matt comments on So, I guess the site redesign is live? - Less Wrong
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We've tried to make it easier to visually track indentation level (and thus which comment replies to which). We could vertically compress while preserving the horizontal extra distance, but it'll look squished.
KDevelop , a c++ integrated development environment , has IMHO an extremely convenient way to visually track "indentation level" in source code. It shows a coloured bar to the left of the source whose colour indicates the "code depth" at that line. See e.g. this screenshot