[1.21.1] Minor improvements

[tmvkrpxl0]

This PR adds these minor improvements:

1. Runs directory is removed. It contained junit jvm parameter containing path "/Users/ekansh". I assume this is from one of contributors. It could interfere running junit in other computers.
2. Enabled Configuration Cache for faster configuration.
3. Bumped Gradle version to 9.3.0, as official neoforge MDK for 1.21.1 uses 9.x
4. Removed vendor limit on gradle/gradle-daemon-jvm.properties as it was requiring microsoft's JVM
5. Switched to use debug logger in NSBiomes.java. Using plain System.out looks out of place in logs and cannot be silenced.
6. Fix neogradle warning about usage of "programArguments"