As JD has said you can ship your application without zipaligning it. It is supposed to increase the performance of your application if it has a lot of uncompressed resources. (Uncompressed audio for example or plain text files).
If you want to zipalign it, I have included the command line utility that is used for the job. Simply write in command line "zipalign 4 <<name of apk>>.apk zip_aligned.apk". There will be zip_aligned.apk file in the folder where you have run the command.
We also are going to add a story in our backlog for this feature. Seems that people will prefer to have their google play apks zipaligned.
Evgeni "Zammy" Petrov
the Telerik team
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