How can I make SmartScreen Filter trust a self-signed certificate

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To quote from MSDN’s website:

Detractors may claim that SmartScreen is “forcing” developers to spend
money on certificates. It should be stressed that EV code signing
certificates are not required to build or maintain reputation with
SmartScreen. Files signed with standard code signing certificates and
even unsigned files continue to build reputation as they have since
Application Reputation was introduced in IE9 last year. However, the
presence of an EV code signing certificate is a strong indicator that
the file was signed by an entity that has passed a rigorous validation
process and was signed with hardware which allows our systems to
establish reputation for that entity more quickly than unsigned or
non-EV code signed programs.

In other words, EV (paid) validation is just one factor in a large algorithm that determines whether the SmartScreen warning is displayed or not. If you have a lot of people that download your program, or if your program download link has not changed in a while, with some work you can get your program not to show the warning. Also, by digitally signing your code, you can increase your Appication Reputation. This is straight from Microsoft’s webpage on the topic.

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