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The settings you chose last time are what the next run opens on — all six of
them, not just some. Every value is shown before anything is converted, so
nothing is applied that you have not seen, and changing one is the same as
it ever was.
If the settings are asked one question at a time, they are remembered there
too, including a colour of your own: the list opens on "Custom colour..."
with your colour already in the prompt behind it.
Changed
Headless runs are unaffected in both directions. A configuration file says
everything about the run it describes, so it neither reads what you chose in
a window nor changes it.
Fixed
A headless configuration file that is valid JSON but is not a set of
settings — null, a number, a string, a list — now says so, instead of
failing later with a message about the failure rather than about the file.