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Actually, I just got it to work .. turns out I was VERY close ...
Following the instructions in the EZ-USB Suite User Guide (NOT the outdated instructions in the "H" revision of the Programmers Manual (they removed those from the "G" version)), they indicate what fields in the Debug Configuration need to be changed.
For the 'Debugger' tab they leave the 'GDB client setup' fields unmodified.
This actually has to be configured as the gdb command that comes with EZ-USB's Eclipse ... in my case (your installation path may differ) it was:
C:\Cypress_FX3\EZ-USB FX3 SDK\1.3\ARM GCC\bin\arm-none-eabi-gdb.exe
Once I fixed that, everything started to work. With the SuperSpeed Kit and its built-in debugger, as well as with the J-Link and Olimex debugger connected to our own design with just plain JTAG. I can single-step through my code, and examine variables just fine.
(Also: don't forget double quotes around paths that contain spaces! Maybe not for the executables, but definitely the config info)
I am looking for a document that explains how to set up an OCD debugger with the FX3 USB dev kits-Eclipse, I am using the E-Con Denebola