Git Rebase vs. Merge: A Deep Dive into Git Internals

If you’ve ever participated in a heated pull request debate, you’ve probably encountered the age-old dilemma: Should we rebase or merge? While this question often sparks opinions based on team culture or aesthetics, there’s a more technical layer that rarely gets discussed — what’s really happening inside .git/, and how these two operations impact your repository under the hood.

This article takes a deep dive into Git internals to demystify rebase vs. merge. We'll explore their structures, effects on commit history, and provide hands-on examples that demonstrate what’s actually being written to your local object database.

Understanding Git’s Data Model

Before we compare rebase and merge, let’s quickly revisit how Git works under the hood.

Git isn’t a series of file diffs — it’s a content-addressable file system made up of:

Blobs – file contents
Trees – directories
Commits – snapshots pointing to trees and parent commits

Each commit creates a new object containing:

A reference to its parent(s)
A snapshot of the file tree
Metadata (author, timestamp, message)

You can inspect any object in Git using:

git cat-file -p <hash>

This internal model is what allows Git to represent operations like merge and rebase as manipulations of commit graphs.

What Happens During a Git Merge?

Scenario

You're on main, and you've branched off to feature.

git checkout -b feature
# make some commits
git checkout main
git merge feature

Under the Hood

Git performs a three-way merge, comparing the tips of main and feature with their common ancestor. This creates a new merge commit with two parents.

Run:

git log --graph --oneline

You'll see:

*   abc123 (HEAD -> main) Merge branch 'feature'
|\
| * def456 (feature) Add new API call
|/
* 789abc Previous main commit

That merge commit (abc123) references both main and feature. No history is lost or rewritten. This is the default and safest strategy — ideal for preserving full context and audit trails.

What Happens During a Git Rebase?

Now, let’s rebase that same feature branch on top of main.

git checkout feature
git rebase main

Under the Hood

Git takes the feature branch’s commits, copies them, and applies them \ on top of the latest commit in main. These are new commits with new hashes.

Original:

main:    A---B
               \
feature:         C---D

After rebase:

main:    A---B---C'---D'

The original C and D are no longer referenced. They still exist (temporarily) in .git/refs/original/, but they will eventually be garbage collected.

This linear history is easier to read and bisect, but at the cost of potentially rewriting shared history, which is dangerous if other developers have pulled the old commits.

Hands-On: Exploring the Object Store

Let’s inspect what actually happens inside .git/objects.

Create a new repo and make two branches:

git init rebase-vs-merge
cd rebase-vs-merge
echo "line 1" > file.txt
git add .
git commit -m "initial commit"
git checkout -b feature
echo "line 2" >> file.txt
git commit -am "feature commit"
git checkout main
echo "line 3" >> file.txt
git commit -am "main update"

Now merge:
```
git merge feature
```
Then:
```
ls .git/objects
```
You’ll see new blobs and trees — but the real star is the new merge commit object with two parents.

Now repeat in a new branch and rebase instead:

git checkout -b feature2 HEAD~2
echo "line 2b" >> file.txt
git commit -am "feature2 commit"
git rebase main

Check:

git log --graph --oneline

You’ll see a flat line — and new object hashes.

When to Use Rebase

Before merging a feature branch into main to keep history clean.
When cleaning up a messy branch, squashing or reordering commits.
On your own branch, never on shared history.

Use:

git rebase -i HEAD~n

to launch an interactive rebase and modify commits before opening a pull request.

When to Use Merge

When working in a collaborative environment, to preserve history and avoid conflicts.
When you need a clear audit trail of integrations.
When using GitOps or deployment tracing that benefits from merge commits.

Pro Tip: Aliases for Safety

git config --global alias.lg "log --graph --oneline --all --decorate"

Always run git lg before pushing rebased branches to double-check your DAG.

AI Enhancements to Merge and Rebase (A Glimpse Ahead)

Modern Git tools are now using AI to:

Auto-generate commit messages from diffs (see: GitHub Copilot CLI)
Suggest rebase vs. merge based on historical patterns
Resolve conflicts intelligently using LLM-powered semantic understanding
Auto-squash or flatten commits with context-aware logic

Expect Git tools to increasingly suggest “the right operation” before you even type it — and one day, perhaps manage the entire flow autonomously.

Conclusion

The rebase vs. merge debate isn’t just philosophical — it’s deeply rooted in how Git structures and stores your data. Understanding the mechanics behind these operations gives you the power to make informed decisions, troubleshoot complex history, and contribute clean, maintainable code.

Want to go deeper into Git internals or explore how AI is reshaping the future of development? Check out more at Slaptijack