Updating lit tests leaves file in source tree

When I run `./scripts/auto_update_tests.py --binaryen-bin=../binaryen-out/bin lit` it leave 3 untracked files in the source tree:

```
	test/lit/debug/source-map-stop.wast.wasm
	test/lit/debug/source-map-stop.wast.wasm.map
	test/lit/downgrade-reftypes.wast.wasm
```