Regression error in 3.87.0

I have reproduced the issue on the latest CLI version.

Yes, I am on the latest version

I have searched existing posts and this report is not a duplicate.

Yes, this isn’t a duplicate

In which of these areas are you experiencing a problem?

App

Expected behavior

Running shopify app config use $ENVIRONMENT should succeed.

Actual behavior

Running shopify app config use $ENVIRONMENT fails with Unsupported section(s) in app configuration: metaobjects, order

Reproduction steps

Upgrading from shopify/cli 3.86.1 to 3.87.0 and running shopify app config use development results in an error.

My shopify.app.development.toml file:

name = "my-dev-app"
client_id = "<id>"
application_url = "<url>"
embedded = true
handle = "app-handle"
web_directories = [ "web", "web/frontend" ]

[access_scopes]
# Learn more at https://shopify.dev/docs/apps/tools/cli/configuration#access_scopes
scopes = "..."

[access.admin]
direct_api_mode = "online"
embedded_app_direct_api_access = true

[auth]
redirect_urls = [
  "https://example.com/auth/callback",
  "https://example.com/auth/shopify/callback",
  "https://example.com/api/auth/callback"
]

[webhooks]
api_version = "2025-07"

[app_proxy]
url = "https://example.com/app_proxy"
subpath = "app"
prefix = "apps"

[pos]
embedded = false

[build]
dev_store_url = "my-store.myshopify.com"
automatically_update_urls_on_dev = true

[metaobjects.app.order_metaobject]
name = "Order Metaobject"
description = "description"
access.admin = "merchant_read_write"
access.storefront = "public_read"

[metaobjects.app.order_metaobject.fields.due_date]
name = "Date Due"
type = "date"

[metaobjects.app.order_metaobject.fields.paid]
name = "Paid"
type = "boolean"

[metaobjects.app.order_metaobject.fields.amount_paid]
name = "Amount Paid"
type = "money"

[order.metafields.app.app_metafield]
name = "My metafield"
description = "A list of metaobjects for this order"
type = "list.metaobject_reference<$app:order_metaobject>"
access.storefront = "public_read"
access.customer_account = "read"

Verbose output

npx shopify app config use development
╭─ error ────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                                                                                        │
│  Unsupported section(s) in app configuration: metaobjects, order                                       │
│                                                                                                        │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────╯

Operating system

Mac OS Sequoia 15.6

CLI version

3.87.0

Shell

zsh

Nodejs version

22.13.1

What language and version are you using in your application?

Ruby 3.4.1