Function bootstrap 

pub fn bootstrap(
    config: &RobitConfig,
    working_dir: &PathBuf,
    base_tool_names: &[&str],
) -> BootstrapResult

Bootstrap both skills and tools in one call.

This is the main entry point for frontends. It:

1. Loads skills from global and project directories
2. Filters skills by config.enabled_skills
3. Creates SkillRegistry
4. Creates ToolRegistry with all standard tools

Returns a BootstrapResult with both registries and metadata.