Inside the Payara Micro UberJar, there is a folder named MICRO-INF/. The configuration of Payara Micro, as well as Microservices deployed at startup, are present in this folder. And much more. A typical structure of this folder is demonstrated as follows:

.
├── classes
├── deploy
├── domain
├── lib
├── payara-boot.properties
├── post-boot-commands.txt
├── pre-boot-commands.txt
└── runtime

The names are self-descriptive. Microservices to be deployed are placed in the deploy/ folder. There may be additional libraries used by those services. Those are placed in the lib/ folder and typically configured in the Payara Micro Maven plugin configuration. The runtime/ folder is of no interest to developers, as it contains implementations of the core functionalities Payara uses. Commands to invoke prior to boot and after the server has booted are placed in separate text files.