The repository that holds cluster state should be structured in a particular way.
Weave Cloud supports pushing to a single repository only. Multiple applications on the same cluster may be supported by creating and configuring multiple instances of Weave Cloud Deploy.
Each Kubernetes component should have its own file.
Files may be separated into subfolders.
A simple example can be found here. A more complex example can be found in the Microservices Demo reference architecture.
Further Reading