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In html it should not matter at all what the directory structure for your unzipped epub files should be. With HTML, as long as you get the paths correct on the hyperlink, everything is great.

As a practical matter though, it is easier to work with flat directories. Maybe one subdir for media files, one subdir for scripts, one subdir for css. This can be unwieldy for ebooks with a lot of chapters though.

Many tools that produce epub files try to follow this convention, if only to prevent path problems later on. I would assume that an HTML-based tool like Calibre would offer more flexibility, while Adobe ID offers less.

There is a separate issue about how reading systems process an epub consisting of a lot of subdirs. But in the 5 or 6 years I have been creating ebooks, I haven't heard of any performance or rendering problems related to that -- but I could be wrong.

It's important to remember that all files in an epub file must be used or the epub won't validate. So you can't have conditional directories (or else you must manually add/remove them for each output).


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