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Becoming a Git pro. Part 1: internal Git architecture

In this article we'll explore internal architecture of Git step by step using practical exercises. We'll see how Git stores content, what is a tree object that underlies a commit and how a branch is just a text file.

Becoming a Git pro. Part 1: internal Git architecture

Git may seem like a complex system. Just ask google. Here are some of the titles that a quick search turns up:

Why the Heck is Git so Hard...
Git is just too hard…
Can we please stop pretending that Git is simple and easy to learn...
Why is Git so complex and confusing…

At first glance these statements may seem to hold true. But, once you understand the underlying concepts, working with Git becomes a delightful experience. The problem with Git is that it’s very flexible - pretty much like Webpack. And the inherent characteristic of all flexible systems is complexity. I strongly believe that the only way to battle this complexity is to get down to the basics underneath the provided user interface and understand the underlying mental model and architecture. Once you do that there will be no magic and unexpected results and you’ll feel right at home working with these complex tools.

Both developers who have worked with Git before and who just start working with this awesome version control tool will benefit from the material in this article. If you’re an experienced GIT user, you will understand the lifecycle checkout -> modify -> commit much better. If you’re just starting with Git, this article will give you a great head start.

I’ll be using low-level so called “plumbing” commands in this post to demonstrate how Git works under the hood. You don’t need to remember them, as they are rarely used during regular workflow. But, they are indispensable when explaining the underlying Git architecture.

The article is a bit lengthy and I believe you can study it in the following way:

  • Skim the article from top to bottom to understand the general flow
  • Read thoroughly and follow along by implementing the exercises I use

By practicing you will reinforce the knowledge you gain here. I use bash commands during exercises so you’re OK if you’re on Unix based OS. If you use Windows, you can run git-bash which is installed alongside Git and can be accessed using context menu option Git Bash here.

Git as a folder

When you run git init in a folder, Git creates the .git directory. So let’s open a terminal, create a new directory where we will be working, and initialize an empty git there:

$ mkdir git-playground && cd git-playground

$ git init
Initialized empty Git repository in path/to/git-playground/.git/

$ ls .git
HEAD config description hooks info objects refs

This is where Git stores all your commits and other relevant information to manipulate these commits.

When you clone a repository:

  • Git copies this single directory into your folder
  • Creates remote-tracking branches for each branch in the cloned repository
  • Creates and checks out an initial branch that is specified by the HEAD file

We will see later what purpose the HEAD file serves in Git architecture but the takeaway here is that cloning a repository is essentially just copying .git directory from the other location.

Git as a database

Git is a simple key-value data store. You put a value into the repository and get a key by which this value can be accessed.

Writing to the database: hash-object

The command that puts values into the database is hash-object and it returns a 40-character checksum hash that will be used as a key. The command creates a plain object in Git repository that is called a blob. Let’s write a simple string f1 content into the database:

     echo 'f1 content' | git hash-object -w --stdin )

For those of you who are not very familiar with shell, the main command in the above snippet is:

echo 'f1 content' | git hash-object -w --stdin

The echo command outputs the f1 content string. By using the pipe operator | we redirect, or "pipe", the output to the git hash-object command. The param -w passed to the hash-object command tells it to store the object; otherwise, the command simply tells you what the key would be. --stdin tells the command to read the content from stdin. if you don’t specify this, hash-object expects a file path at the end. As mentioned earlier, the git hash-object command returns a hash that I then save into the F1CONTENT_BLOB_HASH variable.


We also could have split the main execution and the variable assignment like this:

$ echo 'f1 content' | git hash-object -w --stdin

$ F1CONTENT_BLOB_HASH=a1deaae8f9ac984a5bfd0e8eecfbafaf4a90a3d0

Notice it is the = that does the assignment:

But for convenience I’ll be using the shorter version in the subsequent code snippets to assign outputs into variables. Those variables are used where a hash string is expected.

To read the value of the variable, we need to start the name with $.


Reading from the database: cat-file

To read a value by key from the database we can use the cat-file command with the -p option. This command expects the hash key of the object to retrieve:

$ git cat-file -p $F1CONTENT_BLOB_HASH
f1 content

As I said before .git is a folder and all stored values/objects are kept in this folder. So we can go into .git/objects and you will see the folder created by Git with the name a1 which is the first two letters of the hash key:

$ ls -1 .git/objects/

This is the way Git usually stores objects — one folder per one blob. However, Git can also merge multiple blobs into one file to generate pack files and the pack directory you see above is where these files are stored. Git keeps information related to these pack objects in the info directory. Git generates hashes for blobs based on the blob contents. So objects in Git are immutable because changing the contents would change the hash.

Let’s write another string f2 content into the repository:

     echo 'f2 content' | git hash-object -w --stdin )

As expected you can see that the \.git\objects folder now contains two records 9b/ and a1/:

$ ls -1 .git/objects/

Tree as an integral part

Currently we have two blobs in our repository:

F1CONTENT_BLOB_HASH -> 'f1 content'
F2CONTENT_BLOB_HASH -> 'f2 content'

We need a way to somehow group them together and also associate each blob with a filename. And this is where a tree comes into play. A tree can be created using the git mktree command with the following syntax for each file/blob association:

[file-mode object-type object-hash file-name]

See this answer for an explanation of file-mode. We will use the mode 100644 that defines a blob as a regular file which can be read and written by the user. Those permissions are used when checking out files to a working directory to set permissions on files\directories corresponding to the trees entries.

So to associate two blobs with two files we’ll do the following:

    printf '%s %s %s\t%s\n' \
      100644 blob $F1CONTENT_BLOB_HASH f1.txt \
      100644 blob $F2CONTENT_BLOB_HASH f2.txt |
    git mktree )

Just as with hash-object, the mktree command returns a hash key for the created tree object:


So here is what we have now:

After running the command Git creates a third object in the repository of type tree. Let’s see it:

$ ls -1 .git/objects
e0   <--- initial tree object  (INITIAL_TREE_HASH)
9b   <--- 'f1 content' blob    (F2CONTENT_BLOB_HASH)
a1   <--- 'f2 content' blob    (F2CONTENT_BLOB_HASH)

When using mktree we can specify another tree object as a parameter instead of a blob. That tree will be associated with the directory instead of a regular file. For example, the following command would create a tree with a sub-tree associated with the nested-folder directory:

printf '%s %s %s\t%s\n' 040000 tree e05d9da nested-folder | git mktree

The file-mode 040000 marks a directory and we use the type tree instead of blob. This is how Git stores nested directories in the project structure.

Index is a place where trees are assembled

Everyone working with Git should be familiar with the notion of the index or staging area. You have probably seen the following diagram:

On the right side you can see the Git repository which stores Git objects: blobs, trees, commits and tags. We used the hash-object and mktree commands to directly add a blob and tree objects to this repository. The working directory on the left is your local file system/directory where you checkout all the project files. This section explains the middle stage which we will refer to as the index file or simply the index. It is a binary file (generally kept in .git/index) that resembles the structure of a tree object. It holds a sorted list of path names, each with permissions and the SHA1 of a blob/tree object.

It is the place where Git prepares a tree before it:

  • writes it into the repository or
  • checks it out into a working directory

We now have one tree in the repository that we created in the previous chapter. We can read this tree into the index file from the repository using the read-tree command:

$ git read-tree $INITIAL_TREE_HASH

So now we expect the index file to have two files. We can check the structure of the current index file using the git ls-files -s command:

$ git ls-files -s
100644 a1deaae8f9ac984a5bfd0e8eecfbafaf4a90a3d0 0 f1.txt
100644 9b96e21cb748285ebec53daec4afb2bdcb9a360a 0 f2.txt

Since we haven’t made any changes to the index file, it is exactly the same as the tree we used to populate the index file. Once we have the correct structure in the index file let’s check it out into the working directory using the checkout-index command with the -a option:

$ git checkout-index -a

$ ls
f1.txt f2.txt

$ cat f1.txt
f1 content

$ cat f2.txt
f2 content

All right! We have just checked out the files we added manually into the git repository without any commits. How cool is that?

But the index file doesn’t usually stay in the state of the initial tree. You probably know that it can be modified using git add [file path] and git rm --cached [file path] commands for a single file or git add -A and git reset for the set of modified/deleted files. So let’s put this knowledge into practice and create a new tree in the repository containing one file blob associated with the new f3.txt text file. The contents of the file will be the f3 content string. But instead of creating the tree manually like we did in the previous section we will use the index file for that.

Currently we have the following structure of the index file based on the initial tree tree we used to populate the index:

This is the base to which we will be applying changes. All the changes you make to the index file are tentative until you actually write a tree to the repository. The objects however that you add are written into the git repository immediately. If you discard the current changes to the tree, they will later be picked up by garbage collection (GC) and removed. This also means that if you accidentally discard changes to a file they can still usually be recovered until Git runs GC. And it usually does so only when there are too many loose objects floating around that are not referenced anywhere.

Let’s start by removing two files in the working directory:

$ rm f1.txt f2.txt

If we now run git status, we will see the following:

$ git status
On branch master

Initial commit

Changes to be committed:
  (use "git rm --cached <file>..." to unstage)

        new file:   f1.txt
        new file:   f2.txt

Changes not staged for commit:
  (use "git add/rm <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

        deleted:    f1.txt
        deleted:    f2.txt

That’s a lot of information. It reports two deleted files and two new files and it also says Initial commit. And here is why. When you run git status Git makes two comparisons:

  • it compares the index file with the current working directory — changes are reported as Changes not staged for commit
  • it compares the index file with the HEAD commit — changes are reported as Changes to be committed

So in our case we see that git reports two deleted files for Changes not staged for commit and we know how it got them — it compared the current working directory with the index file and found two files missing in the working directory (because we removed them).

We also see that under Changes to be committed Git reports two new files. This is because currently we don’t yet have any commits in the repository so the HEAD file (which will be explained later) resolves to a so-called “empty tree” object with no files. So Git thinks we just started with the new fresh repository and that’s why it shows Initial commit and treats every file in the index file as a new file.

Now if we run git add . it will modify the index file by removing two files and when we run git status again it will report no changes since we have no files in either the working tree or in the index file:

$ git add .

$ git status
On branch master

Initial commit

nothing to commit (create/copy files and use "git add" to track)

We started with the task to create a new tree with one new file f3.txt. Let’s create this file and add it to the index:

$ echo 'f3 content' > f3.txt
$ git add f3.txt

If we run git status now:

$ git status
On branch master

Initial commit

Changes to be committed:
  (use "git rm --cached <file>..." to unstage)

        new file:   f3.txt

We can see that one new file is detected. Again, the changes are reported under Changes to be committed so we know Git compared the index file with the “empty tree”. So we expect the index file to have this one new file blob. Let’s check it:

$ git ls-files -s
100644 5927d85c2470d49403f56ce27afd8f74b1a42589 0       f3.txt

# Save the hash of the f3.txt file blob
$ F3CONTENT_BLOB_HASH=5927d85c2470d49403f56ce27afd8f74b1a42589

Okay, the index has the correct structure now and we’re ready to create a tree from it in the repository. Let’s do that with the write-tree command:

$ LATEST_TREE_HASH=$( git write-tree )

Great, we’ve just created the tree with the help of index. And we put the hash of the new tree into the LATEST_TREE_HASH variable. We could’ve done it manually by writing the f3 content blob to the repository and then creating a tree with mktree. But, using index is much more convenient.

What’s interesting is that if you run git status now, you will see that Git still thinks that there’s new file f3.txt:

$ git status
On branch master

Initial commit

Changes to be committed:
  (use "git rm --cached <file>..." to unstage)

  new file:   f3.txt

That’s because although we’ve created and saved our tree into the repository, we didn’t update the HEAD file that is used for comparison. We can only put a commit hash or a branch reference into the HEAD file. But since we have neither now, we will leave the HEAD file as it is for now.

So, with this newly created tree we have the following objects in the repository:

A commit is a wrapper around a tree

In this section it gets even more interesting. During our everyday work with Git we don’t usually encounter trees or blobs. We work with commit objects. So what really is a commit in Git then? Actually, to put it as simply as possible, it’s just a wrapper around the tree object that:

  • allows attaching a message to a tree (group of files)
  • allows specifying a parent (commit)

We now have two trees in our Git repository — initial tree and latest tree. Let’s wrap the first tree object in a commit using the commit-tree command that takes a hash of the tree to create a commit for:

    echo 'initial commit' | git commit-tree $INITIAL_TREE_HASH )

After you run the above command we will have the following:

And we can checkout that commit into the working directory:

$ git checkout $INITIAL_COMMIT_HASH
A       f3.txt
HEAD is now at a27a75a... initial commit

Now we can see our two files in the working directory:

$ ls
f1.txt f2.txt

$ cat f1.txt
f1 content

$ cat f2.txt
f2 content

When you run git checkout [commit-hash] Git does the following:

  • reads the tree that the commit points at into the index file
  • checks out the index file into the working directory
  • updates the HEAD file with the commit hash

These are the operations that we did manually in the previous section.

Git history is a chain of commits

So now we know that a commit is just a wrapper around a tree. I also mentioned that it can have a parent commit. We had two trees initially and wrapped one of them into a commit in the previous section so we still have one orphan tree left. Let’s wrap it into the other new commit and make the initial commit a parent of this new commit. We will use the same commit-tree operation we used above but with the -p option to specify the parent:

    echo 'latest commit' | 
    git commit-tree $LATEST_TREE_HASH -p $INITIAL_COMMIT_HASH )

And so here is what we have now:

So now you can run git log to see the history. Pass the hash of the “latest” commit and you will see two commits:

$ git log --pretty=oneline $LATEST_COMMIT_HASH
[some hash] latest commit
[some hash] initial commit

And we can switch between them. Here is the initial commit:

$ git checkout $INITIAL_COMMIT_HASH
$ ls
f1.txt f2.txt f3.txt

Latest commit:

$ git checkout $LATEST_COMMIT_HASH
$ ls

The HEAD is a reference to the checked out commit

HEAD is a simple text file located at .git/HEAD that references the currently checked out commit. Since we checked out the “latest” commit with the hash $LATEST_COMMIT_HASH in the previous section, this is exactly what the HEAD file contains:

$ cat .git/HEAD

$ [ $LATEST_COMMIT_HASH == "88d3b9901d62..." ]; echo 'equal'

However, usually the HEAD file references the currently checked out commit through branch references. When it references the commit directly it is in a detached state. But even when HEAD holds a reference to a branch like this:

ref: refs/heads/master

it still resolves to the commit hash.

You already know that Git uses the commit referenced by the HEAD when executing git status to produce a set of changes between the index file and the currently checked out tree/commit. Another usage for the HEAD is to resolve a commit that will be used as a parent for the future commit.

Interestingly, HEAD file is so important for most operations that if you manually clear its contents Git thinks that it is not a git repository and reports an error:

fatal: Not a git repository (or any of the parent directories): .git

A branch is a text file pointing to a commit

So now we have two commits in our repository that constitute the following history:

$ git log --pretty=oneline $LATEST_COMMIT_HASH
[some hash] latest commit
[some hash] initial commit

Let’s introduce a fork into the existing history. We will checkout the initial commit and modify the f1.txt file contents. After that we will make a new commit using the git commit command that you’re accustomed to:

$ git checkout $INITIAL_COMMIT_HASH
$ echo 'I am modified f1 content' > f1.txt
$ git add f1.txt

$ git commit -m "forked commit"
1 file changed, 1 insertion(+), 1 deletion(-)

The above code snippet:

  • checks out "initial commit" that adds f1.txt and f2.txt to the working directory
  • replaces f1.txt contents with the I am modified f1 content string
  • updates the index file with git add

The last git commit command, as we already know, performs multiple under-the-hood operations:

  • creates a tree from the index file
  • writes this tree to the repository
  • creates a commit object that wraps this tree
  • sets the initial commit as a parent of the new commit since it’s the commit that we currently have in the HEAD file

We also need to save the hash of that commit into a variable. Since Git updates HEAD with the current commit file we can read it from there:


So now we have the following objects in our git repository:

Which creates the following commit history:

Due to the presence of a fork we have two lines of work here. And it means we need to introduce two branches to track each line of work independently. Let’s create a master branch that tracks the linear history starting from latest commit and a forked branch that tracks the history from the forked commit.

A branch is a text file which that contains a hash of a commit. It is part of the Git references — a group of objects that reference a commit. The other reference type is a lightweight tag. Git stores all references under the .git/refs folder and branches are stored in the directory .git/refs/heads. Since branch is a simple text file we can just create a file with the contents of a commit hash.

So this will point to the main branch with the “latest commit”:

$ echo $LATEST_COMMIT_HASH > .git/refs/heads/master

And this will point to the “forked” branch with the “forked commit”:

$ echo $FORKED_COMMIT_HASH > .git/refs/heads/forked

So finally we’ve come to the regular workflow you’re used to — we can now switch between branches:

$ git checkout master
Switched to branch 'master'

$ git log --pretty=oneline
[some hash] latest commit
[some hash] first commit

$ ls -1

And let’s see another forked branch:

$ git checkout forked
Switched to branch 'forked'

$ git log --pretty=oneline
f30305a8a23312f70ba985c8c644fcdca19dab95 forked commit
f30305a8a23312f70ba985c8c644fcdca19dab95 initial commit

$ git ls
f1.txt f2.txt

$ cat f1.txt
I am modified f1 content

A tag is a text file pointing to a commit

You probably know that instead of a line of work that we track with branches, we can also track individual commits by using tags. Tags are usually used to mark important development milestones like releases. Right now we have 3 commits in our repository. And we can give them names using tags. Just as in a branch, a tag is a text file which contains a hash of a commit and is a part of the Git references group.

As you already know Git stores all references under .git/refs folder and tags are stored in the subfolder .git/refs/tags. Since it’s a simple text file we can create a file and put the commit hash into it.

So this will point to the latest commit:

$ echo $FORKED_COMMIT_HASH > .git/refs/tags/forked

And this will point to the initial commit:

$ echo $INITIAL_COMMIT_HASH > .git/refs/tags/initial

Once we’ve done that we can switch between commits using tags. Here is the initial commit:

$ git checkout tags/initial
HEAD is now at 285aec7... second commit

$ cat f1.txt
f1 content

And the forked commit:

$ git checkout tags/forked
$ cat f1.txt
I am modified f1 content

There’s also an “annotated tag” which is different from this light-weight tag. It’s an actual object that can contain a message just like a commit and is stored in the repository alongside other objects.


This is pretty lengthy article, but I’ve tried to make it as transparent and clear as possible. Once you work through the article and understand all the concepts I showed here you will be able to work with Git more effectively and you should never have fear of unexpected results.

If you want to learn more about Git, I highly recommend reading this great book which is also free online. I’m in the process of writing the next article on Git that will explore the concepts of merge, rebase and remote repositories. Do follow me to get notified!