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I made a windows program that runs in the background and lets you re-map keys dynamically per application. It has a pop-up when you're holding a toggle key to show you what each key does.
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There's no logging of the keys being pressed. There are hooks installed on top of the keys configured to be re-mapped and the key used for toggling but these presses aren't logged anywhere. All the configuration is stored in plain text though so you'll want to be careful about what you put in there.