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Do a Google search for a python program called "epubmerge.py" v. 4.1 by Jim Miller, Dec. 2011, available under the Apache 2.0 license. I've used it to merge several separate short stories into one epub. It seemed to get confused with space characters in file names, though, so you may have to rename your (x)html files with underscores in place of spaces to get it to work smoothly.
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