XPC564BADPT176QSB3M_SCH.PDF .The document comes from the official website, TCK is pull up, but the 41.2.1 JTAG Controller (JTAGC) of MPC5646CRM.pdf Description TCK is pull down.
that's a typo in reference manual. There's internal weak pull up resistor. See the "Table 4-3. Functional port pin description" in reference manual. Here it is correct.
I will create ticket for documentation team. Thanks for pointing this out.
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