The reference fasta file in this directory was unpacked from Heng Li's bwakit-0.7.12:

http://sourceforge.net/projects/bio-bwa/files/bwakit/bwakit-0.7.12_x64-linux.tar.bz2/download

Heng's fasta file is based on GRCh38 full analysis set 

ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.fna

The only addition is the HLA sequences.

This fasta file includes:

Chromosomes:
chr{chromosome number or name}
e.g. chr1 or chrX
chrM for the mitochondrial genome.

Unlocalized scaffolds:
chr{chromosome number or name}_{sequence_accession}v{sequence_version}_random
e.g. chr17_GL000205v2_random

Unplaced scaffolds:
chrUn_{sequence_accession}v{sequence_version}
e.g. chrUn_GL000220v1

Alternate loci scaffolds:
chr{chromosome number or name}_{sequence_accession}v{sequence_version}_alt
e.g. chr6_GL000250v2_alt

Patch scaffolds:
chr{chromosome number or name}_{sequence_accession}v{sequence_version}_patch
e.g. chrY_KN196487v1_patch 

Decoy sequences:
chrUn_{sequence_accession}v{sequence_version}_decoy
e.g. chrUn_KN707606v1_decoy

HLA sequences:
HLA-{id}
e.g. HLA-A*02:53N
 
This directory also contains some other files

20150713_location_of_centromeres_and_other_regions.txt contains a list of all the modelled centromeric sequence     
that GRCh8 contains as well as the location of the PAR on chrY and the hetrochromatic sequence on chr7.

This was sourced from ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_assembly_regions.txt on the 13th July

The other_mapping_resources contains a set of vcf files for snps and indels for base quality recalibration
and indel realignment for GRCh38 mapping pipelines.

There is more explanation about these files in

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/other_mapping_resources/README.20150504.other_mapping_resources