How Version Control Systems Work
In 2005, Linux kernel development faced a crisis. The team had been using a proprietary version control system called BitKeeper under a free license. When that license was revoked, Linus Torvalds spent two weeks building a replacement. That replacement—Git—became the most widely used version control system in the world, fundamentally changing how software teams collaborate.
But Git's dominance obscures a deeper question: How does version control actually work? When you type git commit, what happens behind the scenes? How does Git track file history across thousands of commits? How do branches work? How does merging determine what changes to combine and which create conflicts?
Understanding version control at a technical level reveals elegant solutions to hard problems: how to efficiently store thousands of versions of thousands of files, how to enable multiple developers to work independently yet merge their work safely, and how to maintain a complete audit trail without prohibitive storage costs.
The principles extend beyond Git. While implementation details vary, most modern version control systems—Git, Mercurial, Subversion—solve similar problems. Understanding how one works provides insight into them all.
This analysis examines version control architecture from first principles: the data structures that store history, the algorithms that enable branching and merging, the tradeoffs between centralized and distributed systems, and the technical reasons why certain operations are fast while others are slow.
The Core Problem: Tracking Change Over Time
What Version Control Must Solve
The fundamental challenge: Multiple people modifying shared files over time need to:
- See who changed what and when (attribution and audit trail)
- Revert to previous versions (undo mistakes)
- Work simultaneously without overwriting each other's changes (parallel development)
- Merge independent work back together (integration)
- Branch to experiment safely (parallel alternate histories)
- Store all history without prohibitive disk usage (efficiency)
Naive Approaches (And Why They Fail)
Approach 1: File naming conventions (document_v1.txt, document_v2.txt, document_final.txt, document_final_ACTUALLY.txt)
Problems:
- No structured metadata (who, when, why)
- Naming degrades over time
- No way to see differences between versions
- Merging requires manual comparison
- Storage explodes (complete copy per version)
Approach 2: Centralized file copies (server directory with timestamped copies)
Problems:
- Still manually organizing copies
- No atomic grouping (commit might include changes to 50 files—how do you know they're related?)
- No branching support
- Merging still manual
Approach 3: Delta storage (store first version completely, then only differences)
Better: Uses less storage. Centralized VCS like Subversion use this approach.
Problems:
- Checking out old versions requires applying many deltas (slow)
- Branching complex (which deltas apply to which branch?)
- Merging requires reconstructing files from deltas
What we need: A system that:
- Groups related changes atomically (commits)
- Stores complete history efficiently
- Makes branching and merging fast and safe
- Operates independently on each developer's machine (distributed systems)
- Verifies integrity (detect corruption)
Git's architecture solves all of these.
Git's Core Architecture: Content-Addressable Storage
The Big Idea: Everything is a Hash
Git's fundamental design: Every piece of content is identified by the SHA-1 hash of its content. This is called content-addressable storage—content is the address.
Example:
Content: "Hello, world!\n"
SHA-1: 8ab686eafeb1f44702738c8b0f24f2567c36da6d
That 40-character hex string is the "name" of the content. Store the content at .git/objects/8a/b686eafeb1f44702738c8b0f24f2567c36da6d (Git splits into directory and file for filesystem efficiency).
Properties of content-addressable storage:
1. Deduplication: Identical content produces identical hash. If 50 files contain the exact same content, Git stores it once. Saving the same file in different commits doesn't duplicate it.
2. Integrity verification: Content can't change without changing hash. If storage corrupts, you know immediately (hash won't match content). Can't tamper with history without detection.
3. Efficient comparison: Different hash = different content. Don't need to compare file contents; just compare hashes (cheap).
4. Location independence: Content identified by hash, not filename. Moving or renaming files doesn't create storage overhead.
The Four Object Types
Git stores everything as objects identified by SHA-1 hashes. There are four types:
1. Blob Objects (File Contents)
What it stores: Raw file contents. No filename, no metadata—just bytes.
Example: File hello.txt containing "Hello, world!\n" becomes blob object 8ab686ea....
Structure:
blob 14\0Hello, world!\n
(Type, size, null byte, content)
Key insight: Blobs are anonymous content. Multiple files with identical content reference the same blob. Renaming a file doesn't create new blobs.
2. Tree Objects (Directory Structure)
What it stores: Directory listing—what files and subdirectories exist, their names, permissions, and which blob/tree they point to.
Example:
100644 blob 8ab686ea... hello.txt
100755 blob 95d09f2b... script.sh
040000 tree 3c4e9cd3... subdir
Structure: Each entry specifies:
- File mode (permissions)
- Type (blob or tree)
- SHA-1 hash of referenced object
- Filename
Key insight: Trees represent snapshots of directory state. Each commit references a tree representing the complete project state at that moment.
3. Commit Objects (History and Metadata)
What it stores: Metadata about a change—author, timestamp, message, parent commit(s), and tree representing project state.
Example:
tree 3c4e9cd3...
parent a11bef03...
author John Doe <john@example.com> 1610000000 -0800
committer John Doe <john@example.com> 1610000000 -0800
Add hello world script
Structure:
- Tree reference (project state)
- Parent commit(s) (history)
- Author and committer (who and when)
- Message (why)
Key insight: Commits form a directed acyclic graph (DAG). Each commit points to parent(s), creating history chain. Merge commits have multiple parents.
4. Tag Objects (Named References)
What it stores: Annotated tags—permanent names for specific commits, including tagger, date, message.
Structure:
object a11bef03...
type commit
tag v1.0.0
tagger Jane Doe <jane@example.com> 1610000000 -0800
Release version 1.0.0
Key insight: Tags are named commits. Unlike branches (which move), tags are fixed references.
How These Objects Relate
Commit A (dad4a98)
|
├─ tree (72f7e5b) ──────┐
└─ parent: [none] │
↓
Tree (72f7e5b)
├─ hello.txt → blob (8ab686ea)
└─ readme.md → blob (3b18e512)
Commit B (b8ef023)
|
├─ tree (9d2ac3f) ──────┐
└─ parent: dad4a98 │
↓
Tree (9d2ac3f)
├─ hello.txt → blob (8ab686ea) [unchanged]
├─ readme.md → blob (c421e90f) [modified]
└─ new.txt → blob (5f2e091b) [added]
What happens when you commit:
- Git creates blobs for modified files
- Git creates tree(s) representing current directory structure
- Git creates commit object linking tree and parent commit
- Git updates current branch reference to new commit
Storage efficiency: If hello.txt didn't change between commits, both commits' trees reference the same blob. No duplication.
Branches: Just Pointers
The Simplicity of Branches
Misconception: Branches are containers that hold commits or copies of code.
Reality: A branch is a 41-byte text file containing a commit hash.
Example: .git/refs/heads/main contains:
b8ef023a7c9d5e4f3b1a6c2d8e0f7b4a5c9d6e8f
That's it. The branch main is a pointer to commit b8ef023....
HEAD (.git/HEAD) points to the current branch:
ref: refs/heads/main
Operations
Creating a branch: Write new file .git/refs/heads/feature with current commit hash. Done. That's why creating branches is instant in Git.
Switching branches: Update HEAD to point to different branch. Update working directory to match that commit's tree. Fast (Git only modifies changed files).
Committing: Create commit object, update current branch pointer to new commit. Previous commit becomes parent.
The mental model: Commits form the history graph. Branches are movable labels attached to commits. When you commit, the current branch label moves to the new commit.
Before commit:
main → C3 → C2 → C1
After commit on main:
main → C4 → C3 → C2 → C1
Why Branches are Lightweight
In centralized VCS like Subversion, branching copies the entire repository. This is expensive and slow.
In Git, branching creates a 41-byte pointer. That's it. No copying files. No network operations. Instant.
This makes branching cheap enough to use liberally—branch for every feature, experiment, or bug fix. Delete branches when done. No overhead.
Merging: Combining Divergent Histories
The Three-Way Merge Algorithm
Setup: You have two branches that diverged from a common ancestor:
D---E (feature)
/
A---B---C (main)
Commits B, D, and E all modified the same file. How do we merge?
Naive approach: Compare feature's current state to main's current state. Apply differences.
Problem: Can't tell which changes came from which branch. Did feature remove a line, or did main add it?
Three-way merge solution: Use the common ancestor (B) as reference.
Algorithm:
- Find common ancestor (B) using commit graph
- Compare ancestor to main's tip (C): see what changed
- Compare ancestor to feature's tip (E): see what changed
- Combine both change sets:
- If only one branch modified a region: use that version
- If both branches modified different regions: combine both
- If both branches modified same region differently: conflict
Example:
Ancestor (B):
Line 1: original
Line 2: original
Line 3: original
Main (C):
Line 1: changed in main
Line 2: original
Line 3: original
Feature (E):
Line 1: original
Line 2: original
Line 3: changed in feature
Merged result:
Line 1: changed in main [from main]
Line 2: original [unchanged]
Line 3: changed in feature [from feature]
Both changes applied successfully because they modified different lines.
When Conflicts Occur
Conflict example:
Ancestor (B):
def calculate(x):
return x * 2
Main (C):
def calculate(x):
return x * 3 # Changed multiplier
Feature (E):
def calculate(x):
return x + 10 # Changed to addition
Conflict: Both branches modified the same line differently. Git can't automatically decide which to use.
Git's conflict markers:
def calculate(x):
<<<<<<< HEAD
return x * 3 # Changed multiplier
=======
return x + 10 # Changed to addition
>>>>>>> feature
Resolution required: Human must decide: keep one change, combine both somehow, or write something entirely new.
Fast-Forward Merges
Special case: One branch contains all commits of the other:
A---B---C (main)
\
D---E (feature)
Main is ancestor of feature. "Merging" feature into main just means moving main's pointer to E. No merge commit needed. This is a fast-forward.
After fast-forward:
A---B---C---D---E (main, feature)
Git does this automatically when possible (unless you specify --no-ff to force merge commit).
Distributed vs. Centralized Architecture
Centralized Version Control (Subversion, CVS)
Architecture: Single central server stores repository. Developers have working copies, not full repositories.
Operations:
- Commit: Sends changes to server. Requires network. Fails if server down.
- Update: Fetches latest from server.
- Branch: Creates server-side branch (often expensive operation).
- Merge: Server computes merge.
Workflow:
- Update working copy from server
- Make changes locally
- Commit changes to server (conflicts resolved here)
Limitations:
- Requires network for most operations
- Single point of failure (server)
- Slow over slow networks
- Branching often expensive
Distributed Version Control (Git, Mercurial)
Architecture: Every developer has complete repository, including full history.
Operations:
- Commit: Creates commit in local repository. Instant. Works offline.
- Push: Sends commits to remote repository (when you choose).
- Pull/Fetch: Gets commits from remote repository.
- Branch/Merge: Entirely local operations. Fast.
Workflow:
- Clone repository (get complete history)
- Make changes, commit locally (repeatedly, offline if desired)
- Fetch others' changes when ready
- Merge local work with fetched changes
- Push integrated result to remote
Advantages:
- Most operations fast (local disk, not network)
- Work offline (flights, trains, poor connections)
- Full history available locally (blame, log, diff—all instant)
- No single point of failure (every clone is full backup)
- Flexible workflows (multiple remotes, pull requests, etc.)
The key difference: In centralized systems, the repository is the central server. In distributed systems, every clone is a complete repository. The "central" server (GitHub, GitLab) is just one more clone that teams agree to treat as canonical.
How Common Operations Work Internally
Clone
What happens:
- Git creates
.gitdirectory - Fetches all objects (blobs, trees, commits, tags) from remote
- Creates remote-tracking branches (
origin/main, etc.) - Checks out default branch (usually
main)
Why it's efficient: Git uses pack files—compressed deltas of similar objects. Cloning transfers compressed pack, not individual objects. Smart protocol negotiates what's needed.
Network efficiency: If cloning from local filesystem or fast network, cloning is fast. Over slow connections, initial clone can be slow (getting complete history), but subsequent operations are fast (local).
Add (Staging)
What happens:
- Git computes SHA-1 of file content
- Stores content as blob object in
.git/objects/ - Updates index (
.git/index) to reference new blob
The index (staging area): A binary file listing what will be in next commit. Maps filenames to blob hashes and metadata.
Why staging exists: Allows you to craft commits carefully—stage some changes, not others. Working directory is messy; staging area is curated; commits are permanent.
Commit
What happens:
- Git creates tree object from current index (staged files)
- Git creates commit object referencing:
- New tree object
- Parent commit (current branch's commit)
- Author/committer metadata
- Commit message
- Git writes commit object to object database
- Git updates current branch reference to new commit
Why it's fast: All data already in object database (from git add). Just creating commit object and updating pointer.
Branch
What happens:
- Git writes new file
.git/refs/heads/branch-namecontaining current commit hash
That's it. Creating 100 branches takes milliseconds. They're just pointers.
Checkout (Switch)
What happens:
- Git reads tree object for target commit
- Compares to current working directory
- Updates modified files
- Updates
.git/HEADto point to new branch
Optimization: Git only modifies files that changed between commits. If switching between similar branches, most files unchanged—checkout is fast.
Uncommitted changes: Git preserves uncommitted changes during checkout if they don't conflict. Otherwise, requires clean working directory or stashing changes.
Merge
What happens:
- Git finds common ancestor using commit graph (merge base)
- Git computes diff from ancestor to each branch tip
- Git applies both diffs to working directory:
- Clean merge: Create merge commit with two parents
- Conflict: Mark conflicted files, halt merge
- User resolves conflicts, stages resolution, commits
Fast-forward: If one branch contains the other, just move pointer (no merge commit).
Merge commit: Has two parents, representing integration of divergent histories.
Push
What happens:
- Git determines which commits local has that remote doesn't
- Git sends missing objects (commits, trees, blobs) to remote
- Git updates remote branch reference
Safety: Push fails if remote branch moved since your last fetch (someone else pushed). Must fetch, merge, then push. Prevents overwriting others' work.
Force push: Overwrites remote branch regardless. Dangerous—loses others' commits. Use only on personal branches.
Pull
Equivalent to: git fetch (download commits) + git merge (integrate them).
What happens:
- Fetch downloads commits from remote, updates remote-tracking branches (
origin/main) - Merge integrates remote commits into your current branch
Alternative: git pull --rebase does fetch + rebase instead of merge. Replays your local commits on top of remote commits, avoiding merge commits.
Rebase: Rewriting History
What Rebase Does
Setup:
C---D (feature)
/
A---B---E---F (main)
You created feature from B, but main has moved forward (commits E and F added).
Merge approach: Creates merge commit combining D and F:
C---D
/ \
A---B---E---F---M (merged)
Rebase approach: Replays C and D on top of F:
A---B---E---F---C'---D' (rebased)
How Rebase Works
Algorithm:
- Find common ancestor (B)
- Save all commits from current branch since ancestor (C, D)
- Reset current branch to target (F)
- Apply saved commits one by one on top of target
- Each application creates new commit (C', D') with same changes but different parent
The catch: C' and D' are new commits (different hashes) even though they represent the same changes. You've rewritten history.
When to Rebase
Good use case: Update feature branch with latest main:
git checkout feature
git rebase main
Before: feature forked from old main. After: feature based on current main. Keeps history linear.
Good use case: Clean up local commits before pushing:
git rebase -i HEAD~5 # Interactive rebase last 5 commits
Combine commits, reword messages, reorder, drop commits. Make history readable before sharing.
When NOT to Rebase
Never rebase commits that you've already pushed and others might have based work on.
Why: Rebase creates new commits. If others based work on original commits, your rebase orphans their work. Chaos ensues.
Golden rule: Rebase local commits before pushing. Don't rebase pushed commits unless they're on a personal branch no one else uses.
Conflict Resolution Mechanics
Why Conflicts Occur
Conflict = same region modified differently in both branches.
"Region" usually means lines of text, but depends on merge strategy. For binary files, any change in both branches = conflict.
Git's Conflict Format
<<<<<<< HEAD
Content from current branch
=======
Content from merging branch
>>>>>>> branch-name
Conflict markers:
<<<<<<< HEAD: Start of current branch's version=======: Separator>>>>>>> branch-name: End of merging branch's version
Resolution Process
1. Identify conflicts: git status lists conflicted files.
2. Edit files: Open conflicted files, resolve conflicts:
- Choose one version
- Combine both versions
- Write something entirely new
- Remove conflict markers
3. Stage resolution: git add conflicted-file marks it resolved.
4. Complete merge: git commit (for merge) or git rebase --continue (for rebase).
Merge Tools
Manual resolution: Edit files in text editor.
Merge tools: Visual tools showing three-way diff:
- Base (common ancestor)
- Ours (current branch)
- Theirs (merging branch)
- Result (merged output)
Tools: vimdiff, meld, kdiff3, p4merge, IDE integrations.
Configuration:
git config --global merge.tool meld
git mergetool # Launch configured tool
Prevention Strategies
1. Smaller, more frequent merges: Less divergence = fewer conflicts.
2. Modular code: Different people work on different files.
3. Communication: Coordinate when editing same code.
4. Testing: Automated tests catch integration issues before merge.
Storage Efficiency and Garbage Collection
How Git Stays Efficient
Problem: Storing complete snapshots for every commit should consume enormous disk space.
Solution combination:
1. Content deduplication: Identical blobs stored once, referenced multiple times.
2. Pack files: Git periodically runs garbage collection, compressing loose objects into pack files—large files containing many objects with delta compression.
Delta compression: Instead of storing complete files, store first version completely, then deltas (differences) for subsequent versions. Similar to what centralized systems do, but Git applies it as optimization, not core architecture.
3. Shallow clones: git clone --depth 1 fetches only recent commits, not full history. Useful for CI/CD where history isn't needed.
4. Sparse checkout: Check out subset of files in large repositories. Fetches only needed blobs.
Garbage Collection
Command: git gc
What it does:
- Compresses loose objects into pack files
- Removes unreachable objects (commits not referenced by any branch or tag)
- Optimizes pack files for better compression
When it runs: Automatically during certain operations (push, fetch) if many loose objects accumulate.
Manual trigger: git gc --aggressive for maximum compression (slower, rarely needed).
Advanced Concepts
Reflog: History of HEAD
What it tracks: Every time HEAD moves (commit, checkout, reset, merge), Git records it in reflog.
Why it matters: You can recover "lost" commits. Even if you reset to old commit, reflog remembers recent HEAD positions.
Command: git reflog
Output:
a11bef0 HEAD@{0}: commit: Add feature
b8ef023 HEAD@{1}: checkout: moving from main to feature
dad4a98 HEAD@{2}: commit: Initial commit
Recovery: git reset --hard HEAD@{1} goes back to that state.
Expiration: Reflog entries expire after 90 days (configurable). Unreachable commits eventually garbage collected.
Detached HEAD
Normal state: HEAD points to branch, which points to commit.
HEAD → main → commit
Detached HEAD: HEAD points directly to commit, not branch.
HEAD → commit
When it happens: git checkout <commit-hash>
Implication: Commits made in detached HEAD aren't on any branch. If you checkout another branch, they become unreachable (except via reflog).
Fix: Create branch from detached HEAD: git branch new-branch
Cherry-Pick
What it does: Apply changes from specific commit to current branch.
Command: git cherry-pick <commit-hash>
How it works:
- Git computes diff between commit and its parent
- Git applies that diff to current branch
- Git creates new commit with same changes (different hash, different parent)
Use case: Backporting bug fix from main to release branch without merging all main's changes.
Bisect
What it does: Binary search through commits to find which introduced a bug.
Process:
git bisect startgit bisect bad(mark current commit as bad)git bisect good <old-commit>(mark old working commit as good)- Git checks out middle commit
- Test if bug present:
git bisect goodorgit bisect bad - Repeat until Git identifies first bad commit
Efficiency: Finds bad commit among 1000 commits in ~10 steps (log₂1000 ≈ 10).
Key Takeaways
Git's core architecture:
- Content-addressable storage: Everything identified by SHA-1 hash of content—enables deduplication, integrity checking, efficient comparison
- Four object types: Blobs (file contents), trees (directory structure), commits (history + metadata), tags (named references)
- Commits form DAG: Each commit points to parent(s), creating history graph; branches are movable pointers to commits
- Snapshots, not deltas: Each commit represents complete project state (tree), not diffs; delta compression applied later as optimization
Why Git operations are fast:
- Local operations: Most commands query local disk, not network
- Lightweight branches: Just 41-byte pointer files, created instantly
- Index staging: Staging pre-computes objects needed for commit; commit itself is fast
- Content deduplication: Unchanged files between commits reference same blobs; no storage overhead
Branching and merging:
- Branches are pointers: Creating, deleting, switching branches is cheap pointer manipulation
- Three-way merge: Uses common ancestor to determine what changed on each branch; combines non-overlapping changes, conflicts on overlapping
- Fast-forward: When possible, moves pointer instead of creating merge commit
- Rebase rewrites history: Replays commits on new base, creating new commits; useful for cleanup but dangerous on shared branches
Distributed architecture advantages:
- Every clone is full repository: Complete history available locally; no central dependency
- Work offline: Commit, branch, merge, view history—all without network
- No single point of failure: Every clone is backup
- Flexible workflows: Multiple remotes, pull requests, fork-and-PR model all enabled by distributed nature
Conflict resolution:
- Conflicts occur when same region modified differently: Git can't automatically decide which version to use
- Three-way diff shows context: Ancestor, ours, theirs—helps understand what each branch changed
- Manual resolution required: Human judgment needed to decide how to integrate conflicting changes
- Prevention through communication and modularity: Smaller, more frequent merges reduce conflicts
Storage efficiency:
- Content deduplication: Identical content stored once regardless of how many files/commits reference it
- Pack files and delta compression: Periodic garbage collection compresses objects using deltas
- Shallow clones: Fetch only recent history when full history not needed
- Garbage collection: Removes unreachable objects, compresses loose objects into packs
Advanced capabilities:
- Reflog: Safety net tracking HEAD movements; recover "lost" commits
- Cherry-pick: Apply specific commits to different branches
- Bisect: Binary search to identify commit that introduced bug
- Interactive rebase: Rewrite local history before sharing—combine, reorder, edit commits
The fundamental insight: Git's architecture—content-addressable storage with commits forming a DAG—elegantly solves version control's core problems. The complexity comes from powerful features (branching, merging, rebasing) built on this simple foundation.
References and Further Reading
Chacon, S., & Straub, B. (2014). Pro Git (2nd ed.). Apress. Available: https://git-scm.com/book/en/v2 DOI: 10.1007/978-1-4842-0076-6
Torvalds, L. (2007). "Tech Talk: Linus Torvalds on git." Google TechTalks. Available: https://www.youtube.com/watch?v=4XpnKHJAok8
Loeliger, J., & McCullough, M. (2012). Version Control with Git (2nd ed.). O'Reilly Media. DOI: 10.5555/2381967
Spinellis, D. (2005). "Version Control Systems." IEEE Software 22(5): 108-109. DOI: 10.1109/MS.2005.140
de Alwis, B., & Sillito, J. (2009). "Why Are Software Projects Moving from Centralized to Decentralized Version Control Systems?" Proceedings of ICSE Workshop on Cooperative and Human Aspects on Software Engineering. DOI: 10.1109/CHASE.2009.5071408
Bird, C., Rigby, P. C., Barr, E. T., Hamilton, D. J., German, D. M., & Devanbu, P. (2009). "The Promises and Perils of Mining Git." Proceedings of the 6th IEEE International Working Conference on Mining Software Repositories. DOI: 10.1109/MSR.2009.5069475
Kamp, P.-H. (2011). "VCS Trends in Open Source." ACM Queue 9(4). DOI: 10.1145/1966989.1967004
O'Sullivan, B. (2009). Mercurial: The Definitive Guide. O'Reilly Media. Available: http://hgbook.red-bean.com/
Collins-Sussman, B., Fitzpatrick, B. W., & Pilato, C. M. (2008). Version Control with Subversion. O'Reilly Media. Available: http://svnbook.red-bean.com/
Pilato, C. M., Collins-Sussman, B., & Fitzpatrick, B. W. (2004). "Version Control with Subversion." Available: http://svnbook.red-bean.com/
Git Documentation. "Git Internals - Git Objects." Available: https://git-scm.com/book/en/v2/Git-Internals-Git-Objects
Hamano, J. C. (Git maintainer). Various technical discussions in Git mailing list archives. Available: https://lore.kernel.org/git/
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