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A general description is here.
The Tcl timezone files (3Mb on disc) are now an optional part of the installation: they would be very rarely used with R.
When building R, the recommended way is now to supply a file R_HOME/src/gnuwin32/MkRules.local instead of editing MkRules: there is now no MkRules file in the distribution, but one is generated during the build process.
MkRules.local can be generated by copying and editing MkRules.dist.