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Upgrading Waypoint

Recommended path

If Waypoint is installed globally from npm, use:

waypoint upgrade

That does two things:

  1. updates the globally installed waypoint-codex package
  2. refreshes the current repo scaffold using the repo's existing Waypoint config

If you only want to update the CLI and skip the repo refresh:

waypoint upgrade --skip-repo-refresh

If you use npx, no global update step is required:

npx waypoint-codex@latest --help

Manual refresh

If you updated the CLI some other way, refresh the repo scaffold manually:

waypoint init
waypoint doctor

waypoint init is designed to refresh Waypoint-managed files while preserving user-owned repo content outside the managed scaffold.

What to verify after upgrading

Focus on the files that define the default behavior:

  • AGENTS.md
  • .waypoint/MEMORY.md
  • .waypoint/SOUL.md
  • .waypoint/agent-operating-manual.md
  • .waypoint/WORKSPACE.md
  • .waypoint/DOCS_INDEX.md
  • .waypoint/context/
  • .agents/skills/
  • .codex/agents/

What to look for

After an upgrade, sanity-check three things:

  1. The default voice still matches the product. The core contract should read like a strong collaborator with clear judgment and useful next actions.

  2. Heavy workflows still live in tools. Review loops, ship audits, trackers, and retrospectives should stay available without taking over the always-on layer.

  3. Repo memory still has clear boundaries. .waypoint/MEMORY.md, .waypoint/WORKSPACE.md, .waypoint/docs/, and .waypoint/plans/ should still have distinct jobs.

If you customized a repo

Repo-specific guidance should live outside the managed Waypoint block in AGENTS.md.

That means upgrades should be able to refresh Waypoint-owned content without clobbering your custom repo guidance.

If the upgrade changes the product philosophy in a meaningful way, review the repo's custom guidance and make sure it still complements the scaffold instead of fighting it.