It might be easier to do it the other way around. The only really useful things that will be generated are the Project.toml file and the folders src, test etc. (and perhaps the file test/runtests.jl).
So after generating the files in some new directory, I would copy them into the existing project (keeping around the original Project.toml and Manifest.toml temporarily if something goes wrong, e.g. just rename them).
Then you can rename/move/edit all the files as needed and sort them into the right places, add the dependencies to the new (now empty, but containing the UUID and package name) Project.toml, and test if everything is working. At the end, you can make one big commit “reshaping” your existing repo into a package – that way you can keep all the git history without the hassle of duplicating the .git folder.