XcodeGen is a command line tool written in Swift that generates your Xcode project using your folder structure and a project spec.
The project spec is a YAML or JSON file that defines your targets, configurations, schemes, custom build settings and many other options. All your source directories are automatically parsed and referenced appropriately while preserving your folder structure. Sensible defaults are used in many places, so you only need to customize what is needed. Very complex projects can also be defined using more advanced features.