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CLI Reference

atomic-agent is the single command-line tool for running the agent, serving it over HTTP, scheduling background work, managing local models and skills, and inspecting what happened after the fact. This page lists every command and every flag.

If you just want to start chatting, run atomic-agent with no arguments — it opens the terminal UI.

At a glance

Terminal window
atomic-agent [command] [flags]

There are 12 public top-level commands, plus a hidden debug repl. Running atomic-agent with no command opens the TUI.

CommandWhat it does
runInteractive chat loop on stdin/stdout
tuiFull terminal UI (default when no command is given)
serveStart the OpenAI-compatible HTTP server (and any enabled Telegram/Discord channels)
taskManage the durable task queue (schedule, list, run)
traceInspect, export, and replay recorded sessions
skillInstall, list, and toggle skills
modelsManage local llama.cpp models and GPU devices, and search cloud models
configRead, set, or reset keys in config.json
memoryExport the memory store to an Obsidian vault
importMigrate from Claude Code, Codex, Hermes, OpenClaw, Pi or Oh-My-Pi
updateSelf-update the installed binary from GitHub Releases
uninstallRemove the binary and/or all of its data from this machine

A few entry points sit outside the table:

  • atag is a short alias for atomic-agent, installed next to the binary by the install script. atag run and atomic-agent run are the same thing.
  • atomic-agent --version (also -v or version) prints the installed version, for example atomic-agent 0.6.5.
  • atomic-agent help <command> is the same as atomic-agent <command> --help. atomic-agent --help lists every command.
  • atomic-agent repl is a scaffold debug REPL. It is not listed in --help and is not a substitute for run or tui.

Exit codes: 0 success, 1 failure, 2 usage error. The 2 split is implemented by run, skill, memory, update, uninstall, and the dispatcher itself (unknown command). config, serve, trace, task, models and import return 1 for usage errors as well, so a 1 from them does not always mean the work failed. trace replay uses 2 to mean “drift detected”. tui can pass through a relaunched child’s status (for example 130 after Ctrl-C), and repl always returns 0.

flowchart TD
    A["atomic-agent [command]"] --> B{command}
    B -->|none| TUI["tui"]
    B -->|run| RUN["interactive chat loop"]
    B -->|serve| SRV["HTTP server + approval bus"]
    B -->|task| TSK["TaskStore / TaskRunner"]
    B -->|trace| TRC["trace files (NDJSON)"]
    B -->|skill| SK["skill install / toggle"]
    B -->|models| MD["managed llama.cpp daemon"]
    B -->|config| CF["config.json"]
    B -->|import| IM["migration from other agents"]
    RUN --> RT["runtime.runTurn"]
    SRV --> RT
    TSK --> RT

Commands

Run — interactive chat

Starts the agent in a plain stdin/stdout chat loop. Type a message, press Enter, and the agent runs a turn and prints its reply. Diagnostics go to stderr; the assistant’s reply goes to stdout.

Terminal window
atomic-agent run [--cwd DIR] [--max-steps N] [--no-approval]
FlagDefaultDescription
--cwd DIRcurrent directoryWorking directory the agent resolves relative paths against and scopes the session to.
--max-steps Nagent.task.maxSteps (1000)Hard ceiling on steps for one task. Without it, the agent works in legs of agent.maxSteps (25) steps and continues automatically up to agent.task.maxSteps (1000) or agent.task.maxDurationMs (2 hours). --max-steps can also raise the ceiling above 1000.
--no-approvaloffForce approval level 5 (approve everything) for this process. See the caution below.

At the default approval level (1), dangerous tools pause and prompt you over stdin. Approval is serial: a long-running approval blocks later ones in the same turn.

The approval prompt

The stdin prompt takes four answers, not two:

AnswerEffect
yApprove this one call.
sApprove, and allow this whole category (file writes, HTTP, shell…) for the rest of the session.
aApprove, and allow this shell command shape for the rest of the session.
NDeny. Anything that is not y, yes, s, or a is a refusal.

s and a only appear when the request is grantable. Writes to the agent’s own trust config (config.json, .env) are never grantable — those requests only ever offer y/N, because a silent write there could raise the ladder for the next boot.

TUI — terminal UI

Launches the full React/Ink terminal interface: chat plus tabs for tasks, skills, memory, MCP, providers, local models, and Telegram. This is what runs when you type atomic-agent with no command.

Terminal window
atomic-agent tui [--cwd DIR] [--max-steps N] [--no-approval] [--skip-llama-setup]
[--onboarding] [--mouse | --no-mouse]
FlagDefaultDescription
--cwd / --working-dir DIRcurrent directoryWorking directory for the session.
--max-steps Nagent.task.maxSteps (1000)Hard step ceiling for one task, same meaning as for run.
--no-approvaloffForce approval level 5 (approve everything). In the TUI, approvals otherwise appear as a modal.
--skip-llama-setupoffSkip the first-run model setup wizard. Also settable via ATOMIC_AGENT_TUI_SKIP_LLAMA_SETUP=1.
--onboardingoffRun first-time setup again. Providers, keys, and sessions are kept.
--mousetui.mouse (true)Force terminal mouse support on for this run.
--no-mouseoffTurn mouse support off for this run, which restores the terminal’s own drag-to-select.

The TUI needs an interactive terminal. In scripts, use atomic-agent run.

Inside the TUI, slash commands drive everything: /help, /new, /clear, /abort, /quit, /theme, plus panel switches like /tasks, /skills, /memory, /mcp, /llm, /models, /telegram, and /import. Sessions are created lazily on your first message, so opening the TUI just to glance at settings does not litter the session store.

Serve — HTTP server

Starts a Node HTTP server exposing an OpenAI-compatible chat API plus Atomic Agent management endpoints. Listens until SIGINT (Ctrl-C) or SIGTERM.

serve boots the same runtime as the TUI, so enabled Telegram and Discord channels (and swarm bots that have a token) run in this process too. A channel runs in one process at a time; a second process reports it as already running.

Terminal window
atomic-agent serve [--host H] [--port P] [--cwd DIR] [--api-key K] [--no-approval]
FlagDefaultDescription
--host H127.0.0.1Address to bind.
--port P8787Port to listen on.
--cwd DIRcurrent directoryWorking directory for sessions.
--api-key KATOMIC_AGENT_API_KEY env varBearer token required on authenticated routes. If both are omitted, auth is disabled.
--no-approvaloffForce approval level 5 (approve everything) for all requests.

Authenticated routes expect an Authorization: Bearer <token> header. Two routes are intentionally public so OpenAI SDKs can probe them before sending a key: GET /health and GET /v1/models.

HTTP endpoints exposed by serve
Method & pathPurpose
POST /v1/chat/completionsOpenAI-compatible chat, streaming or sync.
POST /v1/chat/completions/{id}/cancelAbort a streaming completion by id.
GET /v1/modelsModel catalog (public, single atomic-agent entry).
GET /healthLiveness probe (public).
GET /api/capabilitiesRuntime wiring summary.
GET|PATCH /api/configRead the user config, or rewrite it. PATCH has a known issue that resets most blocks, see the HTTP server page.
GET /api/skills, GET /api/skills/{name}List / inspect skills.
POST /api/skills/install, /api/skills/uninstallManage skills.
GET /api/sessions, GET|DELETE /api/sessions/{id}List / fetch / delete sessions.
POST|GET|DELETE /api/sessions/{id}/steerSteer a running turn, list steers it never consumed, acknowledge them.
POST /api/approval/resolveResolve a pending approval.
GET /api/eventsSSE stream of approval requests (replays pending on connect).
POST|GET /api/tasks, GET|DELETE /api/tasks/{id}Task CRUD.
POST /api/tasks/{id}/run, POST /api/tasks/drainTrigger task execution.
POST /api/webhooks/{name}Webhook ingress, materialized as a task.

Custom headers: X-Atomic-Session-Id (request/response) pins the session; X-Atomic-Completion-Id is returned on completions (pass it to the cancel route); X-Atomic-Extensions opts into named SSE events (e.g. tool_progress) instead of the strict OpenAI subset; X-Webhook-Secret authenticates webhook posts.

Task — durable task queue

Schedule deferred or recurring agent turns. Tasks persist to SQLite and survive restarts. Reads (list, show) use the task store directly; create for recurring schedules and run boot the full runtime.

Terminal window
atomic-agent task list [--session ID] [--status CSV] [--limit N]
atomic-agent task show <id>
atomic-agent task create [--session ID] --message TEXT
[--at MS | --cron EXPR | --every SEC] [--tz IANA]
[--notify telegram]
[--max-attempts N] [--max-steps N]
atomic-agent task cancel <id>
atomic-agent task run <id> | --all-pending [--session ID]
atomic-agent task tick [--limit N]
SubcommandNotes
listFilter by --session, comma-separated --status, and --limit.
show <id>Print one task record.
create--message is required. Pick at most one schedule: --at (epoch ms one-shot), --cron (cron expression), or --every (interval in seconds). --tz sets the IANA timezone and is only valid together with --cron — passing it with --at, --every, or no schedule at all is an error. --notify telegram pings you over the Telegram channel when the task finishes; telegram is the only accepted value.
cancel <id>Idempotent cancel.
run <id> / --all-pendingExecute now, applying retry backoff between attempts.
tick [--limit N]One-shot drain of all due tasks, then exit. Exits 1 if any task failed or was blocked. Good for cron-style ops.

Trace — inspect & replay sessions

Traces are append-only NDJSON files, one per session, capturing turns, steps, prompts, LLM completions, and tool calls. The trace command reads and replays them.

Terminal window
atomic-agent trace list [--limit N]
atomic-agent trace show <sessionId> [--step N] [--raw]
atomic-agent trace export <sessionId> [--format ndjson|json]
atomic-agent trace replay <sessionId> [--step N]
SubcommandNotes
listRecent trace summaries.
show <sessionId>Human-readable chronology. --step N isolates one step; --raw prints unformatted lines.
export <sessionId>Dump as ndjson (default) or json.
replay <sessionId>Rebuild the stable prefix with current tools/skills/capabilities and compare hashes to detect prompt drift. --step N isolates a step. Exits 0 if no drift, 2 if drift is detected.

Skill — manage skills

Skills are folders (a SKILL.md plus optional scripts) that extend the agent with reusable playbooks.

Terminal window
atomic-agent skill install <path|owner/repo[/path]|@owner/slug> [--force] [--acknowledge-risk]
atomic-agent skill uninstall <name>
atomic-agent skill list
atomic-agent skill show <name>
atomic-agent skill enable <name>
atomic-agent skill disable <name>
atomic-agent skill browse [--source owner/repo]
atomic-agent skill search <query>
atomic-agent skill tap list | add <owner/repo> | remove <owner/repo>
SubcommandNotes
install <target>Install from three kinds of source: a local directory path, a GitHub skill hub tap (owner/repo or owner/repo/path), or ClawHub (@owner/slug). --force overwrites an existing skill of the same name. --acknowledge-risk confirms you accept a remote skill flagged as suspicious by the install scan — without it, a flagged skill is refused.
uninstall <name>Remove a global skill.
listShow all skills with enabled/disabled state and source.
show <name>Print the SKILL.md body.
enable / disable <name>Toggle visibility by mutating skills.disabled in config.json. Disabled skills stay on disk but are invisible to the model.
browse [--source owner/repo]List installable skills from ClawHub plus every configured GitHub tap. --source narrows it to a single tap.
search <query>Search ClawHub and the configured taps by keyword.
tap list|add|removeManage the GitHub repositories browse and search read from. Mutates skills.taps in config.json. Ships with anthropics/skills, openai/skills, and vercel-labs/agent-skills.

Models — local llama.cpp models

Manage the managed-mode local inference daemon: download backends and GGUF models, start/stop the server, and pick GPU devices. models search also looks up models on your configured cloud providers.

Terminal window
atomic-agent models list | status | devices
atomic-agent models pull <id> [--background] [--mmproj]
atomic-agent models downloads [cancel <id> | clear]
atomic-agent models use <id> | remove <id>
atomic-agent models start | stop | update
atomic-agent models use-device <auto|cpu|Vulkan0>
atomic-agent models list-embeddings
atomic-agent models pull-embedding <id> [--background]
atomic-agent models use-embedding <id> | --disable
atomic-agent models search <query> [--provider ID] [--limit N] [--json] [--refresh]
GroupSubcommands
Chat modelslist, pull <id>, use <id>, remove <id>, status, update
Downloadspull --background keeps downloading after the terminal closes; downloads lists background downloads, downloads cancel <id> stops one (the partial file is kept, and pull resumes it), downloads clear forgets finished records. pull --mmproj also fetches the vision projector.
Daemonstart, stop
GPUdevices, use-device <auto|cpu|Vulkan0>
Embeddingslist-embeddings, pull-embedding <id>, use-embedding <id> / --disable
Cloudsearch <query> searches your configured cloud providers’ models by id, vendor, and capability (for example claude vision or free tools). --refresh pulls live model lists first. No local runtime needed.

Config — read & write config

Read and edit the user config file at <stateDir>/config.json, one key at a time or as a whole document.

Terminal window
atomic-agent config get # whole file as JSON
atomic-agent config get <key> # one value, e.g. log.level
atomic-agent config set <key> <value> # one value, rest of the file untouched
atomic-agent config set '<json>' # replace the whole file (missing keys get defaults)
atomic-agent config unset <key> # restore one key to its default
atomic-agent config list # every key as key = value
atomic-agent config path # where config.json lives

Keys are dotted paths such as log.level or agent.approvalLevel. Values are typed by the config schema, so false, 40 and info are written as a boolean, a number and a string. Bounds and enums are checked before anything is written.

Terminal window
atomic-agent config set log.level debug
atomic-agent config set agent.maxSteps 40
atomic-agent config unset log.level # back to "info"

List-valued keys such as projects.roots have no single-value form. Set them with the whole-file JSON form; unset works on them.

Memory: export the memory store

Terminal window
atomic-agent memory export [--vault PATH] [--folder NAME]

One-way export of the memory corpus (notes, lessons, procedures from <stateDir>/memory.sqlite) into an Obsidian vault, as Markdown files with YAML frontmatter and [[wikilinks]] along the memory’s own links.

FlagDefaultDescription
--vault PATH$OBSIDIAN_VAULT_PATHAn existing Obsidian vault directory.
--folder NAMEatomic-agentThe vault subfolder the export owns.

The export is idempotent: re-running it overwrites its own files in place and prunes files whose record is gone. Other files in the vault are never touched, and the database is opened read-only, so nothing syncs back.

Update: self-update the binary

Terminal window
atomic-agent update [--check | --version <tag>]

Checks GitHub Releases for a newer version and re-runs the install script in place, the same as the TUI’s in-app update. It only applies to the installed binary; a source checkout is updated with git. The running process is not restarted, so the new version takes effect on the next launch.

FlagDescription
--checkReport the current and latest version, install nothing.
--version <tag>Install a specific release tag (for example v0.6.5) instead of the latest.

Exit codes: 0 up to date, updated, or check succeeded; 1 the check or the install failed, or this install cannot self-update; 2 usage error.

Uninstall: remove Atomic Agent

Terminal window
atomic-agent uninstall [--dry-run] [--keep-data] [--keep-binary] [--keep-path] [-y | --yes]

Deletes the state directory (config, memory, sessions, tasks, traces, and downloaded models), the installed binary and its atag alias, the asset folders installed beside them, and the PATH line the installer added to your shell rc file. Interactive runs list everything with sizes and ask you to type a confirmation word; non-interactive runs must pass --yes.

FlagDescription
--dry-runPrint exactly what would be removed, remove nothing.
--keep-dataKeep the state directory; remove only the program.
--keep-binaryKeep the binary; remove only the data.
--keep-pathLeave the installer’s PATH line in your rc file.
-y, --yesSkip the typed confirmation (for scripts).

Exit codes: 0 removed, dry run printed, or you declined; 1 something could not be removed; 2 usage error (unknown flag, or no terminal and no --yes).

REPL — debug REPL

Terminal window
atomic-agent repl

A minimal scaffold REPL for debugging. It is hidden from --help and is not a substitute for run or tui.

Import — migrate from another agent

Migrate from Claude Code, Codex, Hermes, OpenClaw, Pi or Oh-My-Pi into Atomic Agent. Imported sessions are prefixed with the source name (claude-code:, hermes:, and so on) so they never collide with native ones. What each source brings is listed in the Import guide.

Terminal window
atomic-agent import hermes [--source DIR] [--preset default|full]
[--include a,b] [--exclude a,b]
[--migrate-secrets] [--limit N]
[--overwrite] [--dry-run] [--yes]
  • --source defaults to ~/.hermes (or HERMES_STATE_DIR).
  • --preset selects what to import (default = sessions + cron). --include / --exclude adjust it.
  • --migrate-secrets is the only way to copy secrets, and is limited to an allowlist (OPENROUTER_API_KEY, AIMLAPI_API_KEY). Secrets are never part of a preset.
FlagDescription
--limit NCap the number of sessions processed (-1 = no limit).
--overwriteOverwrite a differing destination instead of flagging it as a conflict.
--dry-runPreview only — reconciliation runs but nothing is written.
--yesSkip the interactive confirmation.

Environment variables

The CLI reads these at bootstrap. They cover operational and bootstrap values that have no config.json key; the file wins for user-facing settings like model and log level. Three exceptions override a file key for one process: ATOMIC_AGENT_LLAMA_MAX_TOKENS (over localModels.completionMaxTokens), ATOMIC_AGENT_SKILLS_CATALOG_BUDGET (over skills.catalogTokenBudget), and ATOMIC_AGENT_DOWNLOAD_CONNECTIONS (over localModels.download.connections).

VariablePurpose
ATOMIC_AGENT_STATE_DIRRoot for state: config.json, traces, tasks.sqlite, memory, skills. Defaults to ~/.atomic-agent.
ATOMIC_AGENT_LLAMA_API_KEYBearer token for llama-server (optional).
ATOMIC_AGENT_LLAMA_MAX_TOKENSOverrides localModels.completionMaxTokens (default 16384) for this process, clamped 64 to 131072. The CLI’s --help still says 8192; that text is out of date.
ATOMIC_AGENT_API_KEYBearer token for the serve HTTP API (fallback when --api-key is omitted).
ATOMIC_AGENT_RG_PATHOverride the bundled ripgrep binary path.
ATOMIC_AGENT_BROWSER_CHANNELchrome | msedge | chromium (default chrome).
ATOMIC_AGENT_BROWSER_EXECUTABLE_PATHExplicit Chromium binary path (overrides auto-detect).
ATOMIC_AGENT_BROWSER_HEADLESS1 for headless mode (default 0).
ATOMIC_AGENT_BROWSER_NO_SANDBOX1 to pass --no-sandbox (containers/CI only).
ATOMIC_AGENT_BROWSER_CDP_URLAttach to an existing browser via Chrome DevTools Protocol.
ATOMIC_AGENT_DEBUG_ARGV1 logs process.argv to stderr.
ATOMIC_AGENT_UPDATE_CHECK_ON_STARTUPCheck for a newer release at startup (default true).

Task queue

The task queue is configured only through environment variables — there is no tasks block in config.json.

VariableDefaultPurpose
ATOMIC_AGENT_TASKS_ENABLEDtrueMaster switch for the durable task queue.
ATOMIC_AGENT_TASKS_MAX_ATTEMPTS3Default retry budget per task.
ATOMIC_AGENT_TASKS_RUN_ON_CREATEtrueRun a task immediately when it is created with no schedule.
ATOMIC_AGENT_TASKS_SCHEDULER_ENABLEDtrueRun the long-lived background scheduler.
ATOMIC_AGENT_TASKS_SCHEDULER_TICK_MS5000Scheduler poll interval.
ATOMIC_AGENT_TASKS_MIN_INTERVAL_MS1000Floor on --every intervals.

There are many more ATOMIC_AGENT_* tuning vars for the agent loop, tasks, and memory. See the Configuration reference for the full list.

Common config keys

These live in <stateDir>/config.json and back the flags above. Change one with atomic-agent config set <key> <value>, or use the TUI.

KeyDefaultDescription
localModels.modeexternalmanaged runs the daemon; external expects a llama-server you run yourself. models use <id> flips this to managed.
localModels.urlhttp://127.0.0.1:8080HTTP URL for the llama-server API in external mode. In managed mode the URL is http://127.0.0.1:<localModels.managed.port>.
localModels.managed.modelIdnullActive model id in managed mode. Nothing is active until you pull a model.
localModels.managed.port19091Port for the managed chat daemon (embeddings use 19092).
localModels.completionMaxTokens16384Max new tokens per completion. 0 means no client-side cap.
agent.maxSteps25Steps per leg. After a leg the agent reports progress and continues, while agent.task.autoContinue is on.
agent.task.maxSteps1000Hard step ceiling for one task. --max-steps overrides it.
agent.task.maxDurationMs7200000Wall-clock ceiling for one task (2 hours).
agent.task.autoContinuetrueContinue into the next leg automatically instead of stopping after agent.maxSteps.
agent.tokenBudget3000Max prompt tokens per turn.
agent.approvalLevel1Approval ladder, 1 to 5. See below. --no-approval forces 5 for one process.
log.levelinfodebug | info | warn | error.

The approval ladder

agent.approvalLevel replaced the old boolean agent.approvalRequired in schema v37. It is a 1–5 ladder and each level is cumulative — it stops asking about everything the level below it stopped asking about.

LevelNameStops asking about
1paranoidNothing — every gated action asks first. This is the default.
2workspaceFile writes, edits, and patches strictly inside the session working directory.
3homeAdds file writes anywhere under your home directory, moves to Trash, archive extraction, and HTTP requests.
4operatorAdds guarded shell commands, skill scripts, process kills, network git (push, pull, fetch, clone, adding a remote), publishing (PRs, issues), and Fusion fan-out.
5full trustEverything, including browser navigation to non-web URLs, writes to the agent’s own trust config, reads outside the working directory, and sending email.

Hardline shell-guard rules sit outside the ladder and block at every level.

Where to go next

Configuration

The full config.json schema, every environment variable, and precedence rules.

HTTP API

Request/response shapes for serve, including streaming chat completions and the approval SSE stream.

Tasks & scheduling

Schedule syntax (--at / --cron / --every), retry behavior, and session binding.

Skills

The SKILL.md format, script allowlisting, and the approval gate for skill.run_script.