Decide how we want to name the output file

Do we want to:

• Renamed the original file filename.bak and name the cleaned one filename?
• Keep the original file named filename and name the cleaned one filename.cleaned? This is how it's currently done
• Remove the original file, and name the cleaned one filename?

I'm not a big fan of the third option, because should the cleanup process fail (MAT2 is written in Python, so this might happen), the original file is lost.

The first option might be the best way, but it means that for some formats, we must use a temporary file, because some parsers can't work inplace.