Merge pull request #89 from wtangiit/master

bug fix in shock-client pdownload
Dual Auth, mgrast auth, improved logging, reorged indexing, and more
Merge pull request #90 from jaredwilkening/master

Dual Auth, mgrast auth, improved logging, reorged indexing, and more
first round of documention
Merge branch 'master' of github.com:MG-RAST/Shock
fixed chunksize -> chunk_size
more documentation and clean up
Merge pull request #91 from jaredwilkening/master

documentation and bug fixes
Added code to allow for variable length node.  At node creation the user should specify parts=unknown.  Successive parts must be added in order (1, 2, 3, etc.).  The final part should be identified as part=last.
Edits to new feature to allow variable-length nodes. Parts can now be added in non-sequential order and instead of having a part named 'last', the user should send a form with a 'close' parameter to close the node. Node creation in this manner will allow missing parts when node is closed. Also, added deletion of 'parts' directory when node is finished being created from parts.
Changed temporary filenames of parts from 0...N-1 to 1...N
Better error handling and removed a couple debug print commands
Merge pull request #92 from jaredbischof/master

Added code to allow for variable length node.
Minor formatting edit
Changed usage of upload of variable-length file. Instead of accepting close param and ignoring the value to close a variable-length node, looking for parts param equal to close
Merge pull request #93 from jaredbischof/master

Updated convention for closing variable-length node.
Updating bam index documentation
Updating bam index documentation
Updating bam index documentation
Updating bam index documentation