Add optional centroid reporting to Butina clustering

[scal444]

Addresses #74

[greptile-apps]

Greptile Overview

Greptile Summary

Added optional centroid reporting to Butina clustering, allowing users to retrieve the centroid index for each cluster. The implementation threads centroids through all CUDA kernels and properly handles cluster renumbering.

Key changes:

• Added return_centroids parameter to Python API that returns a tuple (clusters, centroids) when enabled
• Centroids are tracked at cluster assignment time in three kernels: attemptAssignClustersFromNeighborlist, butinaWriteClusterValue, and assignSingletonIdsKernel
• Implemented remapCentroidsKernel to handle centroid index remapping when clusters are renumbered by size
• Memory management properly addressed with new toOwnedPyArray helper function
• Both Python and C++ tests added to validate centroid correctness

Tests verify:

• Centroids array has correct size (equal to number of clusters)
• Each centroid is actually in its corresponding cluster
• All cluster members are adjacent to their centroid (within cutoff distance)

Confidence Score: 5/5

• This PR is safe to merge with minimal risk
• The implementation is thorough and well-tested. The feature is backward-compatible (optional parameter with default false), centroids are properly threaded through all kernels, memory management concerns from previous review were addressed with the toOwnedPyArray helper, and comprehensive tests validate correctness at both Python and C++ levels
• No files require special attention

Important Files Changed

Filename	Overview
nvmolkit/clustering.cpp	Added toOwnedPyArray helper and conditional centroid return logic with proper memory management
src/butina.h	Added optional centroids parameter and return value for cluster count to both GPU entry points
src/butina.cu	Threaded centroids through all kernels, added remapCentroidsKernel, and returns cluster count

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[evasnow1992]

Thank you for addressing the user request. Code changes are clean and valid.