The Definitive Guide to Version Control with Git and GitHub

Version control is the foundation of reliable software delivery. This guide teaches Git from first principles, then layers in practical GitHub workflows used by high-performing teams. You’ll learn the mental models, the everyday commands, and the advanced tools to collaborate confidently without fear of breaking anything.

What Is Version Control (and Why It Matters)

Version control systems track changes to files over time so you can collaborate, audit history, and restore previous states. Git is a distributed VCS: every clone contains the entire history, enabling fast local operations and offline work. GitHub is a hosting and collaboration platform built on top of Git.

Git vs GitHubCentralized vs Distributed

Git: command-line tool and file format for versioning
GitHub: remote hosting, Pull Requests, Issues, Actions, Discussions, Packages

Centralized (e.g., SVN): single server of truth
Distributed (Git): many full copies; collaboration via push/pull/fetch

The Git Mental Model

Git tracks content snapshots and references. The three most important zones are the working directory, the staging area (index), and the local repository.

graph LR
    A[Working Directory] -- git add --> B[Staging Area]
    B -- git commit --> C[Local Repository]
    C -- git push --> D[Remote Repository]
    D -- git fetch/pull --> C
    C -- git checkout/switch --> A

Think in small, logical commits that tell a story. Branch to isolate work. Merge or rebase to integrate.

Install and Configure Git

macOSWindows (PowerShell)Linux

brew install git
git --version

winget install --id Git.Git -e
git --version

sudo apt update && sudo apt install -y git       # Debian/Ubuntu
sudo dnf install -y git                           # Fedora
git --version

First-Time Setup

git config --global user.name "Your Name"
git config --global user.email "[email protected]"
git config --global init.defaultBranch main
git config --global core.editor "code --wait"       # VS Code as editor
git config --global pull.rebase false                # start with merges

Optional but recommended:

# Better diffs and helpful aliases
git config --global color.ui auto
git config --global alias.st status
git config --global alias.co checkout
git config --global alias.br branch
git config --global alias.ci commit
git config --global alias.last 'log -1 --stat'

Create or Clone a Repository

Start a new repoClone existing

mkdir hello-git && cd hello-git
git init
echo "# Hello Git" > README.md
git add README.md
git commit -m "chore: initial commit"

git clone https://github.com/owner/repo.git
cd repo

Everyday Workflow

# 1) See what changed
git status
git diff                     # unstaged changes
git diff --staged            # staged vs last commit

# 2) Stage what you want to commit
git add path/to/file
git add -p                   # interactively stage hunks

# 3) Commit with a meaningful message
git commit -m "feat: add user search by email"

# 4) Update your branch from remote
git pull                     # merge-based (default here)
# or: git pull --rebase      # rebase-based

# 5) Push your work
git push -u origin my-feature

Commit Message Best Practices

Use imperative mood: "fix bug", "add feature"
Keep subject ≤ 72 chars; add details in body if needed
Consider Conventional Commits for automation:

<type>(<scope>): <subject>

feat(search): add email filter to users list

Body explaining why, not what. Reference issues if useful.

Branching Strategies

Common strategies include Trunk-Based Development and Git Flow. Most teams today prefer Trunk-Based with short-lived feature branches and frequent merges.

flowchart LR
    main((main)) --> F1[feature/login]
    main --> F2[feature/search]
    F1 --> main
    F2 --> main

Create, Switch, and Delete Branches

git switch -c feature/search-ui   # create and switch
git switch main                   # go back
git branch -d feature/search-ui   # delete merged branch
git branch -D old-experiment      # force delete

Merge vs Rebase

Both integrate changes. Merge preserves history; rebase rewrites your branch to apply on top of a base branch.

Merge (safe, non-destructive)Rebase (linear history)

git switch feature/login
git merge main
# resolves conflicts, creates a merge commit

git switch feature/login
git rebase main
# replay commits atop main; fix conflicts along the way
# if stuck: git rebase --abort   or   git rebase --continue

sequenceDiagram
    participant M as main
    participant F as feature
    Note over F: Before rebase
    F->>F: commits A, B
    M->>M: commits X, Y
    Note over F: Rebase F onto M
    F->>M: pick A'
    F->>M: pick B'

Handling Conflicts

Conflicts occur when the same lines changed in both branches.

# After pull/merge/rebase reports conflicts:
git status                         # see conflicted files

# Edit files, resolve conflict markers <<<<<<< ======= >>>>>>>

git add path/to/conflicted-file
git commit                         # for merge
git rebase --continue              # for rebase

Tips: - Resolve small, logical conflicts first - Prefer consistent formatting to reduce diff noise - Run tests before pushing

Undo and Recover Safely

Unstage changesDiscard local editsAmend last commitRevert a bad commit (public history safe)Time travel with reflog

git restore --staged path/to/file

git restore path/to/file         # careful: this loses changes

git commit --amend -m "fix: correct typo in docs"

git revert <commit_sha>

git reflog                       # shows where HEAD moved
git checkout <sha>

Stashing Work-in-Progress

git stash push -m "wip: partial search filters"
git stash list
git stash show -p stash@{0}
git stash pop     # apply + drop
git stash apply   # apply only

Tags and Releases

git tag -a v1.0.0 -m "First stable release"
git push --tags

Use annotated tags for semantic versioning; create GitHub Releases from tags for changelogs and assets.

GitHub Fundamentals

Repositories: public or private
Issues: track tasks/bugs with labels, assignees, and milestones
Pull Requests (PRs): propose changes; enable reviews and checks
Discussions: community Q&A and proposals
Projects: kanban planning
Wikis: long-form documentation

HTTPS vs SSH (and Tokens)

# HTTPS clone (uses PAT on push)
git clone https://github.com/owner/repo.git

# SSH clone (key-based)
ssh-keygen -t ed25519 -C "[email protected]"
ssh-add ~/.ssh/id_ed25519
git clone [email protected]:owner/repo.git

For HTTPS pushes, create a Personal Access Token (fine-grained) and use it as the password. For SSH, upload your public key to GitHub.

Fork-and-PR vs Shared-Repo

sequenceDiagram
    participant U as You (fork)
    participant O as Origin Repo
    U->>O: fork
    U->>U: clone fork
    U->>U: create branch, commit, push
    U->>O: open Pull Request
    O->>U: review, request changes
    U->>O: update branch, CI passes
    O->>O: merge PR

Opening an Effective PR

Keep PRs small and focused
Write a clear title and description (why, tradeoffs, screenshots)
Link Issues and Discussions
Ensure CI passes and tests are updated
Request specific reviewers and use code owners when applicable

Protecting Main and Enforcing Quality

Protected branches: require PR, reviews, status checks, linear history
Required checks: unit tests, lint, type-check, build
Code owners: automatic review assignment
Bypass rules for admins sparingly

Automate with GitHub Actions (CI/CD)

name: ci
on: [push, pull_request]
jobs:
  build:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-node@v4
        with:
          node-version: 20
      - run: npm ci
      - run: npm test -- --ci

Add environment protections for deploy jobs; use environments, required reviewers, and secrets.

Keep Repos Healthy

.gitignore: avoid committing build artifacts, secrets, large files
LICENSE: make intent explicit
README: quickstart, architecture, contribution guide
CONTRIBUTING.md, CODE_OF_CONDUCT.md, SECURITY.md
Small, coherent commits; squash or rebase before merge if noisy

Large Files and Monorepos

Git LFSSparse Checkout (partial clones)

git lfs install
git lfs track "*.bin"
git add .gitattributes

git clone --filter=blob:none --no-checkout [email protected]:owner/huge-repo.git
cd huge-repo
git sparse-checkout init --cone
git sparse-checkout set apps/web apps/api

Security and Trust

Sign commits and tags (GPG or SSH signatures)
Use branch protections and required reviews
Avoid pushing secrets; scan with GitHub Advanced Security or pre-commit hooks
Rotate tokens; limit PAT scopes

Sign Your Commits (GPG)

gpg --full-generate-key
gpg --list-secret-keys --keyid-format=long
git config --global user.signingkey <KEY_ID>
git config --global commit.gpgsign true

Troubleshooting FAQ

fatal: not a git repositoryPermission denied (publickey)Updates were rejected because the remote contains work that you do not haveHow do I undo the last commit but keep my changes?How do I remove a file from history (secret accidentally committed)?

Run inside a repo or initialize one: git init.

Add your SSH key to the agent and GitHub; or use HTTPS + PAT.

Pull first, resolve, then push: git pull --rebase or git pull then fix conflicts.

git reset --soft HEAD~1

Use git filter-repo or git filter-branch, then force-push and rotate secrets.

Glossary (Quick Reference)

Commit: snapshot with metadata
Branch: movable pointer to a commit
HEAD: your current checked-out commit/branch
Remote: named reference to another repository (e.g., origin)
Merge: combine histories with a merge commit
Rebase: replay commits onto another base
Tag: named pointer for releases

Conclusion

You now have a practical toolbox and the mental models to use Git effectively and collaborate on GitHub with confidence. Start with small, clear commits; branch freely; integrate often; protect main; and automate quality with CI. As your team matures, refine policies and workflows—Git and GitHub will scale with you.

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