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Does/will this enable project references with JS files (composite and allowJs)?

@ajafff No, the scope of this effort is limited to making declaration and allowJs work together.

So... this probably isn't what you wanna hear; but you probably want to use a completely separate transformer for JS files, when compared to the TS one. Because of how JS declarations are merged/inferred in a piecewise fashion, what you probably want to do is something along the lines of iterating over all the exported symbols (rather than the declarations in the file) and attempting to rebuild them from typechecker information, rather than their (potentially non-.d.ts-compatible) original declaration sites. For example, we have an upcoming PR to recognize Object.defineProperty calls in JS files as property declarations - in a .d.ts they would mean nothing (and are expressions, which we generally elide in declarations), yet that information must still be transformed and preserved somehow. (That's in addition to all the special assignments we already recognize.) And while we do have typeToTypeNode already written within the checker (which makes, say, translating a jsdoc'd const into a type annotated const easy (we have a quickfix that does this)), we have not yet written anything like interfaceToInterfaceNode or classToClassNode (I think), so this is probably quite a bit of work. Also things like jsdoc enums I think actually don't even have a precise way to represent them in a .d.ts, I think (although a type plus a namespace probably comes close).

Thanks for the explanations @weswigham. This sounds like a ton of work indeed, requiring more time than I'm able to spend on it. I'm closing this pull request, but won't delete my branch in case anyone else wants to pick it up from here.