This is mostly a personal project, but I will try to keep it neat and tidy for my own sanity as well as anyone reading!
Code in the Shaders directory is written in HLSL, these files can be renamed/converted to .fx and then compiled via Monogame's mgfx compiler. The output of shader compilation is a binary .xnb file that can be added directly into your project using the Microsoft.XNA.Framework.Graphics.Effect class's constructor. Here is an example.
byte[] diffuseShaderBytecode = File.ReadAllBytes(projectDir + "\Shaders\BasicDiffuse.mgfx"); _basicDiffuseShader = new Effect(GraphicsDevice, diffuseShaderBytecode);