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yes, with the packager 0.5, the jailbreak replaces Amazon's default signing certificate, temporarily.
If you don't let the package finish its job, Amazon's certificate has been removed and you won't be able to install Amazon's official packages in the future.
The way the packager 0.5 does is:
-Jailbreak by replacing Amazon's default certificate
-Run the package installer
-Restore Amazon's default certificate
If your package installer reboots (like what Savory was 0.06 doing), the default amazon certificate isn't restored.
Running the freekindle uninstaller however, would restore everything properly
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