GitHub repository does not contain assets (models, textures and other big files). Game will search for this files in path specified in global.props. It's recommended to create file user.props which overrides values from global.props. File user.props is ignored by GitHub, so you won't accidentally commit it.

Example user.props:

<?xml version="1.0" encoding="utf-8"?> 
<Project ToolsVersion="4.0" xmlns="https://schemas.microsoft.com/developer/msbuild/2003">
  <ImportGroup Label="PropertySheets" />
  <PropertyGroup Label="UserMacros" />
  <PropertyGroup>
    <ContentPath>d:\SteamLibrary\SpaceEngineers\Content</ContentPath>
    <EffectsFromSources>true</EffectsFromSources>
    <DataFromSources>true</DataFromSources>
  </PropertyGroup>
  <ItemDefinitionGroup />
  <ItemGroup />
</Project>

Data definitions and Effects are included in repository and you can choose whether you want to use them from repository or from Steam content. EffectsFromSources and DataFromSources are two elements in global.props which influences that; repository is used by default.

GitHub repository can be slightly ahead of content in Steam folder, because it's updated more often than the game. This can cause some minor issues, most of them can be resolved by using Data definitions from Steam content folder by setting

<DataFromSources>false</DataFromSources>

in your user.props.

When you download the sources as ZIP and extract it, all files will be marked as 'potentially dangerous' which can cause some issues (for example with SGen which generates serialization assemblies).

Before extracting the ZIP file, go to it's properties and click unblock button.