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Unfortunately, this isn't currently possible with the current version of SQL Compare. DML triggers and indexes are treated as part of a table, and changing this would require a large rewrite of the core of the SQL Compare engine. It is something that's been requested quite a few times before, so it is something we might consider in a future version.
Simon C
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Currently trigger definitions are appended to the table script file containing the relevant CREATE TABLE statement, which can be a pain if you have triggers that are frequentlly modified. My current workaround is to manually cut and paste the CREATE TRIGGER statements into new files.
Thanks
Chris