WSO2 ESB's configuration is kept in pre defined file structure. However, if you want to have the whole synapse config in one file, you can use synapse.xml for that purpose.
If you want to manage multiple ESB configs, then the best option is to use WSO2 Carbon Studio where you can hot deploy various ESB configuration as applications (so called capp).
WSO2 ESB Config structure:
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synapse-configs
└── default
├── api
├── endpoints
├── event-sources
├── local-entries
├── priority-executors
├── proxy-services
├── registry.xml
├── sequences
│ ├── fault.xml
│ └── main.xml
├── synapse.xml
└── tasks