Update documentation to reflect new mycoder.config.js configuration system

[bhouston]

The MyCoder CLI has been updated to use a mycoder.config.js file for configuration instead of the previous CLI-based config commands (config set, config get, config list). The documentation needs to be updated to reflect this change and remove references to the old configuration system.\n\nTasks:\n- Update usage/configuration.md to document the new mycoder.config.js file\n- Remove references to 'mycoder config' commands throughout the documentation\n- Update examples to use the new configuration method\n- Update configuration file location information\n\nThe new configuration system is similar to ESLint and other modern JavaScript tools, where settings are defined in a JavaScript file in the project root.