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I still use the Restructure tool but that is due to having gotten used to finding images in Images, etc. Old dogs and an adversion to new tricks.
Actually, there are a few rules for ePub structure. The mimetype file is required, must be in the root of the container and must be stored uncompressed. The container.xml file is required and must be stored in a META-INF directory in the root of the container. There are several other optional xml files (encryption.xml (required if obfuscation/encryption is used), manifest.xml, metadata.xml, rights.xml & signatures.xml). You will also commonly find that Apple and Kobo xml files are stored in the META-INF file though this is not required (com.apple.ibooks.display-options.xml & com.kobobooks.display-options.xml) and can cause an error message if they are also listed in the .opf file.
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