Yellow Caution Icon/Glyph on Assembly Reference in Solution Explorer

I am using NuGet to manage dependencies.

I created a fresh Git clone of my solution, and noticed assembly reference problems.

I have Enabled Package Restore and checked settings as suggested here, but I still have these yellow caution icons on various assembly references:

For example, I had previously added AutoMapper through NuGet, so why is it broken here, and why isn't it showing in my packages.config:

<?xml version="1.0" encoding="utf-8"?>
<packages>
  <package id="bootstrap" version="3.0.0" targetFramework="net45" />
  <package id="EntityFramework" version="6.1.1" targetFramework="net45" />
  <package id="jQuery" version="1.10.2" targetFramework="net45" />
  <package id="Modernizr" version="2.6.2" targetFramework="net45" />
</packages>

I manually went and removed all references that had the yellow mark next to them and then added them back one by one. This way, they started showing up in packages.config too.

I think the reason they weren't showing in packages.config previously was because I turned on the [Restore nuget packages] option much later in development. Had I done this as soon as I started my porject, I believe they would have shown up in packages.config.

PS. I used the search on nuget's website to find out if the package was available on nuget, or if it was a framework assembly.