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One of my longer-term goals is to change the way Sigil parses the content files so that it sorts them according to the mimetype given in the opf instead of looking at the file extension. The current version should handle files which have a period as the first character if they also have a valid extension further on (e.g. .splitmangle001.html), but it will get confused if there's no proper extension at all.
Unfortunately right now the best solution is to extract the files and rename them from the command line (e.g. ren * *.xhtml in windows) then reinsert them into the epub (Sigil should rebuild the manifest) and do a global replace to resolve any links.
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