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If you use a built-in TypeScript compilator, files he's got, and that's how you're supposed to be disguised, they're like "children." In addition, starting with 2016.3, these files will be grouping just by name, that is, even if you create them with some external generators, without using built-in funds, they'll still be covered.
If this is for some reason insufficient, a new scope can be created (Settings | Appearance & Behavior | Scopesby deleting it *.js and *.js.map files, and use this scope in Project tool window instead of default scoop