Handle stitching exports when config.output_folder doesn't contain a stitching subdirectory

We can do one of the following:

1. Write stitching export files to the main output folder and overwrite the previous merged profile.
2. Write stitching export files to the main output folder and append a timestamp or some other unique ID to each filename to keep all exported merged profiles.
3. Figure out how to enforce that the stitching directory exists.