Merge pull request #53 from jaredwilkening/master

improved chunkrecord indexer
Merge pull request #54 from jaredwilkening/master

Regex file format checking
Merge pull request #55 from jaredwilkening/master

pre-authenticated downloads and faster checksumming
Merge pull request #56 from jaredwilkening/master

minor bug fixes
Merge pull request #57 from jaredwilkening/master

code reorganisation
Merge pull request #58 from jaredwilkening/master

bug fix
Merge pull request #59 from jaredwilkening/master

pre-authenticated download bug fix
Merge branch 'master' of github.com:MG-RAST/Shock