Refactor dependabot configs. (#2128)

This is to validate we can use app top level folders to config updates
of inner pubspec files.

Bug: flutter/flutter#136983

## Pre-launch Checklist

- [X] I read the [Effective Dart: Style] _recently_, and have followed
its advice.
- [X] I signed the [CLA].
- [X] I updated/added relevant documentation (doc comments with `///`).
- [X] All existing and new tests are passing.

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[Effective Dart: Style]:
https://dart.dev/guides/language/effective-dart/style
[CLA]: https://cla.developers.google.com/
[Discord]: https://github.com/flutter/flutter/wiki/Chat