You really should not have to extract any files if you use CCA to upgrade the UC500. The upgrade process though CCA will extract all the needed files from the Software Pack, and create the directories. All that is required is that you point CCA to the ZIP file, so that CCA can locate the software pack. (The ZIP file does not need to be extracted.)
Darren is correct, placing everything on the root of the flash card is just Insane and asking for problems, the directory structure is in place for a reason and its not just for cleanliness either
If you are not using CCA as Darren has suggested, loading TFTP commands is no harder then if it was on the root directory, the only differences is that you need to use the alias command now rather then back in the old days it was just a straight point to file, an example of how this would look is:
tftp-server flash:/phones/521_524/cp524g-8-1-17.bin alias cp524g-8-1-17.bin
The most easiest way to manage this is to work up the TFTP-SERVER configuration in a txt editor and then just do a CLI dump, although this can sometimes generate errors so if you have never done it then it is best to do it no more than 3 lines at a time.
But in any event you should be using CCA to both build and manage the system, its just one of those things that you might not like, but in the end you learn to appreciate it
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