use only 'separateCompilation' flag when checking of file should be emitted

Author: vladima

src/compiler/utilities.ts

@@ -1438,8 +1438,7 @@ module ts {
  if ((isExternalModule(sourceFile) || !compilerOptions.out)) {
  // 1. in-browser single file compilation scenario
  // 2. non .js file
- return (compilerOptions.separateCompilation && compilerOptions.allowNonTsExtensions) ||
- !fileExtensionIs(sourceFile.fileName, ".js");
+ return compilerOptions.separateCompilation || !fileExtensionIs(sourceFile.fileName, ".js");
  }
  return false;
  }