The Project API has the Status endpoint, which returns a hash of what the current environment looks like. It does not return a list of files which have uncommitted changes as does Git Status.
There is a delete endpoint, but that requires a full path listing of the files. There is no wildcard delete.
So right now there is no way for an automated solution to discover which files are blocking the Git Pull or to remove them en masse.
Please update the Project/{ProjectId}/Status endpoint to also list out all of the files which have uncommitted changes so they can be deleted by automation.