Improve input file handling

Checks if an input FASTA file is actually a FASTA file.
Adds .gff extension if its not present (and it can be parsed as a GFF file).
Checks if the same GFF file has been provided twice by checking MD5. Only the first is used.
If duplicate IDs are found in any file, all gene IDs in the file are changed to MD5_index to avoid clashes.
Fix error getting MAFFT version string.
Dependancy versions for testing with Travis have been increased to latest.