The information for triple-slash directives is missing from the generated AST.

import-ambient-module.ts

/// <reference path="import-in-module.ts"/>
import { X } from "M1";

The ambient module "M1" is declared in import-in-module.ts. The reference path is needed for importing "X" from "M1".

import-in-module.ts

declare module 'M1' {
  export interface X {}
}

declare module 'M2' {
    import { X } from "M1";
    export namespace NS {
    }
}