PEAR installs system wide dependencies which makes things like what you describe hard. Composer on the other hand is exactly what you'd need, because it's a per-project dependency manager with much better support for resolving and installing of dependencies. Basically, compared to Composer, PEAR sucks... it always did, Composer on the other hand rocks!
The first thing I would do for each package you need is to see if it is also provided on https://packagist.org/. If it is, problem solved, include the installation into your build process with composer. If you end up with only a few packages from PEAR, you have several options:
- inspire the author to provide it on packagist
- make your own mirror on packagist (not recommended but sometimes necessary)
- see if the project is on github and install directly from git with composer
- install the PEAR package via composer anyways, it's possible.
Short answer: switch to composer!