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In the readme for the XDS100V2, it states:
KNOWN BUG FOR EVM DESIGNERS
The CPLD programming pins were moved to Port BCBUS 4,5,6,7 to make room for the B port to be used as UART.
....
RECOMMENDED FIX
BCBUS 1, 2, 5, and 6 are the only free pins on BCBUS when
the FTDI chip B port is in UART mode.
Does the CPLD programming tool listed at http://processors.wiki.ti.com/index.php/XDS100#Q:_How_can_I_update_the_CPLD_on_my_XDS100v2.3F
only work with designs with programming pins at BCBUS 4, 5, 6, 7?
Is there a version where it is changed to pins 1, 2, 5, 6?
The CPLD tool is hard coded to only use the pins at BCBUS 4, 5, 6, 7. Your only option would be to take the tool's sources and modify it yourself. The link to the tool on the XDS100 Wiki also points to a zip file with the sources. I'll try uploading the sources zip to this post too. I downloaded the sources and confirmed the project does build cleanly. Note that you do need to install the FTDI driver binaries into the ...\XDS100_TI_PROG\FTDI\CDM directory. You can find the FTDI driver used by CCS in ...\ccsv6\ccs_base\emulation\windows\xds100_drivers\ftdi. Copy the i386 directory from there to the CDM directory you created in the CPLD tool's FTDI directory.
You should then be able to remap the pins to create the custom version of the tool you need. It appears there isn't a simple pin map to function to change; you will have to search the code to make sure you've found the places to be changed. The code is posted without warranty or support. The company that originally created the tool is not providing support for custom versions, and no one in SDO is actually familiar with internal workings.