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epubcheck requires a file to operate, so it would not work on an unsaved version in Sigil.
This might make it difficult to automate. There are two versions, one online and the other a version which works on your own computer. The computer version requires the installation of Java, which poses too much of a security risk for some people to be comfortable with (including me.)
Since epubcheck is used at the end of the epub creation process, there really isn't a big need to have it integrated, IMO. Flightcrew and the cleaning process will do for the vast bulk of problems including everything that would make it invalid.
The main difference I have personally noticed with what I do is that epubcheck makes sure all the references to anchors and links are valid. This Flightcrew does not do.
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