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/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