Duplicate '.kotlin_module' entries

### Expected and Results Related issue: https://youtrack.jetbrains.com/issue/KT-84503/Duplicate-META-INF-serialization.shadow.kotlinmodule-entry-in-kotlin-native-compiler-embeddable-jar After updating to shadow 9.2.1, the kotlin-compiler-embeddable started showing duplicate zip entries. ### Related environment and versions _No response_ ### Reproduction steps - Checkout Kotlin https://github.com/JetBrains/kotlin at 62ccb3cc728090ba8a929a09754744ae66368b08 - Build using ./gradlew publish - Check `build/repo/org/jetbrains/kotlin/kotlin-compiler-embeddable/2.4.255-SNAPSHOT/kotlin-compiler-embeddable-2.4.255-*.jar` ### Anything else? _No response_