Gradle's APT handling seems to significantly differ from Maven's as the Java compilation runs from a completely different base folder than the actual project compiled. Even more so, for multi-module projects, the base folder is always the same, which causes APT output using Java's plain File API to override itself in a multi-module project.
I've tweaked the output folder detection to look up well-known APT parameters provided by either the Spring Boot plugin (org.springframework.boot.configurationprocessor.additionalMetadataLocations) or KAPT (for Kotlin-based projects, kapt.kotlin.generated) and derive the actual output folder from the values set for those. If neither of these is set, we fall back to the original local folder.
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