Fix warnings for Gradle 9 (#38927)

Summary:
Pull Request resolved: https://github.com/facebook/react-native/pull/38927

I've done a pass and fixed most of the warnings for Gradle 9:
- project.buildDir is deprecated in favor of project.layout.buildDirectory
- I've updated 3rd party Gradle Plugins that we depend on

There are still two warnings which are outside of our control:
1. One is inside AGP and will be fixed with AGP 8.2 - Source https://issuetracker.google.com/issues/279306626
2. Another one is inside nexus-publish and should ideally be fixed by 2.0 https://github.com/gradle/gradle/issues/25206 Will bump the release once it's out

Changelog:
[Internal] [Changed] - Fix warnings for Gradle 9

Reviewed By: mdvacca

Differential Revision: D48231760

fbshipit-source-id: 27d704324ea33cfc8aa0164fa437b80aab425960