Fix data race on shared molecule in batched MMFF minimizers

[scal444]

Batch threads built each molecule's MMFF force field inside the OpenMP loop, and RDKit's MMFFMolProperties constructor mutates the molecule it types. Conformers of one molecule can span several batches, so threads raced on the same ROMol, producing wrong atom types and heap corruption. The trigger is thread count, not GPU count.

Build each molecule's MMFFMolProperties once under std::call_once and share it; contribs still build per batch through the non-mutating overload, so preprocessing stays interleaved with GPU work.

Fixes #236

[greptile-apps]

Greptile Summary

Fixes concurrent MMFF preprocessing for conformers belonging to one molecule, but the guard does not cover duplicate references to that molecule.

• Extracts MMFFMolProperties construction into a shared helper.
• Adds per-input-index call_once storage used by the BFGS and FIRE batch minimizers.
• Adds a multithreaded MMFF regression test and adjusts FMCS test include paths.

Confidence Score: 3/5

This PR should not merge until MMFF property initialization is synchronized by molecule identity or duplicate molecule references are explicitly rejected.

The new call_once guard fixes conformers sharing one input index, but duplicate input entries referencing the same ROMol receive independent guards and can still concurrently invoke the mutating MMFFMolProperties constructor.

Files Needing Attention: src/minimizer/mmff_minimize.cpp, tests/test_mmff.cu

Important Files Changed

Filename	Overview
src/minimizer/mmff_minimize.cpp	Shares MMFF properties across batch threads, but indexing the synchronization guard by molIdx leaves aliased ROMol entries able to initialize concurrently.
rdkit_extensions/mmff_flattened_builder.cpp	Extracts MMFF property construction and configuration into a shared-pointer-returning helper.
rdkit_extensions/mmff_flattened_builder.h	Declares the helper and documents the mutation and synchronization requirements.
tests/test_mmff.cu	Adds coverage for one molecule whose conformers span threads, but does not cover the supported duplicate-ROMol input shape.
tests/test_fmcs_primitives.cu	Qualifies three FMCS test includes with their source-tree paths.

_{Reviews (1): Last reviewed commit: "Fix data race on shared molecule in batc..." | Re-trigger Greptile}

[evasnow1992]

Thank you for fixing this!