Refactor skill handling and improve runtime trace capabilities

- Removed the selectSkill method from prepareService and adjusted related logic in the Run method of Service.
- Updated tool catalog to parse agent allowed tool codes directly.
- Simplified Request and RunInput structures by removing unnecessary fields.
- Enhanced the RuntimeTraceCollector to manage skill activation and visibility.
- Introduced a new databaseSkillBackend to manage skill definitions and their metadata.
- Added tests for skill backend functionalities to ensure correct behavior.
- Updated various factory methods to accommodate changes in skill handling.
- Improved documentation and descriptions for better clarity.

internal/services/skill_definition_service.go

@@ -79,6 +79,10 @@ func (s *skillDefinitionService) GetByCode(code string) *models.SkillDefinition
 	return repositories.SkillDefinitionRepository.GetByCode(sqls.DB(), code)
 }
 
+func (s *skillDefinitionService) GetByIDs(ids []int64) map[int64]models.SkillDefinition {
+	return repositories.SkillDefinitionRepository.GetByIDs(sqls.DB(), ids)
+}
+
 func (s *skillDefinitionService) CreateSkillDefinition(req request.CreateSkillDefinitionRequest, operator *dto.AuthPrincipal) (*models.SkillDefinition, error) {
 	if operator == nil {
 		return nil, errorsx.Unauthorized("未登录或登录已过期")