Revert "Update the packrat lockfile version accordingly"

This reverts commit f63eadb22384bb04a6e8a9e7be12a3c6da0fb1f9.
Revert key-value repo storage for now; tackle in alternate branch
Prefix install.packages with utils::

To avoid the RStudio shim, as we don't want prompts to
interrupt at this stage
Merge branch 'master' into feature/repository-lockfile-format