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This page describes linking a work item to a commit in VS. I just updated my VS to make sure I have the latest stuff, it's VS2015 update 3, but I don't have a Related Work Items section in my Changes pane. We are using VSTS and I can work with Git just fine, and I can even link items to commits using the # syntax and that works, but seeing a list would be more useful.

I cloned the repository manually, and it shows up in "Local Git Repositories" in the Connect pane, which makes me think something isn't "hooked up" to VSTS within VS2015. Is there a way to facilitate that connection, or do I just need to re-clone it not through the CLI?

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This is because Team Explorer isn't connected to the project. You don't need to re-clone it, connecting to the project from Team Explorer via following steps should fix it:

1. Click "Manage Connections" link. enter image description here

2. Select the project of your Git repository and then click "Connect" in the pop up dialog.

Now when you go to "Changes", you should see the "Related Work Items" section: 

enter image description here

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