Add flexible CBMC bonded-stage planning

[cai-lx]

Summary

This is the first, deliberately small part of a stacked semiflexible-adsorbate GCMC contribution. It adds:

• host-side molecule topology entries for bonds, bends, and torsions;
• a deterministic planner for the bonded subset of one CBMC growth stage;
• RASPA2-compatible interaction ownership, PreviousBead selection, and orientation policy;
• a focused test covering forward, reverse, grouped rigid-head, duplicate-entry, and invalid-stage cases.

The planner preserves topology-table indices so duplicate bonded terms remain distinct. It also preserves the atoms-to-place outer-loop order used by RASPA2 Interactions().

Scope

This PR does not enable flexible sampling, add PFAA-specific inputs, or change existing simulation behavior. Input parsing, intramolecular energy evaluation, GPU trial scoring, and GCMC moves will be proposed as separate follow-up PRs after this foundation is reviewed.

Validation

• ./tools/test_flexible_incremental_bonded_growth.sh
• (cd src_clean && ./NVC_COMPILE)

Both pass with NVIDIA HPC SDK 24.5.