All the extensions have also been updated:
ANTLR4 extension
Archive extension
Checkstyle extension
Command Line Execution extension
Generated Version extension
JaCoCo Report extension
PIT Mutation Testing extension
PMD extension
Property File extension
Spring Boot extension
TestNG extension
Tests Badge extension
The Kotlin extension has been completely reworked. It now compiles using a local installation of the Kotlin compiler, making it possible to test with multiple versions of Kotlin. Dokka now has its own extension. There's also a Kotlin project template on GitHub with support for the Dokka and Detekt extensions.
Microsoft got back to me, it was indeed the 'reputation' of the binary. It has now established the necessary reputation and when updating the SmartScreen definitions and re-downloading the binary, the warning doesn't appear anymore.