Improve handling of amplify.yml file in repository root and Amplify console settings

### Environment information

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N/A
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### Description

Currently, if an `amplify.yml` file is present at the root of the repository, it takes precedence over the build settings configured in the Amplify console. However, the behavior when both an `amplify.yml` file and Amplify console settings are present can be confusing for users.

We should improve the handling of this scenario to provide a better user experience. Here are some suggestions:
- Clearly communicate to the user that the `amplify.yml` file in the repository root will take precedence over the Amplify console settings.
- Provide a warning or error message in the Amplify console if an amplify.yml file is detected in the repository root, informing the user that the console settings will be ignored.

Start by reviewing how a root amplify.yml file and Amplify console build settings are currently detected and prioritized. Define the user-facing warning or error behavior, including where precedence is communicated and how completion is verified when repository settings override console settings.

Written by the indexing model from the issue text.