Why does the directory structure of pear/ and php4/pear/ differ?

Answer written by Stig Bakken.

The directory structure of php4/pear/ matches that of the install tree (by default /usr/local/lib/php), and are organized as a simple hierarchy. However, the directory structure of pear/ is based on what package the files belong to. Where files are located in each package directory is completely independent from where they end up being installed, this is all determined by the package description file.