Command Reference

Atomic provides a focused set of commands for managing repositories, recording changes, collaborating with remotes, and integrating with AI coding agents.

Every command listed here corresponds to a real subcommand in the atomic CLI binary. Run atomic <command> --help for full usage details.

Quick Reference

Command	Description
init	Initialize a new Atomic repository
status	Show working copy status
add	Add files to be tracked
remove	Remove files from tracking
move	Move or rename tracked files
record	Record changes from the working copy
revise	Revise a change in-place
diff	Show differences in the working copy
log	Show change history
change	Inspect a specific change
apply	Apply changes to a stack
reset	Reset working copy to last recorded state
split	Create a new stack from an existing one
stack	Manage stacks (new, switch, list, delete)
stash	Temporarily save uncommitted changes
tag	Manage tags (create, list, show, delete)
push	Push changes to a remote
pull	Pull changes from a remote
clone	Clone a remote repository
remote	Manage named remote repositories
identity	Manage user identities and signing keys
agent	Manage AI agent integration

Command Categories

Working with Changes

The core workflow — track files, record changes, review diffs:

atomic add src/main.rs           # Track a file
atomic status                     # See what changed
atomic diff                       # Review the diff
atomic record -m "Add main"       # Record a change
atomic log                        # View history

• add — Add files to be tracked
• remove / rm — Remove files from tracking
• move / mv — Move or rename tracked files
• status — Show modified, added, deleted, and untracked files
• diff — Show differences between working copy and last recorded state
• record — Create a new change from tracked file modifications
• revise — Modify a previously recorded change in-place
• log — Display the history of changes on the current stack
• change — Inspect details of a specific change by hash or sequence number

Repository Management

Create, clone, and reset repositories:

atomic init myproject             # Create a new repo
atomic clone https://...          # Clone from remote
atomic reset --force              # Discard uncommitted changes

• init — Initialize a new Atomic repository
• clone — Clone an existing repository from a remote
• reset — Reset the working copy to the last recorded state
• split — Create a new stack from an existing one

Stacks

Stacks are Atomic's equivalent of branches — but they're views of the same graph, not forks:

atomic stack new feature-auth     # Create a stack
atomic stack switch feature-auth  # Switch to it
atomic stack list                 # List all stacks
atomic stack delete old-feature   # Delete a stack

• stack — Create, switch, list, and delete stacks
• stash — Temporarily save uncommitted changes to an orphan stack

Remote Operations

Synchronize with remote repositories:

atomic remote add origin https://api.atomic.dev/acme/project/code
atomic push                       # Push changes to default remote
atomic pull                       # Pull changes from default remote

• push — Upload local changes to a remote
• pull — Download and apply changes from a remote
• clone — Create a new local repository from a remote
• remote — Add, remove, list, and configure named remotes

Tags

Named state snapshots for marking releases and sync points:

atomic tag create v1.0.0 -m "Release 1.0"
atomic tag list
atomic tag show v1.0.0

• tag — Create, list, show, and delete tags

Identity

Manage user identities for signing changes:

atomic identity new alice --email alice@example.com
atomic identity list
atomic identity whoami

• identity — Create, list, show, and delete identities

AI Agent Integration

Turn-level recording for AI coding agents with full provenance:

atomic agent enable --agent claude-code
atomic agent status --verbose
atomic agent explain <session-id> --all --save

• agent — Enable, disable, and manage AI agent hooks for Claude Code, Gemini CLI, and OpenCode

Global Options

These flags are available on every command:

Flag	Description
-v, --verbose	Enable verbose output for debugging
--no-color	Disable colored output (useful for piping)
--version	Print version information
--help	Display help for a command

Basic Workflow

# 1. Initialize
atomic init myproject
cd myproject

# 2. Create and track files
echo 'fn main() {}' > src/main.rs
atomic add src/main.rs

# 3. Record
atomic record -m "Initial commit"

# 4. Create a stack for a feature
atomic stack new feature-auth --switch

# 5. Make changes, record, review
atomic status
atomic diff
atomic record -m "Add authentication module"

# 6. Push to remote
atomic remote add origin https://api.atomic.dev/acme/project/code
atomic push

AI-Assisted Workflow

# 1. Enable agent hooks
atomic agent enable --agent claude-code

# 2. Work with your AI agent — turns are recorded automatically

# 3. Review what happened
atomic log
atomic agent status --verbose

# 4. Generate reasoning summaries
atomic agent explain <session-id> --all --save

# 5. Push everything (changes + provenance + session data)
atomic push

Getting Help

# Top-level help
atomic --help

# Help for a specific command
atomic record --help
atomic stack --help
atomic agent enable --help