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
https://github.com/gitlabhq/gitlabhq/commit/cbb5b000c0c7593673683c08a402ea01a3a7f369,
https://github.com/gitlabhq/gitlabhq/commit/498a4e6b0c8b7cc9266f71dd3337669a9442934d,
https://github.com/gitlabhq/gitlabhq/commit/c33d5e16fe5f5dde4f270adaf7fb6fe5b9552018,
https://github.com/gitlabhq/gitlabhq/commit/485162ec608784dc1cbafe70b3ba3201b0f74098#diff-e1059d0fa0437ffad94facff86210603,
https://github.com/gitlabhq/gitlabhq/commit/72e2fe2c8a48fae4ec72d9d25b1742187afa0c92#diff-d1b4ff7de834bae6008dd49550413a6f,
https://github.com/gitlabhq/gitlabhq/commit/5163a8fcb9cfd63435560fda00173b76df2ccc93#diff-e1059d0fa0437ffad94facff86210603,
https://github.com/gitlabhq/gitlabhq/commit/993af5d0d2d596040195c4109c531c33deeac026#diff-e1059d0fa0437ffad94facff86210603,
&
https://github.com/gitlabhq/gitlabhq/commit/d3f5a0c67f029441537d4f64040bf6454b999120.