The first elements of PEAR were stored in the directory pear-core (once php-src/pear) and so they were bundled with each new PHP release.
For future releases of PEAR this isn't workable because PEAR will become too big to be bundled with every release of PHP. So there was a decision to commit all new elements to an own top level directory pear. The other elements which are currently remaining in php-src/pear will be moved to the new top level directory soon. Only the PEAR package manager code will be bundled with every new release automatically.