refactor: remove subagent references and update CLI tool usage across documentation

docs/skills/custom.md

@@ -257,13 +257,15 @@ describe('my-skill', () => {
 
 ## Debugging
 
-Enable debug logging:
+Enable debug logging and invoke skill directly:
 
 ```bash
 export CCW_DEBUG=1
-ccw skill run my-skill "test input"
+Skill(skill="my-skill", args="test input")
 ```
 
+> **Note**: The CLI command `ccw skill run` is deprecated. Use `Skill()` tool directly.
+
 ::: info See Also
 - [Core Skills](./core-skills.md) - Built-in skill reference
 - [Skills Library](./index.md) - All available skills