Atom-Atom Path Fingerprints + DISE clustering

[scal444]

No description provided.

[scal444]

@greptile-apps please review.

[greptile-apps]

Confidence Score: 5/5

The PR appears safe to merge because no new actionable correctness, security, build, or repository-rule issue remains.

Summary

This PR adds GPU-backed Atom-Atom Path similarity and directed sphere-exclusion clustering, including Python bindings, result modes, validation tests, documentation, and comparative benchmark support.

• Implements AAP descriptor construction and GPU similarity evaluation.
• Adds first-match and nearest-centroid DISE clustering with host and device result forms.
• Adds CSV benchmark loading with preserved molecule properties and reference-workflow comparisons.
• Integrates the native AAP library into the Python extension and API documentation.

_{Reviews (4) · Last reviewed commit: "Merge remote-tracking branch 'official/m..."}

[scal444]

@greptile-apps review and go back to previous comments

[evasnow1992]

Thank you for adding this new similarity + clustering workflow. Implementation is clean and valid.