow/.loop/${loopId}.json`
   const now = getUtc8ISOString()
 
   const state = {
@@ -83,7 +83,7 @@ function createLoopState(loopId, taskDescription) {
 
   // Ensure directories exist
   mkdir -p ".loop"
-  mkdir -p ".loop/${loopId}.progress"
+  mkdir -p ".workflow/.loop/${loopId}.progress"
 
   Write(stateFile, JSON.stringify(state, null, 2))
   return state
@@ -137,7 +137,7 @@ async function runOrchestrator(options = {}) {
     return { status: 'error', message: 'Missing loopId or task' }
   }
 
-  const progressDir = `.loop/${loopId}.progress`
+  const progressDir = `.workflow/.loop/${loopId}.progress`
 
   // 2. Create executor agent (single agent for entire loop)
   const agent = spawn_agent({
@@ -154,7 +154,7 @@ async function runOrchestrator(options = {}) {
 ## LOOP CONTEXT
 
 - **Loop ID**: ${loopId}
-- **State File**: .loop/${loopId}.json
+- **State File**: .workflow/.loop/${loopId}.json
 - **Progress Dir**: ${progressDir}
 - **Mode**: ${mode}
 
@@ -213,7 +213,7 @@ Execution timeout reached. Please:
     state = readLoopState(loopId)
     state.current_iteration = iteration
     state.updated_at = getUtc8ISOString()
-    Write(`.loop/${loopId}.json`, JSON.stringify(state, null, 2))
+    Write(`.workflow/.loop/${loopId}.json`, JSON.stringify(state, null, 2))
 
     // Handle different outcomes
     switch (actionResult.next_action) {
diff --git a/.codex/skills/ccw-loop/phases/state-schema.md b/.codex/skills/ccw-loop/phases/state-schema.md
index e1576b5f..6fc12d9f 100644
--- a/.codex/skills/ccw-loop/phases/state-schema.md
+++ b/.codex/skills/ccw-loop/phases/state-schema.md
@@ -4,7 +4,7 @@ CCW Loop state structure definition for Codex subagent pattern.
 
 ## State File
 
-**Location**: `.loop/{loopId}.json` (unified location, API + Skill shared)
+**Location**: `.workflow/.loop/{loopId}.json` (unified location, API + Skill shared)
 
 ## Structure Definition
 
@@ -208,7 +208,7 @@ Agent checks control signals at start of every action:
  * @returns { continue: boolean, action: 'pause_exit' | 'stop_exit' | 'continue' }
  */
 function checkControlSignals(loopId) {
-  const state = JSON.parse(Read(`.loop/${loopId}.json`))
+  const state = JSON.parse(Read(`.workflow/.loop/${loopId}.json`))
 
   switch (state.status) {
     case 'paused':
@@ -338,17 +338,17 @@ State-to-file mapping:
 
 | State Field | Sync File | Sync Timing |
 |-------------|-----------|-------------|
-| Entire LoopState | `.loop/{loopId}.json` | Every state change (master) |
-| `skill_state.develop` | `.loop/{loopId}.progress/develop.md` | After each dev operation |
-| `skill_state.debug` | `.loop/{loopId}.progress/debug.md` | After each debug operation |
-| `skill_state.validate` | `.loop/{loopId}.progress/validate.md` | After each validation |
-| Code changes log | `.loop/{loopId}.progress/changes.log` | Each file modification (NDJSON) |
-| Debug log | `.loop/{loopId}.progress/debug.log` | Each debug log (NDJSON) |
+| Entire LoopState | `.workflow/.loop/{loopId}.json` | Every state change (master) |
+| `skill_state.develop` | `.workflow/.loop/{loopId}.progress/develop.md` | After each dev operation |
+| `skill_state.debug` | `.workflow/.loop/{loopId}.progress/debug.md` | After each debug operation |
+| `skill_state.validate` | `.workflow/.loop/{loopId}.progress/validate.md` | After each validation |
+| Code changes log | `.workflow/.loop/{loopId}.progress/changes.log` | Each file modification (NDJSON) |
+| Debug log | `.workflow/.loop/{loopId}.progress/debug.log` | Each debug log (NDJSON) |
 
 ### File Structure
 
 ```
-.loop/
+.workflow/.loop/
 +-- loop-v2-20260122-abc123.json         # Master state file (API + Skill)
 +-- loop-v2-20260122-abc123.tasks.jsonl  # Task list (API managed)
 +-- loop-v2-20260122-abc123.progress/    # Skill progress files
@@ -366,7 +366,7 @@ If master state file corrupted, rebuild skill_state from progress files:
 
 ```javascript
 function rebuildSkillStateFromProgress(loopId) {
-  const progressDir = `.loop/${loopId}.progress`
+  const progressDir = `.workflow/.loop/${loopId}.progress`
 
   // Parse progress files to rebuild state
   const skill_state = {
@@ -381,7 +381,7 @@ function rebuildSkillStateFromProgress(loopId) {
 
 ## Codex Pattern Notes
 
-1. **Agent reads state**: Agent reads `.loop/{loopId}.json` at action start
+1. **Agent reads state**: Agent reads `.workflow/.loop/{loopId}.json` at action start
 2. **Agent writes state**: Agent updates state after action completion
 3. **Orchestrator tracks iterations**: Main loop tracks `current_iteration`
 4. **Single agent context**: All state updates in same agent conversation via send_input
diff --git a/ccw/src/tools/claude-cli-tools.ts b/ccw/src/tools/claude-cli-tools.ts
index 9b9b2022..9aed6810 100644
--- a/ccw/src/tools/claude-cli-tools.ts
+++ b/ccw/src/tools/claude-cli-tools.ts
@@ -439,9 +439,9 @@ export function loadClaudeCliTools(projectDir: string): ClaudeCliToolsConfig & {
     const migrated = migrateConfig(parsed, projectDir);
     const needsSave = migrated.version !== parsed.version;
 
-    // Merge tools with defaults and ensure required fields exist
+    // Load user-configured tools only (defaults NOT merged)
     const mergedTools: Record<string, ClaudeCliTool> = {};
-    for (const [key, tool] of Object.entries({ ...DEFAULT_TOOLS_CONFIG.tools, ...(migrated.tools || {}) })) {
+    for (const [key, tool] of Object.entries(migrated.tools || {})) {
       mergedTools[key] = {
         ...ensureToolTags(tool),
         type: tool.type ?? 'builtin',