Git repository layout
$GIT_DIR/*
A Git repository comes in two different flavours:
a .git directory at the root of the working tree;
a <project>.git directory that is a bare repository (i.e. without its own working tree), that is typically used for exchanging histories with others by pushing into it and fetching from it.
Note: Also you can have a plain text file .git at the root of your working tree, containing gitdir: <path> to point at the real directory that has the repository. This mechanism is often used for a working tree of a submodule checkout, to allow you in the containing superproject to git checkout a branch that does not have the submodule. The checkout has to remove the entire submodule working tree, without losing the submodule repository.
These things may exist in a Git repository.
objects
Object store associated with this repository. Usually an object store is self sufficient (i.e. all the objects that are referred to by an object found in it are also found in it), but there are a few ways to violate it.
You could have an incomplete but locally usable repository by creating a shallow clone. See git-clone(1).
You could be using the objects/info/alternates or $GIT_ALTERNATE_OBJECT_DIRECTORIES mechanisms to borrow objects from other object stores. A repository with this kind of incomplete object store is not suitable to be published for use with dumb transports but otherwise is OK as long as objects/info/alternates points at the object stores it borrows from.
objects/[0-9a-f][0-9a-f]
A newly created object is stored in its own file. The objects are splayed over 256 subdirectories using the first two characters of the sha1 object name to keep the number of directory entries in objects itself to a manageable number. Objects found here are often called unpacked (or loose) objects.
objects/pack
Packs (files that store many object in compressed form, along with index files to allow them to be randomly accessed) are found in this directory.
objects/info
Additional information about the object store is recorded in this directory.
objects/info/packs
This file is to help dumb transports discover what packs are available in this object store. Whenever a pack is added or removed, git update-server-info should be run to keep this file up-to-date if the repository is published for dumb transports. git repack does this by default.
objects/info/alternates
This file records paths to alternate object stores that this object store borrows objects from, one pathname per line. Note that not only native Git tools use it locally, but the HTTP fetcher also tries to use it remotely; this will usually work if you have relative paths (relative to the object database, not to the repository!) in your alternates file, but it will not work if you use absolute paths unless the absolute path in filesystem and web URL is the same. See also objects/info/http-alternates.
objects/info/http-alternates
This file records URLs to alternate object stores that this object store borrows objects from, to be used when the repository is fetched over HTTP.
refs
References are stored in subdirectories of this directory. The git prune command knows to preserve objects reachable from refs found in this directory and its subdirectories.
refs/heads/name
records tip-of-the-tree commit objects of branch name
refs/tags/name
records any object name (not necessarily a commit object, or a tag object that points at a commit object).
refs/remotes/name
records tip-of-the-tree commit objects of branches copied from a remote repository.
refs/replace/<obj-sha1>
records the SHA-1 of the object that replaces <obj-sha1>. This is similar to info/grafts and is internally used and maintained by git-replace(1). Such refs can be exchanged between repositories while grafts are not.
packed-refs
records the same information as refs/heads/, refs/tags/, and friends record in a more efficient way. See git-pack-refs(1).
HEAD
A symref (see glossary) to the refs/heads/ namespace describing the currently active branch. It does not mean much if the repository is not associated with any working tree (i.e. a bare repository), but a valid Git repository must have the HEAD file; some porcelains may use it to guess the designated "default" branch of the repository (usually master). It is legal if the named branch name does not (yet) exist. In some legacy setups, it is a symbolic link instead of a symref that points at the current branch.
HEAD can also record a specific commit directly, instead of being a symref to point at the current branch. Such a state is often called detached HEAD. See git-checkout(1) for details.
branches
A slightly deprecated way to store shorthands to be used to specify a URL to git fetch, git pull and git push. A file can be stored as branches/<name> and then name can be given to these commands in place of repository argument. See the REMOTES section in git-fetch(1) for details. This mechanism is legacy and not likely to be found in modern repositories.
hooks
Hooks are customization scripts used by various Git commands. A handful of sample hooks are installed when git init is run, but all of them are disabled by default. To enable, the .sample suffix has to be removed from the filename by renaming. Read githooks(5) for more details about each hook.
index
The current index file for the repository. It is usually not found in a bare repository.
sharedindex.<SHA-1>
The shared index part, to be referenced by $GIT_DIR/index and other temporary index files. Only valid in split index mode.
info
Additional information about the repository is recorded in this directory.
info/refs
This file helps dumb transports discover what refs are available in this repository. If the repository is published for dumb transports, this file should be regenerated by git update-server-info every time a tag or branch is created or modified. This is normally done from the hooks/update hook, which is run by the git-receive-pack command when you git push into the repository.
info/grafts
This file records fake commit ancestry information, to pretend the set of parents a commit has is different from how the commit was actually created. One record per line describes a commit and its fake parents by listing their 40-byte hexadecimal object names separated by a space and terminated by a newline.
Note that the grafts mechanism is outdated and can lead to problems transferring objects between repositories; see git-replace(1) for a more flexible and robust system to do the same thing.
info/exclude
This file, by convention among Porcelains, stores the exclude pattern list. .gitignore is the per-directory ignore file. git status, git add, git rm and git clean look at it but the core Git commands do not look at it. See also: gitignore(5).
info/sparse-checkout
This file stores sparse checkout patterns. See also: git-read-tree(1).
remotes
Stores shorthands for URL and default refnames for use when interacting with remote repositories via git fetch, git pull and git push commands. See the REMOTES section in git-fetch(1) for details. This mechanism is legacy and not likely to be found in modern repositories.
logs
Records of changes made to refs are stored in this directory. See git-update-ref(1) for more information.
logs/refs/heads/name
Records all changes made to the branch tip named name.
logs/refs/tags/name
Records all changes made to the tag named name.
shallow
This is similar to info/grafts but is internally used and maintained by shallow clone mechanism. See --depth option to git-clone(1) and git-fetch(1).
modules
Contains the git-repositories of the submodules.
git-init(1), git-clone(1), git-fetch(1), git-pack-refs(1), git-gc(1), git-checkout(1), gitglossary(7), \m[blue]The Git User\(cqs Manual\m[]\s-2\u[1]\d\s+2
Part of the git(1) suite.
The Git User\(cqs Manual
file:///usr/share/doc/git/html/user-manual.html