Freeze now supports the concept of folders. Although Glacier has a flat structure with no hierarchy, it does that by using forward slashes in archive descriptions as folder separators. This is a common concept used by most Amazon S3 and Glacier clients. You can enable and disable folder view within the app by selecting "Inventory -> Folder View".
When you try to upload a folder that already exists at the destination, Freeze will ask you if the remote folder should be synchronized with the local folder, so that only new and changed files will be transferred. Additionally, you have the option to delete orphaned archives from the destination.
To make uploading more convenient, you can now upload files and entire folders by dragging them from Finder to the desired destination vault/folder.