the bug for adding Pam_mkhomedir to the default stack is 557013 (also 566665) 
although at the end I have used this config file 
(/usr/share/pam-configs/my_mkhomedir):
Name: activate mkhomedir
Default: yes
Priority: 900
Session-Type: Additional
Session:
        optional                        pam_mkhomedir.so umask=0077 
skel=/etc/skel

both bugs have been stopped for 2 years so perhaps it's a good idea to
tweak the freeipa package to do the work of including this in pam

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https://bugs.launchpad.net/bugs/997990

Title:
  fail joining to a freeipa server with ipa-client-install

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