TS5074:  Failed to update timestamp of file with --build

Follow up from #1182, I've updated the [repro](https://github.com/joshcartme/tsgo-ts6305)

Using the above repo:
```
yarn run tsgo --build --clean
yarn run tsgo --build
```
gives:
```
message TS5074: Failed to update timestamp of file '`/path/to/repo/lib/foo.js'.
```
That file doesn't exist because the `outDir` is `./dist`. `/path/to/repo/lib/dist/foo.js` does exist.