Gradle generated files
Answered
Why Idea stopped seeing generated files by Gradle?
Environment
Idea 2018.2
Gradle 4.9-4.10
MapStruct 1.2.0.Final
id "net.ltgt.apt" version "0.18"
id "net.ltgt.apt-idea" version "0.18"
Gradle build config checkbox check
On old environment
Idea 2017.x
Gradle 4.6 all work fine
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Do you use annotationProcessor scope? It is not yet supported, see https://youtrack.jetbrains.com/issue/IDEA-187868.
Try enabling Settings(Preferences) | Build, Execution, Deployment | Build Tools | Gradle | Runner | Delegate IDE build/run actions to gradle option.
Check also https://stackoverflow.com/a/51169211/2000323 and https://stackoverflow.com/a/51476415/2000323.