I was the PM on MOTODEV Studio. The cert was in a different format than what ADT uses (long story). I believe the storage formats were either JKS (the standard Java keystore), JCEKS (a Java keystore that provides much stronger protection of private keys), or PKCS12.
It might be possible to use with jarsigner directly with
jarsigner -storetype JKS -keystore file:my_motodev_keystore.key
http://docs.oracle.com/javase/7/docs/technotes/tools/windows/jarsigner.html
I'll ping a couple of the engineers who were on the project and see if they can shed some light on how to convert that format into something jarsigner can use.
EDIT: One of the guys sent me this note...
How to sign an APK with more than one certificate?
Second answer. It says how to convert the motodev keystore to jks by runing the following command:
keytool -importkeystore -srckeystore motodev.keystore -srckeystoretype JCEKS -destkeystore android.keystore -destkeystoretype JKS