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The opf is machine parsed and managed/controlled by Sigil. So direct editing of the opf is rarely needed or desired. There are tools to add and remove resources, etc. So you should not need to ever manually edit the manifest. As you "Add Existing ..." new resources to Sigil it will store them inside its standard epub structure, and automatically update the manifest. You can then edit the appropriate xhtml file to add links, etc. For epub 3, there is a tool to update the manifest properties before your final save.
Does this make things clearer?
KevinH
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