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You can open files directly from an archive in the Archive Browser view and then edit them in the main editor pane. To open a file, simply double-click it or select Open from the contextual menu.

When saving the file back to the archive, you are prompted to choose if you want the application to make a backup copy of the archive before saving the new content. If you choose Never ask me again, you will not be asked again to make backup copies. You can re-enable the pop-up message from the Messages preferences page.