As a general rule food that is prepared for you is taxed. If it is something you have to prepare - no sales tax.
There are some areas open for interpretation, your bagels are a good example. If they had sliced them for you I would say they prepared them. You say yours are unsliced, I would say no tax should be charged.
The easy cop-out, "the computer sets the tax" is a pretty lame response. Law sets the tax and it is the store owner's responsibility to correctly charge those taxes.
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New York, California, Pennsylvania, Florida
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