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/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) {