hydrogen/Bump cli-hydrogen to 13.0.0 (main)

[fredericoo]

WHY are these changes introduced?

The latest Hydrogen release published @shopify/cli-hydrogen@13.0.0. Shopify CLI needs to bundle that version so shopify hydrogen commands pick up the latest Hydrogen CLI release.

Hydrogen release notes: https://github.com/Shopify/hydrogen/releases/tag/%40shopify/cli-hydrogen%4013.0.0

WHAT is this pull request doing?

• Bumps @shopify/cli-hydrogen from 11.1.10 to 13.0.0.
• Updates the lockfile for the new Hydrogen CLI package.
• Updates the generated CLI manifest, README, and shopify.dev generated docs for the new Hydrogen deploy command metadata.
• Updates the existing patch changeset for @shopify/cli.

Release notes included in this Hydrogen CLI release:

• Add hydrogen deploy flags and environment variables for configuring Oxygen client assets and worker output directories.
• Resolve deployment output directories from explicit flags, Vite output directories, then dist/client and dist/server fallbacks.
• Default custom output deployments and 0.0.0-preview-* Hydrogen versions to node --run build when no build command is provided.
• Update @shopify/mini-oxygen to 4.2.0.

How to test your changes?

• npm view @shopify/cli-hydrogen@13.0.0 version
• shadowenv exec pnpm -- i --frozen-lockfile
• node -e 'JSON.parse(require("fs").readFileSync("packages/cli/oclif.manifest.json", "utf8")); JSON.parse(require("fs").readFileSync("docs-shopify.dev/generated/generated_docs_data_v2.json", "utf8"));'
• shadowenv exec pnpm -- build-api-docs
• git diff --check
• shadowenv exec pnpm -- graphql-codegen fails because local schema files are missing for bulkOperations, storeBusinessPlatformDestinations, and storeBusinessPlatformOrganizations.
• shadowenv exec pnpm -- refresh-manifests fails before packages/cli generation because @shopify/store currently hits an @oclif/core@4.8.3 / @oclif/core@4.11.4 type split.
• shadowenv exec pnpm -- build-dev-docs fails on the same @shopify/store build issue.

Post-release steps

No stable patch PR for this bump because this is a major @shopify/cli-hydrogen version bump.

After the Shopify CLI release that includes this PR, Hydrogen should follow up by updating the skeleton template's @shopify/cli version if this Hydrogen CLI release contained actual CLI code changes.

Checklist

• I've considered possible cross-platform impacts (Mac, Linux, Windows)
• I've considered possible documentation changes
• I've considered analytics changes to measure impact
• The change is user-facing - I've identified the correct bump type and updated the existing changeset