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Stuff i did

Signing BlackBerry BAR files for publishing to the AppWorld
20.01.2013

Using the command line tools:
blackberry-signer -verbose -storepass [your store pass] [your bar file name] RDK
blackberry-signer -verbose -storepass [your store pass] [your bar file name] author

After signing you can verify your BAR file with:
blackberry-signer -verbose -verify [your bar file name]

Everything except:
META-INF/MANIFEST.MF
META-INF/AUTHOR.SF
META-INF/AUTHOR.EC
META-INF/RDK.SF
META-INF/RDK.EC

should be prefixed with "sm", which means that the entry is listed in the manifest and signed properly. The AUTHOR.* files are author signatures and the RDK.* are RIM's signatures. You need both:)

The problem i encountered was that the BAR packager (marmalade sdk in my case) left the actual directories inside the zip file.
They are seperate from files and can be removed without removing the files in them and you should do it with:
zip -d SolidDefence.bar META-INF/ native/

Don't forget to add all the directories you have in your zip file to this list, otherwise you will encounter cryptic error messages minutes before the deadline:)

This will solve the "Error: Some files are missing signatures" problem reported by verify and AppWorld:)

For more common signing errors check here: http://developer.blackberry.com/native/documentation/bb10/com.qnx.doc.native_sdk.devguide/com.qnx.doc.native_sdk.devguide/topic/app_signing_errors.html

Now go develop! 
https://developer.blackberry.com/