It doesn't matter whick cmake version you use, but how you write your Cmakelists.txt file.
I am hoping the Cmakelists.txt file in the root folder or the one in the tests folder could consider this situation.
The one in tests folder could try not to run exe file with relative path for Windows. If it not achievable, then the root one may have separate targets: build fltk, install and build tests.

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