I imagine that you can call these through Team Build - the Exec task available within MSBuild can execute any custom command-line you would like. As for whether this is a good idea - I have no idea, since I don't know what your scripts are for! Things to watch out for, however:
* You will need to make sure that the scripts are installed on all your build machines. In general, if you are going to use scripts within your build process it is a good idea to version them (so that builds can be recreated), so I would recommend adding them to version control and relying on the standard Get task behavior within Team Build to pull them down to the build machine.
* The directory structure on your build machine is likely to be different than on your development boxes - watch out for fully qualified paths (i.e. keep things relative), try to keep things in sync between the two environments, etc.
-Aaron
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