Screen SubstructLibrary queries with pattern fingerprints

[scal444]

This matches RDKit's pattern fingerprint prescreening, with a ~5-6x speedup.

Final PR for #350

[greptile-apps]

Confidence Score: 5/5

[Medium risk] Adds pattern fingerprint screening to substructure search.

The PR appears safe to merge; no new actionable defect was established.

What we checked:

• Selected targets keep their results: The planner stores original target indexes. Result collection reads those indexes rather than the candidate’s position.
• Recursive queries keep contiguous targets: Queries with recursive patterns turn off selected-target batching. After matching, the caller clears results for targets outside the candidate list.

Summary

Adds default-on RDKit pattern fingerprint screening to SubstructLibrary, with an option to disable it.

• Stores fingerprints alongside finalized molecules and builds GPU bit slices.
• Searches selected targets for ordinary queries. Recursive queries search contiguous targets and then keep candidate results.
• Adds benchmark controls and tests for screening, selected indexes, and repeated finalize() calls.
• The earlier freed-pointer concern is addressed by reserving fingerprints_ before committing replacement targets.
• scal444 accepted the extra pinned host-memory cost because GPU memory already limits query slots and a host limit would complicate the pinned-buffer path. That finding remains withdrawn.

_{Reviews (3) · Last reviewed commit: "Screen SubstructLibrary queries with pat..." · Reviewed by Greptile}

[evasnow1992]

Changes look good to me.