Ensconce has the ability to deploy files either performing a copy function to add files, or a replace option to completely remove all existing files and replace with new files.
If the files you are deploying are applications, you should see the Deploying Applications page.
ensconce --deployFrom=[sourcePath] --deployTo=[destinationPath] --copyTo
ensconce --deployFrom=[sourcePath] --deployTo=[destinationPath] --replace