Does setup assistant overwrite applications and operating system?

I want to give my wife my old laptop and transfer her data over. I want her to have my applications. Will the setup assistant overwrite my applications and remove them if she doesn't have them on her mac? Will it overwrite my version of OS with hers?
Thanks

Paranoia is understandable; however, misplaced. Just follow the steps in Pondini's Setup New Mac guide.

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