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Documentation Index

Fetch the complete documentation index at: https://bastani.mintlify.app/llms.txt

Use this file to discover all available pages before exploring further.

Atomic workflows run coding agents with all permission checks disabled. The agent can read, write, and delete files, execute arbitrary shell commands, and make network requests without prompting. This is required for unattended pipelines. Run workflows in a devcontainer or a git worktree, not on your host machine.

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The tradeoff

A workflow that pauses on every Write or Bash prompt isn’t a pipeline — it’s a chat session with extra steps. To get unattended execution (Ralph running for hours, CI runs, scheduled jobs), the agent’s interactive permission prompt has to be turned off. That choice has a cost: the agent can do anything its process can do. Atomic doesn’t try to sandbox tool calls at the agent layer — it pushes you toward sandboxing at the process layer.

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How each agent’s prompts are bypassed

AgentHow permissions are bypassedKey flags / settings
Claude CodeCLI flag disables the interactive permission prompt--dangerously-skip-permissions
GitHub Copilot CLICLI flag enables auto-execution; SDK auto-approves all tool requests--yolo, COPILOT_ALLOW_ALL=true, onPermissionRequest: approveAll
OpenCodePermissions handled programmatically through the event streamPermission requests auto-replied via SSE events
Defaults can be overridden per-project via providers in .atomic/settings.json — chatFlags replaces defaults entirely; envVars are merged. See settings.

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Safe patterns

A devcontainer is the safest place to run a workflow — agent actions are bounded by the container. Add one feature to .devcontainer/devcontainer.json:
FeatureInstalls
ghcr.io/flora131/atomic/claude:1Atomic + Claude Code
ghcr.io/flora131/atomic/opencode:1Atomic + OpenCode
ghcr.io/flora131/atomic/copilot:1Atomic + Copilot CLI
Each feature bundles Atomic, Bun, playwright-cli, agent configs, and the agent CLI itself. See installation.

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Git worktree

For autonomous coding workflows like Ralph, a git worktree keeps the agent’s changes off your working tree: 
git worktree add ../my-project-ralph feature-branch
cd ../my-project-ralph
atomic workflow -n ralph -a claude "Build the auth module"
A worktree is not a security boundary — the agent can still touch anything outside it. Use a devcontainer when isolation matters.

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Chat vs workflow

atomic chat does not disable permissions — it spawns the native agent CLI, so you get the agent’s normal prompts. The disabled-prompt behavior only applies during atomic workflow runs.