just some remarks

-APDU are stored in a dedicated apdu buffer, separated from the main ram
-cards that support both T=0 and T=1 are generally used in T=0 mode since
the readers try this one before ;)
-command apdu is sent as a whole even if only the 5 first bytes are
available before setIncomingAndReceive, this is what the oscilloscope said
to me yesterday.
-new Truc() creates an eeprom object. To get a RAM object, create it as a
local variable and give this local variable as a parameter to other methods
that will use it.

-muscle card spec: the best I know is
http://www.linuxnet.com/musclecard/files/mcardprot-1.2.1.pdf

sebastien
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