Nexus: First step to ridding us of Particles

[brockdyer03]

Proposed changes

First step from #6010.

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

• Refactoring (no functional changes, no api changes)

Does this introduce a breaking change?

• No

What systems has this change been tested on?

Laptop, Fedora Linux 43 (KDE Plasma Desktop Edition)
AMD Ryzen 7 PRO 7840U (8 cores, 16 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'

[jtkrogel]

Update physical system interface to fully hide particles classes. See comments.

[jtkrogel]

See new comments

[jtkrogel]

Looks good now.

[prckent]

Test this please

[prckent]

Note that due to scheduled maintenance the self-hosted CI will likely go down before the initial invocation completes. We'll restart on ~Tuesday.