It's a mySQL problem, but there's a Perl solution: SQL::Translator, aka SQLFairy.

So yes, other people have had the problem before you. I've never used it for what you're describing, as I only came across it last week, but it has a 'sqldiff', which will attempt to take two schemas, and give you the changes necessary to turn the first into the second. (see the documentation, as there are some special notes about the diff it generates)