Nexus: replace optparse in __init__.py with argparse

[brockdyer03]

Proposed changes

Python's optparse module is very outdated and requires a significant amount of extra work to do the same thing as argparse. In this PR I have updated the main __init__.py of Nexus to use argparse instead of optparse, and have organized and trimmed down the code for handling command line arguments, as well as added options for common/convenient aliases of some command line arguments.

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 44 (KDE Plasma Desktop Edition)
AMD Ryzen 7 PRO 7840U (8 cores, 16 logical processors)

Python        3.14.6
uv            0.12.5
cif2cell      2.1.0
coverage      7.15.4
h5py          3.16.0
matplotlib    3.11.1
numpy         2.5.2
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'
• • Code added or changed in the PR has been clang-formatted
• • This PR adds tests to cover any new code, or to catch a bug that is being fixed
• • Documentation has been added (if appropriate)

[jtkrogel]

Need time to look