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The content.opf uses manifest ids. A manifest id is any unique identifier name. To make dure the id is unique, some people and somesofrware will copy the file name and use it as the manifest identifier. This is a simple way to assure uniqeness but can be confusing as both the actual filename based on the manifest href and the manifest id can look identical but need not be. That is why using the filenam part of the href is recommended as the id for that same manifest entry could be something like "c1" instead of "chapter1.xhtml".
Hope this explains things.
KevinH
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