feat(analysis): bind CIF source identities to H5MD atom order

[xiaoxuan-yu]

This pull request introduces support for source atom identity order binding in the CIF/H5MD bundle workflow, ensuring that exported atom order and provenance are verifiable and consistent across tools and analysis pipelines. The changes add a new binding schema, implement order binding and validation logic, and update the bundle saver and analysis routines to use these features.

Source order binding and validation:

• Added a new source_order.py module implementing versioned source atom order binding, hash calculation, and validation methods, including make_source_order_binding, validate_source_order_binding, bind_bundle_source_order, and validate_trajectory_source_order (src/XpongeCPP/io_bundle/source_order.py).
• Updated the bundle saver to support binding source atom identities in the final serialization order, writing binding information and hashes to the output files, and validating source_atom_ids for uniqueness and completeness (src/XpongeCPP/io_bundle/saver.py) [1] [2] [3] [4].

Analysis and validation integration:

• Integrated source order binding validation into the CIF/H5MD analysis pipeline, verifying mapping files and trajectory hashes against the new binding schema, and exposing validation results in metadata (src/XpongeCPP/analysis/cif_mdanalysis.py) [1] [2] [3] [4].

Documentation:

• Added a comprehensive markdown document explaining the source-order binding schema, hash contract, mapping sidecar, and analysis validation, including expected file outputs and validation logic (docs/source_order_binding.md).

Compatibility:

• Provided a compatibility import for the new source order binding logic in the Xponge Python interface (src/Xponge/io_bundle/source_order.py).