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Most of it goes in the black bag which then goes in a real backpack or a pannier along with a jacket and Clif bars. I could fit the tubes, lights, and locks in the bag too but I keep the lights out to charge and bring with when I don't bring my full kit, and I keep the tubes out because I bring different tubes depending on what bike I ride, and I keep the locks out because I don't always bring the cable lock and I occasionally bring the folding lock but not the rest of the kit if I'm using a saddle bag with less stuff.
>inb4 nice blogpost