Deprecate files does not delete files when requested

[briangow]

Attempting to deprecate files on a published project and choosing "Yes" to delete files gives this error: [Errno 13] Permission denied. This is because a published projects files are set to read-only (-r--r--r--). This will need to be solved if the files are actually to be deleted.

@bemoody also suggested that it would probably be better to separate the deprecate files and delete files operations.