[Gradle Extension] Move source to right folder

[TheMeinerLP]

Proposed changes

After patching the source, the files ended up in the wrong place, this PR moves them to the right place and deletes certain duplicates from the build-logic folder

Types of changes

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• Bugfix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation Update (if none of the other choices apply)

Checklist

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• I have read the CONTRIBUTING.md
• I have added tests that prove my fix is effective or that my feature works
• I have added necessary documentation (if appropriate)

Further comments

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