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Since you don’t have any history of your changes to preserve I think your best bet is to clone the repo normally, and then copy your changes into that repository. Your question is a bit sparse on details, but something like the following should work
git clone <git hub project> <new folder on your system>
# maybe you can use a tag here for the SHA
git checkout -b my_branch SHA_THAT_REPRESENTS_YOUR_ZIP_DOWNLOAD
cp -r <your existing directory> <your new git repository>
git status # abort if this step doesn't look right
git add # add all your changed files
git commit # commit your work
git rebase <main dev branch> # catch up
Source:stackexchange.com