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There is a uservoice page for MySQL Compare where you can put your suggestions:
http://redgate.uservoice.com/forums/210413-mysql-tools
It may be helpful to include exactly which attributes of the indexes that you want to ignore. You can already ignore index names in the options and I would imagine we could add more options as to which parts of the index can safely be ignored during comparison.
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the only thing i would need is, that i would love to have options to ignore key- and index- differences.
i am working on a productive mysql server which table-design is quite old and it seems like the mysql-dumps did not import all the key- and index-differences to the development server.
i don't wanna touch the keys and indices on the productive environment unless i decide to do it manually someday.
so such an option would be very helpful for me and i rather would decide to buy your product.
(currently i work around this problem by editing the deployment script on my own)