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Conversion does many, many things to make sure its output works across all devices.
1. I'd guess this is because of a non-linear spine item
2. That's an ecoding declaration, it's there for redundancy.
3. Splittling files at page breaks is a good tyhing, makes your epub work faster on limited devices. There is a conversion option to turn it off.
4. IIRC that file is obsolete with newer versions of ibooks, though since I never touch ibooks with a 10 foot barge pole, I cant be sure.
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