Please confirm that you have:

• Searched existing issues to see if your issue is a duplicate. (If you’ve found a duplicate issue, feel free to add additional information in a comment on it.)
• Reproduced the issue in the latest CLI version.

In which of these areas are you experiencing a problem?

App

Expected behavior

Running npm run deploy after migrating the toml config to App-specific Webhook Subscriptions:

[webhooks]
api_version = "2024-07"

[[webhooks.subscriptions]]
topics = [ "app_subscriptions/update", "app/uninstalled", "orders/paid", "shop/update" ]
uri = "webhooks"
compliance_topics = [ "customers/data_request", "customers/redact", "shop/redact" ]

should not produce an error if legacy install flow is enabled and the scope has always been included:

[access_scopes]
# Learn more at https://shopify.dev/docs/apps/tools/cli/configuration#access_scopes
scopes = "read_all_orders,read_customers,read_discounts,read_orders,read_price_rules,read_script_tags,write_customers,write_discounts,write_price_rules,write_script_tags"
use_legacy_install_flow = true

Actual behavior

I'm getting the following error even thought read_orders and read_all_orders are in the scopes, and have been before the migration;

│
│  Version couldn't be created.   
│
│  Missing scope for webhook topic: orders/paid (read_orders or read_marketplace_orders) 
│

Verbose output

Not really comfortable sharing the whole verbose output, but happy to for any specifics portions required.

Reproduction steps

1. Have an app with include_config_on_deploy = true and read_orders in scope using the shop-specific webhook subscriptions
2. Migrate to the new app-specific webhook subscriptions as per https://shopify.dev/docs/apps/build/webhooks/subscribe#app-specific-subscriptions
3. Run npm run deploy

Operating System

Fedora 18 on WSL

Shopify CLI version (check your project's package.json if you're not sure)

3.66.1

Shell

zsh

Node version (run node -v if you're not sure)

v20.14.0

What language and version are you using in your application?

No response