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How I Accidentally Pushed Extra Folders to GitHub — And How to Fix It

Introduction

If you've ever worked with Git repositories, you might have experienced an odd situation where you pushed your code to GitHub — only to realize that not just your intended project folder got uploaded, but some unexpected folders or files appeared too.

This usually happens because of a confusion about where your Git repository is actually initialized (the “Git root”) versus where your project folder lives on your computer.

In this blog post, I’ll share my experience with this issue, how I diagnosed it, and the steps I took to fix it, so you can avoid this headache.

The Problem: Extra Folders Uploaded Alongside Your Project

I was working on a project called job_email_classifier inside a directory called MISC. I thought I was pushing only the job_email_classifier folder to GitHub.

But when I checked the remote repository, I noticed another unrelated folder inside MISC was also uploaded!

How did this happen?

Diagnosing the Issue: Understanding Your Git Root

The key to solving this problem is to understand that Git tracks files starting from a repository root folder — the folder where you run git init or clone a repo.

I ran this command inside my job_email_classifier folder:

git rev-parse --show-toplevel
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It returned:

C:/Users/arafa/projects/MISC
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This meant the actual Git root was the MISC folder, not job_email_classifier!

All files and folders under MISC are part of the same Git repository, so when I pushed changes, everything under MISC (including other unrelated folders) got pushed to GitHub.

Why Did This Happen?

Probably, I ran git init in the MISC folder earlier, making it the root of my Git repository.

Even though I worked inside job_email_classifier, Git sees it as a subfolder within the repo, and tracks all siblings alongside it.

The Solution: Create a Git Repo Only in Your Project Folder

To fix this, I wanted only the job_email_classifier folder to be a Git repository.

Steps I followed:

  1. Remove the old Git repo initialized at MISC: 
cd C:/Users/arafa/projects/MISC
rm -rf .git
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On Windows PowerShell, you can use:

Remove-Item -Recurse -Force .git

This deletes the Git tracking data for MISC.

  1. Go into the project folder and initialize a new Git repo there: 
cd job_email_classifier
git init
git add .
git commit -m "Initial commit"
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  1. Add the remote GitHub repository: 
git remote add origin https://github.com/arafatruetbd/job_email_classifier.git
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  1. Push the project to GitHub: 
git push -u origin main
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Verifying Your Git Repository Root

To avoid confusion in the future, you can always check your Git root folder by running:

git rev-parse --show-toplevel
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Make sure it points to your intended project folder before pushing changes.

Best Practices to Avoid This Issue

  • Always initialize your Git repository inside the specific project folder, not a parent folder that contains multiple projects.
  • Use .gitignore to exclude files or folders you don't want to push.
  • Regularly check your repo root with git rev-parse --show-toplevel.
  • Use git status to review what files are staged or tracked before committing.

Conclusion

Git is a powerful tool, but understanding how the repository root works is crucial to avoid pushing unintended files or folders.

By keeping your repository initialized only in the folder you want to track, you prevent accidentally including unrelated files.

I hope this story helps you troubleshoot and fix similar issues in your Git workflow!

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