refactor/modernize md_crds legacy bundle to mdanalysis new bundle

[alphataubio]

• amber
• dcd
• gromacs
• lammps
• psf

AI TOOLS DISCLOSURE

code generated with Gemini 3 Pro

[alphataubio]

Here is the rewritten md_crds bundle. This refactoring centralizes all file reading through MDAnalysis, replacing the legacy MDTools and ad-hoc parsers.

This solution provides:

1. Unified Structure Reading: A single read_structure module that handles PSF, GRO, LAMMPS Data, and other formats supported by MDAnalysis.
2. Unified Coordinate Reading: A generic read_coords module that uses MDAnalysis to stream trajectories (DCD, XTC, TRR, Amber NetCDF, LAMMPS Dump) into ChimeraX structures.
3. Modern Dependencies: Updates pyproject.toml to require MDAnalysis.

1. mdanalysis/pyproject.toml

Added MDAnalysis to dependencies.

2. mdanalysis/src/util.py

Added universe_to_atomic_structure helper.

3. mdanalysis/src/read_structure.py

Replaces read_psf, read_gro, read_lammps with a unified reader.

4. mdanalysis/src/read_coords.py

Replaces the old trajectory reader.

5. mdanalysis/src/__init__.py

Updated to route all calls to the new modules.

[zjp]

We typically put prerequisites in the top-level pyproject.toml in the repo root. Other than that, I'm unfamiliar with MD coords so I would be an unhelpful reviewer.

[e-pettersen]

I realize this is still a draft pull request at this stage, but nonetheless I cloned your repository and tried to build (after putting mdanalysis in src/bundles/Makefile and removing md_crds) and the build failed because there is no Makefile in src/bundles/mdanalysis. So I guess I will wait until the pull request is no longer a work in progress to check it out.

One other minor point is that one would normally start the version number of the mdanalysis bundle at 1.0 (or 1.0.0) rather than 3.0.0