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Default charset on deployment

I am running a trial of the MySQL compare and it looks pretty good so far; however, when I copied the deployment script and ran a mock deployment to another test instance I noticed a lot of Foreign Key errors.  Upon closer inspection the create table statements from the MySQL script end with ENGINE=InnoDB; however, if I do a create table statement from the database that has the table it ends with ENGINE=InnoDB DEFAULT CHARSET=utf8;

That CHARSET is very important when dealing with foreign keys and the like.  A quick find and replace fixes the script; however, this would preclude me from being able to do a true "deploy" from the tool.  I haven't been able to find a way to dictate this.

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