Upgrading

Update the installed CLI and package-managed UI runtime with npm:

npm install -g co-auto-research@latest

Check the installed version:

co-auto-research version

Each generated project includes:

.co-auto-research-template/manifest.json

The manifest records the template version used to create the project. co-auto-research upgrade reports the installed CLI version, the detected project template version, and the npm update command.

Updating the npm package updates the CLI, dashboard, and default UI runtime used by co-auto-research ui and co-auto-research attach. Existing project research files are not rewritten automatically.

Update Project Instructions

Reviewer and trial-protocol instructions are part of the quality gate. If the UI or doctor reports that an older project has outdated core instructions, update only the managed core instruction files:

co-auto-research upgrade-project

For all projects in the default dashboard folder:

co-auto-research upgrade-project --all --projects-dir co-autoresearch-projects

The command writes a backup under archive/template_migrations/, installs the latest core reviewer and protocol files, and leaves research content plus custom extra reviewers or other instruction files alone.

Adopt The Critical-Path Deliverable Model

Recent templates add Critical Path accounting, mandatory ongoing-work conversion, research-critical acquisition decisions, and the two-artifact manuscript model. Existing projects remain readable by the server, but older projects should adopt the new fields before long autoresearch runs:

  • Re-sync core instructions with co-auto-research upgrade-project.

  • Add a ## Critical Path section to research_trajectory/STATE.md with the current bottleneck and any open data, method, evaluation, figure/table, or deliverable dependencies.

  • Add manuscript/PAPER_PLAN.md for planned evidence obligations and blockers. Keep manuscript/BLUEPRINT.md for real, source-backed manuscript content only.

  • If resources/ongoing_work/ contains code, data, checkpoints, metrics, or manuscript sources, run a conversion trial before normal trials continue.

  • For research-critical resources, record acquisition/substitution decisions under the trial’s artifacts/resource_scout/ directory.

The UI now gates the Paper-Writing Pack. If the blueprint is still a stub, contains planned slots, lacks real result sources, or has blocking missing evidence, export a Research Status Pack instead. The status pack is compatible with legacy projects and is intentionally labeled as incomplete.