Problems, Safety, and GitHub Hygiene

Last updated on 2026-03-06 | Edit this page

Estimated time: 60 minutes

Overview

Questions

  • What common problems will I encounter when using git?
  • How do I undo mistakes safely?
  • How should I organise my repository and collaborate with others?

Objectives

  • Handle common git pitfalls (empty directories, wrong commits)
  • Undo changes using revert, discard, and reset (beginner-safe)
  • Explain the difference between public and private repositories
  • Describe protected branches, collaborators, and permissions
  • Use GitHub issues effectively

Common Problems

Empty Directories

Git tracks files, not directories. If you create an empty folder, git will ignore it.

Workarounds:

  • Add a placeholder file called .gitkeep inside the directory.
  • Make sure every directory contains at least one meaningful file.

BASH 

# Create a directory with a placeholder
mkdir data
touch data/.gitkeep
git add data/.gitkeep
git commit -m "Add empty data directory with .gitkeep"

Accidentally Committed the Wrong File

If you committed a file by mistake (for example a large data file or credentials):

  1. Don’t panic. The commit is only local until you push.
  2. In GitHub Desktop, right-click the commit in History and choose Revert this Commit.
  3. Add the file pattern to .gitignore so it is not tracked in the future.
Callout

Credentials and secrets

Never commit passwords, API keys, or other secrets. If you accidentally push a secret to GitHub, consider it compromised — rotate the credential immediately and remove it from the repository history.

Undoing Changes

There are several ways to undo work in git. Here is a beginner-friendly overview:

Situation Action in GitHub Desktop What happens
Changed a file but have not committed Right-click the file → Discard changes File returns to the last committed state
Committed but have not pushed Right-click the commit → Revert this Commit A new commit is created that undoes the changes
Already pushed Use Revert this Commit and push again A new revert commit is added to the remote

BASH 

# Discard changes to a file (before commit)
git checkout -- filename.md

# Revert the last commit (creates a new commit)
git revert HEAD

# Unstage a file (keep changes but remove from staging)
git reset HEAD filename.md
Callout

A note on rebase

You may encounter the term rebase in online tutorials. Rebasing rewrites commit history and is an advanced technique. Do not use rebase on shared branches unless you fully understand the implications — it can cause serious problems for collaborators. Stick with merge for now.

Repository Visibility

Setting Who can see the repo Who can contribute
Public Anyone on the internet Only collaborators (unless forked)
Private Only you and invited collaborators Only collaborators

Choose private for sensitive or unfinished work. Choose public when you want to share your project with the world.

Protected Branches

Teams often protect the main branch so that:

  • No one can push directly to main.
  • All changes must go through a pull request.
  • Pull requests require at least one approving review before merging.

This prevents accidental breakage on the stable branch.

  1. Go to your repository on GitHub.
  2. Click Settings → Branches.
  3. Under “Branch protection rules”, click Add rule.
  4. Enter main as the branch name pattern.
  5. Check Require a pull request before merging and other options as needed.

Collaborators and Permissions

To give someone access to your private repository (or push access to a public one):

  1. Go to Settings → Collaborators.
  2. Click Add people and search for their GitHub username.
  3. Choose a permission level (Read, Write, or Admin).

GitHub Issues

Issues are used to track tasks, report bugs, and discuss ideas. Good practices:

  • Clear title: summarise the problem or request in a few words.
  • Description: explain the context, steps to reproduce (for bugs), and expected behaviour.
  • Labels: use labels like bug, enhancement, question to categorise.
  • Linking: reference issues in commit messages or PRs using #123 syntax.

Documentation and README files

Challenge

Exercise: Your Troubleshooting Checklist

Create a short checklist titled “What to do when something went wrong”. Include at least five items covering the scenarios discussed above.

  1. Unwanted changes to a file? → Discard changes in GitHub Desktop.
  2. Wrong commit (not yet pushed)? → Revert the commit in GitHub Desktop.
  3. Wrong commit (already pushed)? → Revert and push the revert commit.
  4. Committed a secret? → Rotate the credential immediately. Remove from history if possible.
  5. Empty directory not showing up? → Add a .gitkeep file.
  6. Merge conflict? → Open the file, resolve the markers, commit, and push.
  7. Cannot push to main? → The branch is probably protected. Create a branch and open a pull request instead.
Key Points
  • Git does not track empty directories — use .gitkeep as a placeholder.
  • Use Discard changes for uncommitted edits and Revert for commits.
  • Never commit secrets; rotate any that are accidentally pushed.
  • Protected branches enforce a pull request workflow.
  • Issues help organise work; use clear titles, descriptions, and labels.