PEAR organization best practice - have files, will install?

I have just upgraded PHP to the latest CGI version 4.1.2 using the windows .zip package.(on Apache 2.0.28 Win32) I have also attained the complete PEAR repository through CVS. My question is: It is best practice to drop the complete repository I got through CVS on top of my PHP/PEAR directory? With updated versions found in /PEAR , won't combining this with the files already found in PHP/PEAR overwrite already stable code with more recent versions? I have read that the plans are to keep the packaged PHP/PEAR directory in PHP distros to a minimum, and /PEAR will be its own distro. Does this effect the folder structure I should be using? I understand the reason given for the separate distros. Why is it not taken to the extreme and leave all of PEAR completely separate from PHP? Is this just so people have easy access to the web installer, and a quick introduction to PEAR? thanks to all clarifying the fuzzy... ~ b r y a n