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Thanks for your post.
Can I ask how you originally added the table without the collation to subversion? The reason I ask is because SQL Source control will include the column collation when it adds the new object.
There isn't currently an option to ignore the collations, but there isn't any reason why we couldn't add it to a future version if enough people would find it useful.
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When I looked at the script I saw that it had added the Collation on the column I've changed.
That's not a wanted behavior on my behalf. If it should remain it needs to be configurable so it can be turned off.