This issue can be closed. This system was modified at some point with no notice in the configuration file.

I pulled the deb package from /var/cache/apt, extracted the data.tar.gz and inspected my.cnf

---

Additional debugging used to verify:


user@hostname:~$ apt-cache policy mysql-server*
mysql-server-core-5.0:
  Installed: (none)
  Candidate: (none)
  Version table:
mysql-server-core-5.1:
  Installed: (none)
  Candidate: (none)
  Version table:
mysql-server-core-5.5:
  Installed: 5.5.62-0ubuntu0.14.04.1
  Candidate: 5.5.62-0ubuntu0.14.04.1
  Version table:
 *** 5.5.62-0ubuntu0.14.04.1 0
        500 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/main amd64 Packages
        500 http://security.ubuntu.com/ubuntu/ trusty-security/main amd64 Packages
        100 /var/lib/dpkg/status
     5.5.35+dfsg-1ubuntu1 0
        500 http://us.archive.ubuntu.com/ubuntu/ trusty/main amd64 Packages
mysql-server-core-5.6:
  Installed: (none)
  Candidate: 5.6.33-0ubuntu0.14.04.1
  Version table:
     5.6.33-0ubuntu0.14.04.1 0
        500 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/universe amd64 Packages
        500 http://security.ubuntu.com/ubuntu/ trusty-security/universe amd64 Packages
     5.6.16-1~exp1 0
        500 http://us.archive.ubuntu.com/ubuntu/ trusty/universe amd64 Packages
mysql-server-5.0:
  Installed: (none)
  Candidate: (none)
  Version table:
mysql-server-5.1:
  Installed: (none)
  Candidate: (none)
  Version table:
mysql-server-5.5:
  Installed: (none)
  Candidate: 5.5.62-0ubuntu0.14.04.1
  Version table:
     5.5.62-0ubuntu0.14.04.1 0
        500 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/main amd64 Packages
        500 http://security.ubuntu.com/ubuntu/ trusty-security/main amd64 Packages
        100 /var/lib/dpkg/status
     5.5.35+dfsg-1ubuntu1 0
        500 http://us.archive.ubuntu.com/ubuntu/ trusty/main amd64 Packages
mysql-server-5.6:
  Installed: (none)
  Candidate: 5.6.33-0ubuntu0.14.04.1
  Version table:
     5.6.33-0ubuntu0.14.04.1 0
        500 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/universe amd64 Packages
        500 http://security.ubuntu.com/ubuntu/ trusty-security/universe amd64 Packages
     5.6.16-1~exp1 0
        500 http://us.archive.ubuntu.com/ubuntu/ trusty/universe amd64 Packages
virtual-mysql-server-core:
  Installed: (none)
  Candidate: (none)
  Version table:
mysql-server:
  Installed: (none)
  Candidate: 5.5.62-0ubuntu0.14.04.1
  Version table:
     5.5.62-0ubuntu0.14.04.1 0
        500 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/main amd64 Packages
        500 http://security.ubuntu.com/ubuntu/ trusty-security/main amd64 Packages
     5.5.35+dfsg-1ubuntu1 0
        500 http://us.archive.ubuntu.com/ubuntu/ trusty/main amd64 Packages
mysql-server-core:
  Installed: (none)
  Candidate: (none)
  Version table:
virtual-mysql-server:
  Installed: (none)
  Candidate: (none)
  Version table:

user@hostname:~$ ls /var/run/mysqld/
mysqld.sock  mysql.pid


user@hostname:/etc/mysql$ sudo grep -R "mysql.pid" .
./my.cnf:pid-file                       = /var/run/mysqld/mysql.pid


user@hostname:/etc/mysql$ dpkg -S /etc/mysql/my.cnf
mysql-common: /etc/mysql/my.cnf

user@hostname:/etc/mysql$ apt-cache policy mysql-common
mysql-common:
  Installed: 5.5.62-0ubuntu0.14.04.1
  Candidate: 5.5.62-0ubuntu0.14.04.1
  Version table:
 *** 5.5.62-0ubuntu0.14.04.1 0
        500 http://us.archive.ubuntu.com/ubuntu/ trusty-updates/main amd64 Packages
        500 http://security.ubuntu.com/ubuntu/ trusty-security/main amd64 Packages
        100 /var/lib/dpkg/status
     5.5.35+dfsg-1ubuntu1 0
        500 http://us.archive.ubuntu.com/ubuntu/ trusty/main amd64 Packages


user@hostname:/var/cache$ sudo find .  | grep mysql-common
./apt/archives/mysql-common_5.5.62-0ubuntu0.14.04.1_all.deb
...

user@hostname:/var/cache$ cp ./apt/archives/mysql-common_5.5.62-0ubuntu0.14.04.1_all.deb ~
user@hostname:/var/cache$ cd ~
user@hostname:~$ ar x mysql-common_5.5.62-0ubuntu0.14.04.1_all.deb
user@hostname:~$ tar xvf data.tar.xz

user@hostname:~$ cat etc/mysql/my.cnf | grep pid
pid-file	= /var/run/mysqld/mysqld.pid