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Checkpoints, unlike per editor undo/redo, allow you to undo operations that affect the entire book such as global search and replace, renaming files, running font subsetting and so on. They also serve as a temporary version control. So you can create a checkpoint, give it an arbitrary name and then revert your book back to the state it was in when you created the checkpoint, regardless of what you have done since then. As far as I know, there was no way to recover from global operations in Sigil.
Renaming is implemented, I just haven't added the UI for it. You will be able to right click on files and rename them.
Pre-filling the search box is trivial to implement, remind me about it after I make a first release.
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