Solution
In my experience, the solution I’ve outlined below offers me an excellent approach for long term reproducibility and code stability:
Lock down your R package versions using MRAN snapshots
Lock down your working environment using a Docker image
Do all your development within Docker containers
Accompany all projects with a Docker image
This has worked so well that I haven’t bothered using R/Rstudio on my local machine in well over half a year now. (View Highlight)