I attempted to deploy workflow "convertraw" to proteomics2.ucsd.edu using: make deploy-debug-update. Previously this workflow was present in the proteomics2 workflows directory, but with only a result.xml owned by ccms:ccms-dev having 664 permissions (i.e. group write was set). The deployment failed due to a permissions error.
This should not have happened since the user account I used to make the deployment (jjcarver) is a member of the ccms-dev group. Although the result.xml file already in place was not owned by my user account, it did have group write permissions so the deployment should have been able to overwrite it.
Running chown jjcarver:nunoLab on this file solved the problem and allowed the deployment to work in full.