I propose that the color of the code changes to red just before it expires. (Perhaps 7 seconds?)
Steam Guard has this and I think it will look really good in Aegis.
more visual cues means less time looking for the bar at the top ^^
I agree that the single, slowly moving bar at the top is inadequate. However, I don't feel like something discrete like changing colors is ideal behavior for me. If I'm tying a TOTP in my computer, 2 seconds may be more than enough to get those six digits submitted. If I have to switch apps on my cell phone and find a TOTP field that has lost focus, I could miss longer windows.
My "minimum effort" change would probably be to repeat the countdown progress bar between each set of codes. I've seen other things that I like (like a bar that circles around each icon), but the usability is more important than the specific visual.
Yeah, I liked that feature in LastPass Authenticator (codes were red for the last 5 seconds I think). Of course it could be optional feature, maybe even with option to change the duration.
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more visual cues means less time looking for the bar at the top ^^