Announced at reinvent 2017 in a CloudFormation Deep Dive session for “early 2018” - now (almost at the end of 2018) the time has come. AWS has added a new and long awaited feature to CloudFormation that will help in many cases: “Drift detection”.

With this feature you can see in the CloudFormation console which stacks have been changed manually. Simply select the desired stack, select “Detect drift” under actions and confirm.

In AWS words: Drift detection lets you detect whether a stack’s actual configuration has been changed outside of CloudFormation. To detect drift on a stack, select the stack, and then select Detect drift for current stack from the Actions menu.
Read more in the official documentation.
Read more in the official blog.