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/ai/runtime/instruction/helpers.go

@@ -27,6 +27,10 @@ func BuildSelectedSkillActivationInstruction(skill *models.SkillDefinition) stri
 }
 
 func BuildSelectedSkillDocument(skill *models.SkillDefinition, toolDefinitions []runtimetooling.MCPToolDefinition) string {
+	return BuildSkillDocument(skill, toolDefinitions)
+}
+
+func BuildSkillDocument(skill *models.SkillDefinition, toolDefinitions []runtimetooling.MCPToolDefinition) string {
 	if skill == nil {
 		return ""
 	}