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AXF files are in ELF format, not sure if there any quirks to them, but given their age I'd have to imagine conversion tools exist.
u-boot isn't going to compile under Windows, or in Keil/RVT, things like AT91Bootstrap will. And Keil is certainly capable of compiling C code and downloading/debugging directly in to the SRAM or SDRAM on 9260/9G20 parts.
The way you want to attack it, you're pretty much limited to GDB. You should go look for some tutorials, or FAQ's, or consult your documentation.
Other more practical ways to debug C code include wrapping it in a harness that emulates the interfaces and test the bulk of the code in Visual Studio, et al, or provide enough instrumentation and interactivity to your broken code to trace the problem, and walk through the code.
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