There is some debate about what should and should not be in your repository, and ultimately it comes down to personal preference. Previously, I added only user files and files that I changed from the Umbraco installation, for example, configuration files, however, since the appearance of the Nuget package, I put everything except the binary files in the original control, because when I update through Nuget later, I can easily see the changes and merge the settings back.
This saves a lot of problems with Umbraco directly (IMO), especially if you make any changes using the user interface, and if you do not use it directly, then it makes little sense to use the Nuget package because you will get a bunch of unused files in your project. In your situation, you can keep your project clean and perform a manual installation in the place that IIS uses for the site, and save the files in the project you created.
This is just my opinion, so take away from him what you want, but I hope this helps.
Simon
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