We promote use of jgit or similar Git libraries to manipulate the underlying repositories rather than providing a REST API to manipulate assets.

That said you don't need to worry unduly about manipulating assets with a low level Git library; you can clone workbench repositories, manipulate assets at the file system level - e.g. add, edit or delete files and folders - git add, git commit and git push and the changes will appear in the Workbench.

You'll need to go to the Administration Perspective, get the ssh url for the repository you want to manipulate.