Merge pull request #15 from MG-RAST/master

update devel
Merge pull request #16 from braithwaite/master

update version number
Merge pull request #17 from MG-RAST/devel

Devel
Merge pull request #18 from braithwaite/master

demos updated for tutorial
Merge pull request #19 from braithwaite/master

demos updated for tutorial
Merge pull request #20 from braithwaite/master

functionality in this version is accurately documented in quick reference
Merge pull request #21 from braithwaite/master

datasets and demos rebuilt
Merge pull request #22 from MG-RAST/devel

Devel
Merge pull request #23 from braithwaite/master

API2, ggplot, and other
Merge pull request #24 from MG-RAST/devel

update master
Merge pull request #25 from braithwaite/master

row hierarchies implemented
Merge pull request #26 from MG-RAST/devel

merge devel
Merge pull request #27 from braithwaite/master

rm quickref
Merge pull request #28 from MG-RAST/devel

merge devel
Merge pull request #29 from braithwaite/master

row hierarchy error patch
Merge pull request #30 from MG-RAST/devel

merge devel
Merge pull request #31 from braithwaite/master

hotfix m5rna m5nr to uppercase
Update R/collections.R

Hotfix 9 Jan 2013 per discussion via RT
changed chooser test from <= to < 
Certain views had been inaccessible.
Update data/mconfig.R

change setAuth() to accept connection argument to read key from file (for non-interactive uses).
Update R/transfer.R

Completed support for rowname hierarchies