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Found out the root cause from AGP source code, all NonIncrementalTask will delete outputs before the main TaskAction.

There is a documentation how to affect merged manifest: <https://developer.android.com/studio/build/extend-agp#access-modify-artifacts>
There are also a few examples in <https://github.com/android/gradle-recipes> Make sure to pick branch that corresponds to your AGP version.
For example, <https://github.com/android/gradle-recipes/blob/agp-7.2/Kotlin/manifestReplacementTest/app/build.gradle.kts|manifest replacement> or <https://github.com/android/gradle-recipes/blob/agp-7.2/Kotlin/manifestTransformerTest/app/build.gradle.kts|manifest transformer>.