BREAKING: remove deprecated files config

[dsherret]

The long form "files" config has been flattened into the parent.

Old:

{
  "test": {
    "files": {
      "include": ["**/*.ts"],
      "exclude": ["ignore.ts"]
    }
  }
}

New:

{
  "test": {
    "include": ["**/*.ts"],
    "exclude": ["ignore.ts"]
  }
}

This was deprecated some time ago, but we're removing it now in Deno 2.0.

Closes #25415