feat: prioritize user config, do not merge default tools

Changed loadClaudeCliTools() to only load tools explicitly defined
in user config. Previously, DEFAULT_TOOLS_CONFIG.tools was spread
before user tools, causing all default tools to be loaded even if
not present in user config.

User config now has complete control over which tools are loaded.

.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

.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