Add comprehensive documentation for tool usage and integration

- Introduced a new "Tool Use Overview" document detailing the tool system, including core concepts, available tools, calling mechanisms, and best practices.
- Created individual documentation for the `use_mcp_tool`, `write_to_file`, and other tools, outlining parameters, functionality, and usage examples.
- Updated links throughout the documentation to reflect the new structure under "advanced-usage/available-tools".
- Enhanced the sidebar navigation to include a dedicated section for available tools.
- Adjusted references in various documents to ensure consistency with the new tool documentation paths.
- Improved error handling and recovery strategies in tool documentation.
- Updated update notes to reflect changes in tool functionality and improvements.

Author: hannesrudolph