The GIT repository that is configured with a Cartridge should have the correct folder structure to add artifacts to synchronize with the Cartridge and add to the correct location of the server to get deployed.
For most of the Carbon server Cartridges the corresponding GIT repository should have the folder structure of <CARBON_HOME>/repository/deployment/server.
Example:
For an Application Server Cartridge the folder structure should be as follows:
axis2modules, axis2services, aggeryapps, jaxwebapps, jsservices, modulemetafiles, servicemetafiles, webapps.
PHP Cartridge users have to create a folder named www inside the GIT repository to be able to upload PHP artifacts.