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.

Doesn't make sense to add this to old install guides as most users have already passed those install guides and this doesn't address specific issues they would have encountered during upgrading.

Main purpose of these instructions are to get old installations more up to speed with latest recommended setup as per installation.md and database_mysql.md.
InnoDB added in https://github.com/gitlabhq/gitlabhq/commit/498a4e6b0c8b7cc9266f71dd3337669a9442934d