I just installed Backup and Migrate Files. I then asked it to create a backup of the Files Directory. The directory I wanted backed up was DOCUMENT_ROOT/sites/default/files, but instead it backed up DOCUMENT_ROOT/files. I can't find any way to tell it to back up the directory where the uploaded files actually are.
BTW, the version I installed was backup_migrate_files-6.x-1.x-dev.tar.gz
Mark Rosenthal mbr@arlsoft.com mailto:mbr@arlsoft.com