Accept multiple fasta files as input

[cmorganl]

Users shouldn't have to resort to either concatenating fasta files or running treesapp assign in a loop to classify query sequences in multiple fasta files.

treesapp assign should support both directories as input types (along with a file extension argument e.g. '.faa' and '.fasta') and a list of fasta files.

Simultaneous support for fastq files needs more thought.