How do I create a project in C# without using scaffolding I want to create code manually

There's nothing magic in working with C# - there are no binary files hidden behind the scenes when you start creating your C# applications. The answer to what you are asking is; it depends. If you just want to try out some casual C# statements and aren't bothered about this becoming an application, you could try LINQPad[^]. This utility is, basically, a C# scratchpad conveniently bundled together so you could write code like this without any trouble

List<int> values = new();
values.Add(10);
values.Add(5);
values.Add(7);
foreach (int value in values)
{
  Console.WriteLine(value);
}

If, however, you want to write something that persists - and, from your question we can see that you do, that's no trouble. As long as you are using a relatively up to date version of dotnet. Open up a text editor of your choice, and start writing the various files. You could start with your csproj file. For this example, I'm going to create a C# project file as if I were building a .NET 8 web api.

<Project Sdk="Microsoft.NET.Sdk.Web">

  <PropertyGroup>
    <TargetFramework>net8.0</TargetFramework>
    <Nullable>enable</Nullable>
    <ImplicitUsings>enable</ImplicitUsings>
  </PropertyGroup>

  <ItemGroup>
    <PackageReference Include="Microsoft.AspNetCore.OpenApi" Version="8.0.4" />
    <PackageReference Include="Swashbuckle.AspNetCore" Version="6.4.0" />
  </ItemGroup>

</Project>

Next, create an appsettings.json file like so:

{
  "Logging": {
    "LogLevel": {
      "Default": "Information",
      "Microsoft.AspNetCore": "Warning"
    }
  },
  "AllowedHosts": "*"
}

Create a Properties folder and, inside that, create a filed called launchSettings.json - this is going to be used when you actually run your project

{
  "$schema": "http://json.schemastore.org/launchsettings.json",
  "iisSettings": {
    "windowsAuthentication": false,
    "anonymousAuthentication": true,
    "iisExpress": {
      "applicationUrl": "http://localhost:63483",
      "sslPort": 44330
    }
  },
  "profiles": {
    "http": {
      "commandName": "Project",
      "dotnetRunMessages": true,
      "launchBrowser": true,
      "launchUrl": "swagger",
      "applicationUrl": "http://localhost:5187",
      "environmentVariables": {
        "ASPNETCORE_ENVIRONMENT": "Development"
      }
    },
    "https": {
      "commandName": "Project",
      "dotnetRunMessages": true,
      "launchBrowser": true,
      "launchUrl": "swagger",
      "applicationUrl": "https://localhost:7126;http://localhost:5187",
      "environmentVariables": {
        "ASPNETCORE_ENVIRONMENT": "Development"
      }
    },
    "IIS Express": {
      "commandName": "IISExpress",
      "launchBrowser": true,
      "launchUrl": "swagger",
      "environmentVariables": {
        "ASPNETCORE_ENVIRONMENT": "Development"
      }
    }
  }
}

Finally, add your Program.cs file:

WebApplicationBuilder? builder = WebApplication.CreateBuilder(args);

builder.Services.AddEndpointsApiExplorer();
builder.Services.AddSwaggerGen();

WebApplication app = builder.Build();

if (app.Environment.IsDevelopment())
{
    app.UseSwagger();
    app.UseSwaggerUI();
}

app.UseHttpsRedirection();

string[] summaries = new[]
{
    "Freezing", "Bracing", "Chilly", "Cool", "Mild", "Warm", "Balmy", "Hot", "Sweltering", "Scorching"
};

app.MapGet("/weatherforecast", () =>
{
    var forecast =  Enumerable.Range(1, 5).Select(index =>
        new WeatherForecast
        (
            DateOnly.FromDateTime(DateTime.Now.AddDays(index)),
            Random.Shared.Next(-20, 55),
            summaries[Random.Shared.Next(summaries.Length)]
        ))
        .ToArray();
    return forecast;
})
.WithName("GetWeatherForecast")
.WithOpenApi();

app.Run();

Finally, run the following command:

dotnet build

Congratulations, you have just built your own API style application entirely from scratch. With only a little bit of work, you could adapt the technique I followed here to build your MVC program complete with MVC support.