Public bug reported:

$ lsb_release -rd
Description:    Ubuntu 12.04 LTS
Release:        12.04

$ apt-cache policy php-pear
php-pear:
  Installed: 5.5.4+dfsg-1+debphp.org~precise+1
  Candidate: 5.5.4+dfsg-1+debphp.org~precise+1
  Version table:
 *** 5.5.4+dfsg-1+debphp.org~precise+1 0
        500 http://ppa.launchpad.net/ondrej/php5/ubuntu/ precise/main amd64 
Packages
        100 /var/lib/dpkg/status
     5.3.10-1ubuntu3.8 0
        500 http://us.archive.ubuntu.com/ubuntu/ precise-updates/main amd64 
Packages
        500 http://security.ubuntu.com/ubuntu/ precise-security/main amd64 
Packages
     5.3.10-1ubuntu3 0
        500 http://us.archive.ubuntu.com/ubuntu/ precise/main amd64 Packages

With PHP 5.4, ini files were stored in /etc/php5/mods-available/ and
symlinked into a global ini directory /etc/php5/conf.d/, which inturn
was symlinked as the conf.d directory in all the flavors of PHP. When
PEAR installed an extension it would add the file to /etc/php5/conf.d/
and so would be avaliable regardless of how you ran php (cli, cgi, fpm).

With PHP 5.5 there no longer is a /etc/php5/conf.d/ directory, modules
are still installed into /etc/php5/mods-available/ but are directly
symlinked into the flavor conf.d directory. When PEAR installs a module
it either fails to create the ini file if the directory does not exist,
or if you create the directory it will create the ini fine but not
symlink it into the php flavors.

I would expect either PHP 5.5. to use the old directory structure so
that PEAR modules are loaded as expected, or for PEAR to create the base
conf.d directory and symlink its own inis into the php flavors.

** Affects: php5 (Ubuntu)
     Importance: Undecided
         Status: New

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https://bugs.launchpad.net/bugs/1238160

Title:
  pear puts config in wrong directory

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