R 2.8->2.9 change that breaks some upgrade scenarios

R 2.9.x? uses? R code instead of the previous perl code for 
INSTALL. That's the explanation for the difference.

I agree that it would be quite useful if they supported features
as you mention, and we (R-core) will be very willing to accept
(well-tested) patches enabling that.

I just checked R trunk - only "SHLIB", "INSTALL", "REMOVE" has undergone the shell/perl script->R routine transformation. I would suggest just adding --vanilla to those three. (personally I have never used the last one - just dumping the package directory from within the library directory normally remove almost all trace of a package anyway).

Hin-Tak