Add option to save the output of fix_arb_fasta.py

One usage example was added plus an update to the fix_arb_fasta folder
in the qiime_test_data.

This should fix item 2 of #633
Change -i to -f in script_usage examples
Merge pull request #872 from ElDeveloper/fix_arb_fasta_633

Add option to save the output of fix_arb_fasta.py