First, I never used that particular kit so I don't know that board of those samples.
Just in general with HIWAVE the "command file does not exist." messages are printed if a command file is enabled but does not actually exist. In the CW wizard generated projects those command files are almost always empty, so the lack of them is usually not an issue. I guess that the sample creator did remove the empty files without disabling the command files, if so then this would be not the real problem, just a cosmetic thing.
The "ERROR: programmer is not enabled" and "Code loading overlap detected in range 0x00000400..0x00000417" messages though look suspicious to me, although I'm not sure if they are the actual problem you have either, sorry.
When I look further down the command window then it apears to me that the debugger was able to set a breakpoint run and did hit it. Does this mean the app reaches main? Or where did it stop?
I would also try to reset the device, and if it is on reasonable code, where it would go by stepping throught the code.
Daniel