If I understand correctly, you are asking if the -ccs.buildCommandFlags option can be set differently for different build configurations, is that correct? I am not certain and haven't tested it myself but there is also a -ccs.configurations option supported by projectCreate that you could try to use in conjuction with -ccs.buildCommandFlags, (ie) specify one build configuration followed by its buildCommandFlags and then the next build config with its flags. Again, I don't know for certain if this will work but might be worth a try.
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