save of extensive changes to be detailing in subsequent, finalizing commit.
second save of extensive changes to be detailed in next message
save of extensive changes...
Merge pull request #32 from braithwaite/master

initial commit of extensive changes for integration meeting
(these notes refer also to the previous 2-3 commits)
new R-style runtime doc skeleton completed, with examples to double as test suite.
passes R CMD CHECK with only negligible warnings.
small fixes: contact email addresses updated; "normalize" exported; loading message re. docs and bug reporting; user-reported pco method bug; dataset compression changed to xz.
handling of views revised and clarified; new view addition mechanism; additional new default views (singletons removed).
wrappers for all API resources begun.
new session dump debugging tool.
functioning of signficance testing checked; minor structural change to result list.
command quick reference included as pdf vignette.
changelog for users started.
added change log tex source and pdfs
Merge pull request #33 from braithwaite/master

Extensive update including decent docs (continued)
merge hotfixes
Merge pull request #36 from braithwaite/master

merge hotfix from MG-RAST/master and extensive development from braithwaite/matR (last approx dozen commits)
Merge pull request #37 from MG-RAST/devel

Merge Devel (big)