Fix config link from extension directories

[isaacroldan]

Why

Running shopify app config link from an extension directory could scan the extension folder for app TOMLs, decide none existed, and overwrite the root shopify.app.toml when creating a new linked app.

What

• Use the resolved app root when choosing the config filename.
• Preserve the root prompt behavior when existing app TOMLs are present.
• Add regression coverage for linking a new app from an extension directory.

Testing

• pnpm vitest run packages/app/src/cli/services/app/config/link.test.ts