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Thanks for that - you're correct, SQL Compare doesn't register this difference. I've raised an issue in our bug tracking system for this. (Unless it turns out to be very trivial to fix, I doubt it will be fixed in the 6.0 release, as code freeze is very close now - but it will be considered for the point release.)
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Sample Scenario:
create database firstDB
go
use firstDB
go
create table t(a int, b int, c int)
go
create index x on t(a) include(b,c)
go
create database secondDB
go
use secondDB
go
create table t(a int, b int, c int)
go
create index x on t(a, b, c)
go