Calibre is amazing, but I have one big gripe with it: In its default settings, both the main application and the ebook reader insist on modifying the source file even when only viewing it (to store the current page).<p>I think I've even seen (self-published) ePubs getting contaminated with these annoying bookmark tags, and as a result had Calibre open them on some random page (presumably precisely the one at which the editor or author have closed it before deciding that it's now fit for publishing).<p>Imagine VLC storing the current playback position in every audio or video file! I think not even iTunes does/did that, unless the user actively edits some metadata, and that wasn't very considerate with source files either.<p>And then, on the other hand, Calibre does not automatically propagate actual metadata updates to the ePub file even after explicitly editing them in the library manager view – the one place where that's usually arguably user intent... (Except when opening and closing the book source editor without touching anything, because <i>that</i> rewrites the metadata <i>at every opening time</i> in its default settings, i.e. not at saving time! Make it make sense...)<p>The most infuriating thing is that these decisions can all be overridden with some preferences – it just happens that the default is exactly the opposite of what I'd expect to happen. (The reader should not write things by default, but if it must, the metadata editor should damn well too.)