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How can I change the package name of my apk using java program?

Changing the package name is a pain in the ass. It looks like different methods work for different people. My solution is quick and error free. Looks like no cleaning or resetting eclipse is needed.

Right-click on the package name then Refractor > Rename.

Right-click on the project name Android tools > Rename Application Package.

Manually set the package names in the Manifest that have not been changed by the previous steps.