Cleanup MySQL database

Addresses changes made to installation guide and config files but never
applied in update process. Relevant changes to installation guide and
config files were made in
gitlabhq@cbb5b00,
gitlabhq@498a4e6,
gitlabhq@c33d5e1,
gitlabhq@485162e#diff-e1059d0fa0437ffad94facff86210603,
gitlabhq@72e2fe2#diff-d1b4ff7de834bae6008dd49550413a6f,
gitlabhq@5163a8f#diff-e1059d0fa0437ffad94facff86210603,
gitlabhq@993af5d#diff-e1059d0fa0437ffad94facff86210603,
&
gitlabhq@d3f5a0c.