Nexus: Remove Matter, Particle, Particles, Ion, and PseudoIon

[brockdyer03]

Proposed changes

This PR is the next step after #6030. It removes all of the old classes, and all related functions, and updates the appropriate tests/library code.

What type(s) of changes does this code introduce?

• Other: Legacy code removal

Does this introduce a breaking change?

• Maybe

What systems has this change been tested on?

Desktop, Fedora Linux 43 (KDE Plasma Desktop Edition)
AMD Ryzen 9 7900X (12 cores, 24 logical processors)

Python        3.14.5
uv            0.11.26
cif2cell      2.1.0
coverage      7.15.0
h5py          3.16.0
matplotlib    3.11.0
numpy         2.5.1
pycifrw       4.4.6
pydot         4.0.1
pytest        9.1.1
pytest-cov    7.1.0
pytest-order  1.5.0
scipy         1.18.0
seekpath      2.2.1
spglib        2.7.0
sphinx        9.1.0

Checklist

• • I have read the pull request guidance and develop docs
• • This PR is up to date with the current state of 'develop'
• • This PR adds tests to cover any new code, or to catch a bug that is being fixed
• • Documentation has been added (if appropriate)