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The mergeDebugJniLibFolders command in react-native-reanimated refers to a Gradle task that merges the JNI (Java Native Interface) libraries of all dependencies and the project into a single folder. This is necessary because when an app is built, it must include the appropriate JNI libraries for the processor architecture of the device it will run on. The mergeDebugJniLibFolders task ensures that all necessary libraries are included and properly configured for the app to function correctly.