To reproduce:

1. Open any project that has a few scripts in different folders
2. Build it for Windows store with a C# project
3. Open the C# solution

Result: The Folder Structure missing from Assembly-CSharp.csproj in the solution

Note: 2 pictures included showing expected and actual results

Reproduced on: 5.6.0b1, 5.5.0p1
Regression introduced with: 5.5.0b4 or 5.5.0b3
Not reproducible on: 5.4.3p1, 5.4.0f3-HTP