I assume the JavaCard has to be initialized with bitcoin-specific software (for signing). I wonder which step does that? Or is that not covered by this guide?
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Loading the Satochip java applet to the javacard is what I refer to as the DIY version of Satochip. It takes seconds to prepare them. Here are my notes, follow the links and readmes in the linked repos for more details: 
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Smartcard applets for Bitcoin and PGP on Debian Linux
Smartcard applets for Bitcoin and PGP on Debian Linux - Satochip javacard applet install