Output cleaned fasta files to output folder instead of input folder

[the-lay]

Hi Kiarash!

Since 1.0.8, there are additional checks/rewrites for .fasta files (write_fasta_only_aa and write_fasta_no_gaps). Both of those checks output the reformatted file next to the input file. I propose the reformatted files are written to the output folder instead.

While this is a very minor change, that would really help in our use case, where we enforce that inputs and input folders are always read-only. Thanks!