Update acceptance tests for new knitr, and remove markdown
respect the status code on the error if it exists
Merge branch 'master' of https://github.com/sharelatex/clsi-sharelatex
err != error
Allow python to be executed and return output
Add R as a supported language
Fix unit test
Update R Command
Allow configurable CPU, memory and process limits
Factor out all file reading and writing into CommandRunner
Call initProject to set up CommandRunner
Do all filesystem reading and writing in command runner
Pull out filesystem manipulation into its own module
Fix misnamed method in FilesystemManageR