CakePHP has specific conventions for organizing files and naming different components. The app folder contains subfolders for configuration, controllers, models, views, and plugins. Controllers are named in CamelCase and end in "Controller", models are singular CamelCase, and views match controller functions in lowercase. Database tables are plural lowercase names matching models, and fields are lowercase with underscores. Foreign keys match the singular table name plus "_id". Many-to-many tables are named by joining table names alphabetically ordered and underscore separated.