In CVS, PEAR code is organized by package instead of hierarchical like it would finally be installed. For example, if you want to use the XML_RPC class, you include "XML/RPC.php". It's easy to think that in CVS, this file should be in pear/XML/RPC.php, but that's not the case. XML_RPC is an independent package with its own directory in CVS, in this case the RPC.php file is actually located at pear/XML_RPC/RPC.php. The package description file (package.xml) is used to say where the files should finally be installed.
The reason CVS is organized this way is that it makes package administration much easier.