Symptom

Autopilot looks healthy. gbrain autopilot --status returns the cheerful [cycle] score=N elapsed=1s next=150s line. autopilot.log shows cycles dispatching every 5 minutes. gbrain doctor stays at 90/100. But Embedded 0 chunks across N pages on every cycle, and the real story is buried in ~/.gbrain/autopilot.err:

Error embedding inbox/2026-04-23-...: The OPENAI_API_KEY environment variable is missing or empty
Error embedding inbox/2026-04-23-...: The OPENAI_API_KEY environment variable is missing or empty
... (3.4 MB of these in my case, accumulated over weeks)

Per-page embed failures are caught and warn-logged rather than propagated, so the cycle exits status=success with chunks_embedded: 0. No healthcheck flags it. New pages stop being searchable; nothing tells you.

Root cause

writeWrapperScript() (src/commands/autopilot.ts) generates this wrapper:

source ~/.zshrc 2>/dev/null || source ~/.bashrc 2>/dev/null || true
exec '...gbrain/src/cli.ts' autopilot --repo '/path/to/brain'

It sources the shell profile to pick up API keys exported there. That works for users who keep OPENAI_API_KEY in ~/.zshrc. But Bun also auto-loads .env from CWD (the whole point of "no dotenv needed" in a Bun project), and many users put their gbrain secrets in brain/.env — alongside the brain content, not in shell-init. Since launchd starts the wrapper with CWD = / or $HOME (not --repo), Bun's auto-load looks in the wrong directory and the daemon never sees brain/.env.

The interactive gbrain invocation works because users typically run it from inside the brain repo, where Bun does find brain/.env. So this only bites the daemon path, and only for users whose keys are in brain/.env.

Fix

cd '\${safeRepoPath}' || exit 1 before exec. Bun's CWD-based auto-load now finds brain/.env on every wrapper invocation. Existing shell-init env vars still take precedence (Bun's auto-load doesn't overwrite), so users with keys in ~/.zshrc are unaffected.

writeWrapperScript() is shared across launchd / systemd / crontab / ephemeral installers, so one site covers all four.

Repro

1. Move OPENAI_API_KEY from ~/.zshrc to ~/brain/.env. Confirm in a fresh shell that echo \$OPENAI_API_KEY is empty.
2. `gbrain autopilot --install --repo ~/brain`
3. Wait one cycle (5 min default), then `tail ~/.gbrain/autopilot.err` — embed errors flood.
4. Apply this PR's fix, `gbrain autopilot --install --repo ~/brain` to regenerate the wrapper, kickstart, wait one cycle. `tail ~/.gbrain/autopilot.log` shows `Embedded N chunks` and `autopilot.err` is quiet.

I confirmed the fix locally by patching ~/.gbrain/autopilot-run.sh directly and checking ps eww on the spawned Minions worker — OPENAI_API_KEY was visible in the worker child's env after the fix, absent before.

Possible follow-ups (not in this PR)

• gbrain autopilot could also read --repo/.env itself at startup, so the fix works regardless of how the daemon is invoked. Wider blast radius — left for a separate change.
• gbrain doctor could aggregate per-page embed failures into a warn-status check when failure rate exceeds a threshold. Would have caught this within one cycle. Happy to file a separate issue if there's interest.

Tests

No new test in this PR — writeWrapperScript is a string-template function and the change is two lines of generated shell. Happy to add a snapshot test if reviewers prefer.