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/application/runtime/tool_catalog.go

@@ -41,7 +41,7 @@ func (c *toolCatalog) resolveForRun(req *Request) (*registry.ToolSet, error) {
 		AIAgent:          req.AIAgent,
 		AIConfig:         req.AIConfig,
 		UserMessage:      req.UserMessage,
-		AllowedToolCodes: c.resolveAllowedToolCodes(req.AIAgent, req.SelectedSkill),
+		AllowedToolCodes: c.parseAgentAllowedToolCodes(req.AIAgent),
 	})
 }