Nim is MIT, not GPL v3, not sure if there is some confusion here?
I'm not a lawyer but code generated by Nim's tools falls under the same licence that you chose for your project. So if your project is GPL 3, so is your config.nims. Same for the makefile if you wrote it or niminst generated it for you.
@sls1005 it's common to include a file named LICENCE or COPYING at the root of a repository to hint that all files in the project are under the same license unless stated otherwise. A safer option is to also include a little header on top of every file, for better clarity.
You are not required to use the same license for every file. E.g. some games use GPLv3 for the code files and CC BY-SA for artwork.
If you were to pick a combination of licenses that cannot be satisfied together other people would not be able to use your project.
Also FYI by using Nim's standard library you are required to carry a copy of its license https://github.com/nim-lang/Nim/blob/devel/copying.txt