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You choose the deposit a credit upload sets aside: 0 to 64 credits per file, 64 unless you change it, with a default of your own in account settings.
The deposit pays the chain fee of a later action on that file, such as releasing its storage early. It is now spent only as much as that action actually costs, at least one credit per fee, and what is left returns to your bundle when the storage period ends. A file with no deposit, whether you chose 0 or uploaded it before deposits existed, pays twice that fee from your balance at the time, and the action is refused before anything is touched if the balance does not cover it. The payment sheet shows the deposit beside the price, the release sheet says which pocket the fee came from, and the command-line tool 0.31.0 takes --deposit on put and push and a deposit command for the default.