I've attached a Vagrant config that reproduces this problem.

To run it, install vagrant, put the attached file into a folder, cd into it and run 'vagrant up'.

All it does is get an ubuntu trusty image, adds the percona repo and installs the percona-server-server package (5.6.22-71.0-726.trusty). The resulting installation has these bad directives in the /etc/my.cnf file.

I noticed during the installation that it installs mysql-common (5.5.40-0ubuntu0.14.04.1) as a dependency, which is probably where this is coming from.

I see that although percona-server-server-5.6 lists percona-server-common-5.6 as a dependency, percona-server-common-5.6 does not say it provides mysql-common - could that perhaps be the problem?

If I modify the vagrant file to explicitly install percona-server-common-5.6, the problem still occurs because mysql-common is still installed. Perhaps one of the sub-dependencies like libdbi-mysql-perl relies on it explicitly?

==> default: The following NEW packages will be installed:
==> default:   libaio1 libdbd-mysql-perl libdbi-perl libmysqlclient18
==> default:   libperconaserverclient18.1 mysql-common percona-server-client-5.6
==> default:   percona-server-common-5.6 percona-server-server percona-server-server-5.6
==> default: 0 upgraded, 10 newly installed, 0 to remove and 30 not upgraded.
==> default: Need to get 15.8 MB of archives.
==> default: After this operation, 143 MB of additional disk space will be used.
==> default: Get:1 http://repo.percona.com/apt/ trusty/main percona-server-common-5.6 amd64 5.6.22-71.0-726.trusty [11.5 kB]
==> default: Get:2 http://archive.ubuntu.com/ubuntu/ trusty/main libaio1 amd64 0.3.109-4 [6,364 B]
==> default: Get:3 http://repo.percona.com/apt/ trusty/main libperconaserverclient18.1 amd64 5.6.22-71.0-726.trusty [566 kB]
==> default: Get:4 http://archive.ubuntu.com/ubuntu/ trusty-updates/main mysql-common all 5.5.40-0ubuntu0.14.04.1 [14.1 kB]
==> default: Get:5 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libmysqlclient18 amd64 5.5.40-0ubuntu0.14.04.1 [598 kB]
==> default: Get:6 http://repo.percona.com/apt/ trusty/main percona-server-client-5.6 amd64 5.6.22-71.0-726.trusty [1,392 kB]
==> default: Get:7 http://repo.percona.com/apt/ trusty/main percona-server-server-5.6 amd64 5.6.22-71.0-726.trusty [12.2 MB]
==> default: Get:8 http://archive.ubuntu.com/ubuntu/ trusty/main libdbi-perl amd64 1.630-1 [879 kB]
==> default: Get:9 http://archive.ubuntu.com/ubuntu/ trusty/main libdbd-mysql-perl amd64 4.025-1 [99.3 kB]
==> default: Get:10 http://repo.percona.com/apt/ trusty/main percona-server-server amd64 5.6.22-71.0-726.trusty [11.4 kB]
==> default: dpkg-preconfigure: unable to re-open stdin: No such file or directory
==> default: Fetched 15.8 MB in 19s (812 kB/s)
==> default: Selecting previously unselected package libaio1:amd64.
==> default: (Reading database ... 60964 files and directories currently installed.)
==> default: Preparing to unpack .../libaio1_0.3.109-4_amd64.deb ...
==> default: Unpacking libaio1:amd64 (0.3.109-4) ...
==> default: Selecting previously unselected package mysql-common.
==> default: Preparing to unpack .../mysql-common_5.5.40-0ubuntu0.14.04.1_all.deb ...
==> default: Unpacking mysql-common (5.5.40-0ubuntu0.14.04.1) ...
==> default: Selecting previously unselected package libmysqlclient18:amd64.
==> default: Preparing to unpack .../libmysqlclient18_5.5.40-0ubuntu0.14.04.1_amd64.deb ...
==> default: Unpacking libmysqlclient18:amd64 (5.5.40-0ubuntu0.14.04.1) ...
==> default: Selecting previously unselected package percona-server-common-5.6.
==> default: Preparing to unpack .../percona-server-common-5.6_5.6.22-71.0-726.trusty_amd64.deb ...
==> default: Unpacking percona-server-common-5.6 (5.6.22-71.0-726.trusty) ...
==> default: Selecting previously unselected package libdbi-perl.
==> default: Preparing to unpack .../libdbi-perl_1.630-1_amd64.deb ...
==> default: Unpacking libdbi-perl (1.630-1) ...
==> default: Selecting previously unselected package libperconaserverclient18.1.
==> default: Preparing to unpack .../libperconaserverclient18.1_5.6.22-71.0-726.trusty_amd64.deb ...
==> default: Unpacking libperconaserverclient18.1 (5.6.22-71.0-726.trusty) ...
==> default: Selecting previously unselected package percona-server-client-5.6.
==> default: Preparing to unpack .../percona-server-client-5.6_5.6.22-71.0-726.trusty_amd64.deb ...
==> default: Unpacking percona-server-client-5.6 (5.6.22-71.0-726.trusty) ...
==> default: Selecting previously unselected package libdbd-mysql-perl.
==> default: Preparing to unpack .../libdbd-mysql-perl_4.025-1_amd64.deb ...
==> default: Unpacking libdbd-mysql-perl (4.025-1) ...
==> default: Processing triggers for man-db (2.6.7.1-1ubuntu1) ...
==> default: Setting up percona-server-common-5.6 (5.6.22-71.0-726.trusty) ...
==> default: Selecting previously unselected package percona-server-server-5.6.
==> default: (Reading database ... 61224 files and directories currently installed.)
==> default: Preparing to unpack .../percona-server-server-5.6_5.6.22-71.0-726.trusty_amd64.deb ...
==> default: Unpacking percona-server-server-5.6 (5.6.22-71.0-726.trusty) ...
==> default: Selecting previously unselected package percona-server-server.
==> default: Preparing to unpack .../percona-server-server_5.6.22-71.0-726.trusty_amd64.deb ...
==> default: Unpacking percona-server-server (5.6.22-71.0-726.trusty) ...
==> default: Processing triggers for man-db (2.6.7.1-1ubuntu1) ...
==> default: Processing triggers for ureadahead (0.100.0-16) ...
==> default: Setting up libaio1:amd64 (0.3.109-4) ...
==> default: Setting up mysql-common (5.5.40-0ubuntu0.14.04.1) ...
==> default: Setting up libmysqlclient18:amd64 (5.5.40-0ubuntu0.14.04.1) ...
==> default: Setting up libdbi-perl (1.630-1) ...
==> default: Setting up libperconaserverclient18.1 (5.6.22-71.0-726.trusty) ...
==> default: Setting up percona-server-client-5.6 (5.6.22-71.0-726.trusty) ...
==> default: Setting up libdbd-mysql-perl (4.025-1) ...
==> default: Setting up percona-server-server-5.6 (5.6.22-71.0-726.trusty) ...