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Using linux with 2 partitions, how do you do it and how do you organize your files?

So recently tried zorin os and now im dual booting it with windows, and because of that I need a have NTFS partition between them. Now I have a 256gb windows partition, a 256 linux partition and a 1.7 Tb shared ntfs partition shared between them and I wonder how do you organize your files if you need to have them on another partition and cant use ~.

For programs they will always end up on / and I cant install them on another partition (dont know why) but what do you do for files? What folders do you have and where are they?

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