See changelog of debian/ubuntu apache2 changelog for version 2.4.1-1

+ Move per-site global configuration from conf.d to conf-available and
      manage it similar to modules and sites. To do so, the new tools
      "a2enconf" and "a2disconf" are provided.

The symbolic link is a workaround. 
The phppgadmin apache configuration file should really be moved to 
"/etc/conf.d/conf-available/phppgadmin.conf"

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https://bugs.launchpad.net/bugs/1311489

Title:
  Apache config should be placed in conf-available, not conf.d

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