dramatically cleaned up script, also now grabs some MAF files from
directories that use a different naming convention than was previously
used at the DCC
minor update to wget_ALL_parse_biotab_untar.sh to grep for beginning and ends of the three scripts
major clean-up / restructure
fixing typo in env var usage.
Merge branch 'develop' into feature/common-utilities

Conflicts:
	commands/maf_processing/bash/archive/describe_variants.sh
	commands/maf_processing/bash/archive/get_file.sh
	commands/maf_processing/bash/archive/knowngene_mapping.sh
	commands/maf_processing/bash/archive/knowntranscript_knowngene_mapping.sh
	commands/maf_processing/bash/archive/new_knowngene_mapping.sh
	commands/maf_processing/bash/archive/non_exonic_variant.sh
	commands/maf_processing/bash/archive/prepareEntrezGeneUniprotReferences.sh.orig
	commands/maf_processing/bash/archive/refseq_mapping.sh
	commands/maf_processing/bash/download_daily_gene_data.sh
	commands/maf_processing/bash/download_monthly_annovar_build_data.sh
	commands/maf_processing/bash/download_monthly_tools_data.sh
	commands/maf_processing/bash/download_monthly_tools_data_andhg19.sh
	commands/maf_processing/bash/final_maf_diagnostics.sh
	commands/maf_processing/bash/prepareEntrezGeneUniprotReferences.sh
	commands/maf_processing/bash/refseq_prepareEntrezGeneUniprotReferences.sh
	commands/maf_processing/bash/updateMAF.sh