Update README.md
Update README.md
add additional gms command aliases
update ggplot and plyr versions, add new dependencies
Merge branch 'ubuntu-12.04' of https://github.com/genome/gms into ubuntu-12.04
fix typo in aliases
add chown statement to ensure that ~/.vagrand.d is owned by the current user before attempting to add a vbox
fix typo so that the latest r package archive actually gets used
Merge branch 'ubuntu-12.04' of github.com:genome/gms into ubuntu-12.04
update ggplot2, plyr1.8 and add new dependencies of ggplot2.  Remove redundant installation of base packages
update to very latest version of ggplot to ensure compatibility with plyr 1.8
make sure .vagrant dir within gms install dir is owned by the installing user
ask for sudo pwd up front
complete sandboxing of custom R installation.  All CRAN and Bioconductor packages and versions thereof are now installed explicitly and without reliance on CRAN or BioC servers
Merge branch 'ubuntu-12.04' of github.com:genome/gms into ubuntu-12.04
Merge branch 'ubuntu-12.04' into ubuntu-12.04-testmerge3