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The unaligned apk is just an intermediate product. the unaligned apk is generated. the unaligned gets aligned and produces the aligned apk.
Unsigned Apk, as the name suggests it means it is not signed by any Keystore. A Keystore is basically a binary file that contains a set of private keys. Every App that we install using the Google Play App Store needs to be signed with a Keystore.
It is a two step process. The unaligned apk is just an intermediate product.
The unaligned(signed) APK is needed because signing an aligned apk will undo the alignment.
From the docs:
Caution: zipalign must only be performed after the .apk file has been signed with your private key. If you perform zipalign before signing, then the signing procedure will undo the alignment.
See this answer for more. Here is the detailed build process:
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