Fixes#1471
The spec-required tool YAML format includes a top-level 'tool:' wrapper key,
but the CLI was expecting flat format without the wrapper.
This change:
- Detects and extracts the 'tool:' wrapper key if present
- Silently ignores 'cleveragents:' version header
- Maintains backward compatibility with flat format YAML files
Spec reference: Tool Configuration section in docs/specification.md