it is common for users to have "use strict" as their first line in a module anyways, now we will emit two.

Correct! But this change would bring us inline with both babel and our own parser (since we parse in strict mode in modules). There's also no harm in it. (And users can easily remove the extra "use strict" form their own code if it bothers them)

An interesting behavioral quirk this fixes is this:

export function what() {
  return this;
}
var x = what.call(2);
assert(typeof x === "number");

That assertion changes truthiness based on the strict mode status of the containing code. (Specifically, its only true in strict mode.)
So compiling this code in babel, the assertion is true, but with TS it is false at present.

You could just check if the first statement is a "use strict" directive and omit it if it is.

@DanielRosenwasser So you have asked, so you shall recieve

Look good 👍 Could you add a test when users already have "use strict" and we omit the emitting.

💯

@yuit tests/baselines/reference/modulePrologueAMD.js, tests/baselines/reference/modulePrologueCommonjs.js, tests/baselines/reference/modulePrologueSystem.js, and tests/baselines/reference/modulePrologueUmd.js got ya covered

@weswigham can you add a blurb about this change and what breaks in the breaking changes page; mainly issues that the compiler will not catch but will break at runtime, e.g. eval introducing new variables, value of this, errors on calling function.caller, etc.. possibly reference https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Strict_mode