Originally Posted by greenapple
I think the viewer, fine as it is (though I do wish drag-and-drop from the explorer is supported), should store the bookmarks elsewhere, and not alter the source file in any way.
I don't want two files when one will do. I like to be able to add bookmarks and share with others and not have to worry about a second file. If you don't like the way Calibre's viewer works, why not use another EPUB viewer?