feat: Introduce MCP connection timeout handling and enhance configuration

feat: Introduce MCP startup greeting timeout and PocketTTS connection timeout settings

refactor: Consolidate LLM runtime configuration using LLMSettings

feat: Add support for extra MCP server URLs and enhance assistant instructions

feat: Update LLM runtime configuration and tests for thinking behavior

feat: Introduce turn pipeline summary and enhance tool execution metrics

feat: Update Ollama configuration and validation for cloud usage

feat: Add post-tool response timeout and enhance error handling in channel metrics

refactor: Restructure agent components and remove unused files