I ran into this issue when originally setting up my project for source control. After talking with Noland and some browsing on the AnswerHub I found why they recommend this.
Here’s all I store in my repository for a UE4 project.

So when we pull the proejct we go to the folder where it’s stored locally, right click on the .uproject, and click “Generate Visual Studio Files”

.gitignore
Binaries/
DerivedDataCache/
Intermediate/
Saved/
*.filters
*.opensdf
*.sdf
*.sln
*.suo
*.user
*.vcxproj