Incorrect display of syntax

Something happened and now Atom does not mark out such things like “console”, some variables and I can’t see them while typing them.

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When did it change? What do you see when you start Atom from the command line with atom --safe?

It changed some months ago. When Atom start from the command line I see nothing special.

You may be thinking of changes that happened when Atom adopted the Tree-sitter system for parsing code. You can disable the new grammar system in Settings, under Core.