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A general description is here.
Help in base and recommended packages is no longer zipped: text, HTML, latex and examples files are now built when needed.
Options --use-zip and --use-zip-help in R CMD INSTALL are no longer available and --auto-zip only zips data (or not).
Help in packages installed under 2.9.x may not work correctly, and a warning is given when such a package is attached by library(). Re-installation of all packages is advised (use update.packages(checkBuilt = TRUE)).