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I'm creating my first github repo in C# (compatability has only just been added), and I'm really unsure of how to structure my project.

I know that many languages have folders like:

/src
/builds

though i'm not sure how this would apply to C#.

There's this C# project, although it looks quite messy, and I'm not sure whether this is appriopriate.

Structure it however you want. It takes time and experimentation to find a project structure that works for you though. As an example, I tend to use something like this:

/codebase
/documentation
/libraries
/media
/output
/tools