Post-fire verify loses run-scoped acceptance commands

[samfoy]

Bug description

autoloop verify <project> <run-id> forgets run-scoped acceptance.verify_cmds supplied with autoloop run --set ... and can report an acceptance-verified run as unverifiable.

Steps to reproduce

1. Launch a run with a run-scoped override:

autoloop run autocode "task" \
  --set 'acceptance.verify_cmds=python3 -m compileall -q .,python3 -m pytest -q'

2. Allow it to complete. The registry can show:

{"status":"completed","acceptance_verified":true,"outcome":"verified"}

3. Run independent post-fire verification:

autoloop verify /path/to/project <run-id> --json

Actual:

{"reconcile":"unverifiable","ranChecks":0,"failures":[]}

Root cause

In autoloop-cli/dist/commands/verify.js, post-fire verify does:

const cfg = config.loadProject(record.project_dir || projectDir);
const cmds = postFireCheckCommands(config.getList(cfg, "acceptance.verify_cmds"), ...)

The effective run-scoped overrides are not persisted in the run record, so a later process reloads only project/preset config and loses the commands used by the run.

The compatibility path is confirmed: setting AUTOLOOP_CONFIG to a temporary TOML containing the same acceptance.verify_cmds makes post-fire verify return confirmed.

Expected behavior

A later autoloop verify should reuse the exact effective acceptance contract from that run without requiring callers to resupply it.

Suggested solution

Persist the effective post-fire acceptance commands and timeout in run metadata/journal at launch, then have verify prefer the recorded immutable contract. Avoid reinterpreting mutable project config for historical runs.

Also consider preserving commands as a true array: AutoLoop 0.10.1's string-list parser splits commas inside command strings, so CSV serialization is lossy.

Environment

• AutoLoop 0.10.1
• Node 22.23.1
• Linux