I am starting to use MySQL Workbench tool especially for data modeling. So, the first I would like to do is reverse engineering of my existing database on web server. But I
I use MAMP on mac and failed to upgrade the my databases via command line as suggested above, but it worked when i used MAMP PRO->TOOLS menu options (top of OS X screen) to 'Check', 'Repair' and 'Upgrade' databases.
I presume that the GUI supplies the underlying CLI tools with the necessary options, so that you don't have to think about what those options need to be (as opposed to running the CLI tools manually).
Upgrading my MAMP in this way (via MAMP PRO's GUI Tools) made my (separate) Oracle mysqlWorkbench 6.0 app work just fine with my local MAMP PRO 2.0.5 databases on OS X 10.8.5 (Mountain Lion), which mysqlworkbench had said were corrupt previously (but MAMP's phpmyadmin worked fine on them whilst they were "corrupt", curiously). Now, both mysqlWorkbench 6.0 and MAMP PRO's phpmyadmin tools are both happy, and so am I.