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Hi,
In order to perform debugging in any makefile-based project (including linux kernel and u-boot), CCSv5 has the concept of Standard Makefile (or Unmanaged) project, a specific type of project that simply requires an existing Makefile and all required source/include files in the same directory structure. It differs from the traditional CCS (Managed) project as it only allows control of the parameters passed to the make (or gmake) tool - all compiler and linker parameters are entirely contained in the Makefile.
Therefore, to debug the u-boot source code in a Windows machine you will need access to the u-boot source directory (typically via samba share) and the u-boot binary with debug symbols (file <u-boot> if I am not mistaken). You will also have to create a Standard Makefile project to allow CCS to properly correlate the memory address in the target with the correct source code in the u-boot tree.
The process of creating a standard make project and loading the symbols is very similar to performing Linux kernel debug. Check the section Stop Mode debug of the following page:
http://processors.wiki.ti.com/index.php/Linux_Debug_in_CCSv5
Hope this helps,
Rafael