VS Code - The git repository has too many active changes, only a subset of Git features will be enabled

I am setting up VS Code to work on an existing Salesforce project saved in BitBucket.

I cloned the repository down to my device and now when I open VS Code I get the message

The git repository at 'C:\Users[my repository directory]' has too many active changes, only a subset of Git features will be enabled.

When I go to Git in the left hand menu, it says I have 5000 staged changes and it appears to think those changes are that I deleted the files even though I can see them when I go to the file path myself.

Suggestions?

Visual Studio Code details:

• Version: 1.42.0 (user setup)
• Commit: ae08d5460b5a45169385ff3fd44208f431992451
• Date: 2020-02-06T10:51:34.058Z
• Electron: 6.1.6
• Chrome: 76.0.3809.146
• Node.js: 12.4.0
• V8: 7.6.303.31-electron.0
• OS: Windows_NT x64 10.0.18362

Check with git ls-files --eol (Git 2.8+) if this is an eol issue.

If yes, then:

• type git config --global core.autocrlf false
• re-clone your repository
• check if the issue persists on VSCode: since core.autocrlf attemps to modify all files, disable it could avoid VSCode considering "too many active changes".

That being said, other answers refer to a large number of untracked files, as in sivann's answer, so double-check your untracked files with:

git status --untracked-files=all

It will also show individual files in untracked directories, helping you assess the (possible large) number VSCode Git plugin has to consider.