Moving up a level in that directory you will find this README

This directory includes RefSeq data from fungal genomes if any one of the genome records were designated as NC_ (Complete genomic molecules) or NT_ (Intermediate genomic assemblies) or annotated by multi-genome Gnomon.

Directories of each taxon contain the following file formats:

.asn - nucleotide record in asn.1 format

.faa - protein sequences in fasta format

.ffn - nucleotide sequences of CDS features in fasta format

.fna - total nucleotide sequence in fasta format

.frn - nucleotide sequences of structural RNAs in fasta format

.gbk - full Genbank flat file format

.gff - feature annotation in GFF3 format

.ptt - protein table

.rnt - structural RNA table

.rpt - report file

.val - binary file

You can download all the staff directly by typing "wget -r ftp://ftp.ncbi.nih.gov/genomes/Fungi/Aspergillus_fumigatus_uid14003/".