Fruit - include the core/peel in the weight?
Bananas, oranges or fruit that I peel I weigh without the peel.
Any fruit that I eat with the peel on I weigh whole.
Cores and pits weigh almost nothing, I don't worry about them.
The same with veggies, if I am going to eat the skin, I weigh it with the skin on.
I am the same, things that I eat without the peel, I try to weigh without but it can be difficult.
I have banana on my breakfast every morning, I peel it, chop it up and weigh it when i put it with my cereal. Normally, the banana's in the bunch are all about the same size so I can pretty much guess the weight it I don't have access to scales, if say I took a banana to work with me.
If I were you and were eating a lot of fruit on the go, I would do a bit of a trial at home. Eg. weigh an orange/banana etc before, peel it and weigh afterwards and see what the difference is. If you can work out a rough % per fruit, then you could weigh the whole fruit in the morning, take it to work/where ever and take off an estimated amount when you log it based on your % findings.
Or you could log the whole weight, but then it would over calculate as you said.
:)

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