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I managed to tune Thunderbird to darker scheme for everything except the messages, so it looks like this:
I tried changing colors for messages in Options - Display - Colour, but regardless of Allow content to chose its own colours checkbox, this makes too many HTML messages unreadable, because they assume the white background.
Also it's impossible to change the quoted text color (I tried plugins, but found none working), and blue becomes unreadable on darker backgrounds.
So is it possible to change background and foreground font color just for plain text messages, and not HTML messages and not plain-text replies (or also change colors for quoted text)?

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I've put up a bug for part of this : https://bugzilla.mozilla.org/show_bug.cgi?id=1136626 : the quoted text colour in plain text emails. HTML mail : if it doesn't specify back/fore colours, you'll get the preferred colours. Alas, Thunderbird itself is one of the few clients that DOES set them in HTML, see : https://bugzilla.mozilla.org/show_bug.cgi?id=690644
– Adrian – 2015-02-26T10:44:51.743