Using Atomic

This page collects day-to-day usage details that do not fit on the quickstart page.

Interactive Mode

The interface has four main areas:

Startup header - shortcuts, loaded context files, prompt templates, skills, and extensions
Messages - user messages, assistant responses, tool calls, tool results, notifications, errors, and extension UI
Editor - where you type; border color indicates the current thinking level
Footer - working directory, session name, token/cache usage, cost, context usage, and current model

The editor can be replaced temporarily by built-in UI such as /settings or by custom extension UI.

Editor Features

Feature	How
File reference	Type `@` to fuzzy-search project files
Path completion	Press Tab to complete paths
Multi-line input	SHIFT+Enter, or CTRL+Enter on Windows Terminal
Images	Paste with CTRL+V, ALT+V on Windows, or drag into the terminal
Shell command	`!command` runs and sends output to the model
Hidden shell command	`!!command` runs without sending output to the model
External editor	CTRL+G opens `$VISUAL` or `$EDITOR`

See Keybindings for all shortcuts and customization.

Slash Commands

Type / in the editor to open command completion. Extensions can register custom commands, skills are available as /skill:name, and prompt templates expand via /templatename.

Command	Description
`/login`, `/logout`	Manage OAuth or API-key credentials
`/model`	Switch models
`/scoped-models`	Enable/disable models for CTRL+P cycling
`/fast`	Toggle Codex fast mode for chat and workflow stages when `openai/` or `openai-codex/` models are available
`/workflow`	List/run workflows; manage runs (connect/inspect/pause/interrupt/resume/kill); reload workflow resources
`/settings`	Thinking level, theme, message delivery, transport
`/resume`	Pick from previous sessions
`/new`	Start a new session
`/name <name>`	Set session display name
`/session`	Show session file, ID, messages, tokens, and cost
`/tree`	Jump to any point in the session and continue from there
`/fork`	Create a new session from a previous user message
`/clone`	Duplicate the current active branch into a new session
`/compact [prompt]`	Manually compact context, optionally with custom instructions
`/copy`	Copy last assistant message to clipboard
`/export [file]`	Export session to HTML
`/share`	Upload as private GitHub gist with shareable HTML link
`/reload`	Reload keybindings, extensions, skills, prompts, and context files
`/hotkeys`	Show all keyboard shortcuts
`/changelog`	Display version history
`/exit`	Exit Atomic
`/quit`	Quit Atomic

Message Queue

You can submit messages while the agent is still working:

Enter queues a steering message, delivered after the current assistant turn finishes executing its tool calls.
ALT+Enter queues a follow-up message, delivered after the agent finishes all work.
Escape aborts and restores queued messages to the editor.
ALT+Up retrieves queued messages back to the editor.

On Windows Terminal, ALT+Enter is fullscreen by default. Remap it as described in Terminal setup if you want Atomic to receive the shortcut. Configure delivery in Settings with steeringMode and followUpMode.

Sessions

Sessions are saved automatically to ~/.atomic/agent/sessions/, organized by working directory.

atomic -c                  # Continue most recent session
atomic -r                  # Browse and select a session
atomic --no-session        # Ephemeral mode; do not save
atomic --session <path|id> # Use a specific session file or session ID
atomic --fork <path|id>    # Fork a session into a new session file

Useful session commands:

/session shows the current session file and ID.
/tree navigates the in-file session tree and can summarize abandoned branches.
/fork creates a new session from an earlier user message.
/clone duplicates the current active branch into a new session file.
/compact summarizes older messages to free context.

See Sessions and Compaction for details.

Context Files

Atomic loads AGENTS.md or CLAUDE.md at startup from:

~/.atomic/agent/AGENTS.md for global instructions
parent directories, walking up from the current working directory
the current directory

Use context files for project conventions, commands, safety rules, and preferences. Disable loading with --no-context-files or -nc.

System Prompt Files

Replace the default system prompt with:

.atomic/SYSTEM.md for a project
~/.atomic/agent/SYSTEM.md globally

Append to the default prompt without replacing it with APPEND_SYSTEM.md in either location. Use /export [file] to write a session to HTML. Use /share to upload a private GitHub gist with a shareable HTML link. If you use Atomic for open source work and want to publish sessions for model, prompt, tool, and evaluation research, see badlogic/pi-share-hf. It publishes sessions to Hugging Face datasets.

CLI Reference

atomic [options] [@files...] [messages...]

Package Commands

atomic install <source> [-l]     # Install package, -l for project-local
atomic remove <source> [-l]      # Remove package
atomic uninstall <source> [-l]   # Alias for remove
atomic update [source|self|atomic] # Update Atomic and packages; skips pinned packages
atomic update --extensions       # Update packages only
atomic update --self             # Update Atomic only
atomic update --extension <src>  # Update one package
atomic list                      # List installed packages
atomic config                    # Enable/disable package resources

See Atomic Packages for package sources and security notes.

Modes

Flag	Description
default	Interactive mode
`-p`, `--print`	Print response and exit
`--mode json`	Output all events as JSON lines; see JSON mode
`--mode rpc`	RPC mode over stdin/stdout; see RPC mode
`--export <in> [out]`	Export a session to HTML

In print mode, Atomic also reads piped stdin and merges it into the initial prompt:

cat README.md | atomic -p "Summarize this text"

Model Options

Option	Description
`--provider <name>`	Provider, such as `anthropic`, `openai`, or `google`
`--model <pattern>`	Model pattern or ID; supports `provider/id` and optional `:<thinking>`
`--api-key <key>`	API key, overriding environment variables
`--thinking <level>`	`off`, `minimal`, `low`, `medium`, `high`, `xhigh`
`--models <patterns>`	Comma-separated patterns for CTRL+P cycling
`--list-models [search]`	List available models

Session Options

Option	Description
`-c`, `--continue`	Continue the most recent session
`-r`, `--resume`	Browse and select a session
`--session <path\|id>`	Use a specific session file or partial UUID
`--fork <path\|id>`	Fork a session file or partial UUID into a new session
`--session-dir <dir>`	Custom session storage directory
`--no-session`	Ephemeral mode; do not save

Tool Options

Option	Description
`--tools <list>`, `-t <list>`	Allowlist specific built-in, extension, and custom tools
`--no-builtin-tools`, `-nbt`	Disable built-in tools but keep extension/custom tools enabled
`--no-tools`, `-nt`	Disable all tools

Default built-in tools: read, bash, edit, write, ask_user_question, todo. Additional built-in read-only tools are available through tool options: grep, find, ls.

Resource Options

Option	Description
`-e`, `--extension <source>`	Load an extension from path, npm, or git; repeatable
`--no-extensions`	Disable extension discovery
`--skill <path>`	Load a skill; repeatable
`--no-skills`	Disable skill discovery
`--prompt-template <path>`	Load a prompt template; repeatable
`--no-prompt-templates`	Disable prompt template discovery
`--theme <path>`	Load a theme; repeatable
`--no-themes`	Disable theme discovery
`--no-context-files`, `-nc`	Disable `AGENTS.md` and `CLAUDE.md` discovery

Combine --no-* with explicit flags to load exactly what you need, ignoring settings. Example:

atomic --no-extensions -e ./my-extension.ts

Other Options

Option	Description
`--system-prompt <text>`	Replace default prompt; context files and skills are still appended
`--append-system-prompt <text>`	Append to system prompt
`--verbose`	Force verbose startup
`-h`, `--help`	Show help
`-v`, `--version`	Show version

File Arguments

Prefix files with @ to include them in the message:

atomic @prompt.md "Answer this"
atomic -p @screenshot.png "What's in this image?"
atomic @code.ts @test.ts "Review these files"

Examples

# Interactive with initial prompt
atomic "List all .ts files in src/"

# Non-interactive
atomic -p "Summarize this codebase"

# Non-interactive with piped stdin
cat README.md | atomic -p "Summarize this text"

# Different model
atomic --provider openai --model gpt-4o "Help me refactor"

# Model with provider prefix
atomic --model openai/gpt-4o "Help me refactor"

# Model with thinking level shorthand
atomic --model sonnet:high "Solve this complex problem"

# Limit model cycling
atomic --models "claude-*,gpt-4o"

# Read-only mode
atomic --tools read,grep,find,ls -p "Review the code"

Environment Variables

Variable	Description
`ATOMIC_CODING_AGENT_DIR`	Override config directory; default is `~/.atomic/agent`
`ATOMIC_CODING_AGENT_SESSION_DIR`	Override session storage directory; overridden by `--session-dir`
`ATOMIC_PACKAGE_DIR`	Override package directory, useful for Nix/Guix store paths
`ATOMIC_OFFLINE`	Disable startup network operations, including update checks, package update checks, and install/update telemetry
`ATOMIC_SKIP_VERSION_CHECK`	Skip the Atomic version update check at startup. This prevents the latest-version request
`ATOMIC_TELEMETRY`	Override install/update telemetry: `1`/`true`/`yes` or `0`/`false`/`no`. This does not disable update checks
`PI_CACHE_RETENTION`	Provider/upstream-specific prompt-cache retention knob; set to `long` where supported
`VISUAL`, `EDITOR`	External editor for CTRL+G

PI_* aliases are also supported for app-specific ATOMIC_* variables for legacy compatibility. PI_CACHE_RETENTION is not one of those aliases and has no ATOMIC_* equivalent. Use PI_CACHE_RETENTION=long when configuring prompt-cache retention for providers/upstreams that support long-lived caches.

Design Principles

Atomic keeps the core CLI small, while this distribution bundles first-party package extensions for workflows, subagents, MCP, web access, and intercom. Other workflows can still be installed as extensions or packages, or handled externally with tools such as containers and tmux. For the full rationale, read the blog post.

​Using Atomic

​Interactive Mode

​Editor Features

​Slash Commands

​Message Queue

​Sessions

​Context Files

​System Prompt Files

​Exporting and Sharing Sessions

​CLI Reference

​Package Commands

​Modes

​Model Options

​Session Options

​Tool Options

​Resource Options

​Other Options

​File Arguments

​Examples

​Environment Variables

​Design Principles