jtag: cut down on usage of unintended modification of global end state

jtag: cut down on usage of unintended modification of global end state

jtag_get/set_end_state() is now deprecated.

There were lots of places in the code where the end state was
unintentionally modified.

The big Q is whether there were any places where the intention
was to modify the end state. 0.5 is a long way off, so we'll
get a fair amount of testing.

Signed-off-by: Øyvind Harboe <oyvind.harboe@zylin.com>