Replace cyan with (or just add) pink flags
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It's really hard to tell the difference between the cyan and blue flags, but red and pink are different enough to easily distinguish.
The ability to toggle flags on and off in the UI based off of color (and secondary color) would be nice.
I think black flags also could be useful, especially now that there are two possible colors (so a flag with black on it can still be highly visible with the other color).
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Being able to use RGB color codes (ie: #FF34AB) would be amazing.