feat(cv): support inline H5 RMSD references with end-to-end coverage

[xiaoxuan-yu]

This pull request introduces comprehensive support for native inline RMSD reference coordinates in the H5 protocol format, improves validation and error handling for RMSD collective variables, and adds robust end-to-end and unit tests to ensure compatibility and correctness across both native and legacy H5 input formats. The changes also update documentation and test instructions to reflect the new features and workflows.

Support for native inline RMSD references and improved validation:

• Refactored the ProtocolCVH5Reader to support reading RMSD reference coordinates directly from the protocol dataset (/cv/<name>/coordinate) in addition to the legacy restart path, with validation for shape, finiteness, and CV type. Conflicting references are detected and rejected. [1] [2]

Documentation updates:

• Updated the input reference documentation to describe the new native RMSD reference workflow, including dataset requirements, compatibility, and conflict handling between native and legacy references.
• Expanded the H5 bundle test README to explain the new end-to-end RMSD CV test suite and its requirements for both Xponge and XpongeCPP producers.

Testing enhancements:

• Added an end-to-end test (test_rmsd_cv_e2e.py and rmsd_cv_e2e_producer.py) that generates native and legacy RMSD H5 input using both Xponge and XpongeCPP, runs SPONGE, and independently verifies RMSD values and bias forces against a NumPy/Kabsch oracle. Also tests restart behavior for reproducibility. [1] [2]
• Added a unit test to validate all combinations of inline and restart RMSD references, including error cases for shape, finiteness, and conflicts, directly in the protocol reader. [1] [2] [3]

[xiaoxuan-yu]

@codex review