jtag_debug_module_reset and custom_instruction_maser ?

I am a new NIOS and Qsys user. I’m starting to build my Cyclone IV NIOS system in Quartus and Qsys. I’m starting small with the NIOS processor, EPCS and internal memories. There are two NIOS signals that I am not familiar with and I can’t find any explanation of their operation in the NIOS data sheet.

Can someone please explain what the purpose of the jtag_debug_module_reset and custom_instruction_maser ports are, or point me to a document that describes how I should use those?

thanks,

-phil