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From the Appearance preference page and/or colors and fonts page, it would be good to provide an action "create custom theme via CSS". User could click that and edit a local theme.css file. Change to this CSS files would be applied to the IDE if this CSS file is the one used by the current theme.
Sounds like this has the same target as Bug 502581. *** This bug has been marked as a duplicate of bug 502581 ***