Running an agent overnight without breaking things

It’s 23:30 and Claude Code is halfway through a migration. You want progress by morning, not a wrecked branch or a turn stuck on a permission prompt since 01:00.

The safe overnight run is a bounded one: a turn limit, a permission mode you’d leave alone and a throwaway branch. Then the worst case is a wasted night, not a mess.

Claude Code’s own wait only resumes once after a usage limit, in an open session. Agent Auto-Continue handles the turn limit and the sending; the rest is on you.

Before you go to bed

1. Work on a branch (git switch -c overnight), so the worst case is deleting it.
2. Put the plan in the repo. A PLAN.md beats anything you’ll type at 23:30.
3. Ask Claude Code for a commit per step. What to say has a message for that. Codex keeps .git read-only by default, so there a commit needs approval.
4. Pick Up to a few turns, not Until done. A stop phrase like TASK COMPLETE helps; the limit is the real guard.
5. Keep the Mac awake and plugged in. Keep-awake is off by default, and a closed lid sleeps anyway outside closed-display mode.
6. Quit claude or codex in the terminal. An open Claude Code session counts as busy; the chain waits. Codex waits too while another process holds the thread’s writer lock.

Pick a permission mode you’d leave alone

The app runs Claude Code headless in the session’s last permission mode, and headless denies anything that would prompt. So the mode decides what gets done:

• Manual only runs reads without asking, so overnight it mostly reads.
• Auto runs everything with background safety checks, and Anthropic lists it for long tasks. Blocked actions are skipped and Claude keeps working.
• bypassPermissions is for isolated containers and VMs only, in Anthropic’s words. Not your laptop at 03:00.

For progress by morning, Auto on a throwaway branch is the reasonable pick.

Codex stops instead. Its default Auto preset asks before editing outside the workspace or using the network. Nobody’s there to approve, so the turn stops and the chain pauses. One npm install at 02:00 can end your night.

What can go wrong, and what stops it

Risk	What stops it
It carries on after the task’s done	The turn limit. Three sub-minute turns in a row pause it
It keeps hitting the usage limit	Those turns don’t count, and three in a row pause it
A turn never ends	After 24 hours the chain pauses and lets the Mac sleep
The same message twice	Stable message IDs; an unclear send is marked unconfirmed, never retried
You typed in the thread at 02:00	A re-check before each send pauses it; a gone or archived thread stops it
The agent asks you something	The chain pauses, turn unsent
A restart or sleep	Jobs survive; missed schedules catch up after wake
You want it stopped	Stop, or Stop all in the queue; a running turn finishes, nothing more is sent

The morning review

What’s still going is in the queue; Recent and All history show how the rest ended. Click a run for each turn’s outcome.

A paused run says why, and Resume never resends a delivered turn. If it’s unconfirmed, Check delivery first; it only reads the conversation.

The app knows what it sent, not whether the work’s any good. That’s git and you:

git log --oneline main..overnight
git diff --stat main

Read the diff, run the tests, then decide whether to stay in this thread. Unattended isn’t the same as unreviewed.

Honest limits

• It can’t tell when the task’s done. No harness reports it, so Until done ends at the stop phrase, a pause or you.
• The Mac has to be awake and the app running. Quitting interrupts Claude Code and private Codex turns.
• Claude Desktop and the ChatGPT app need the Mac unlocked, so a locked screen waits for morning.