another round of refactoring / cleaning

[dantzert]

no more god functions like delay_io_train in train.py.
use inheritance and abstract base classes to give more structure when we have choices.
follow guidance in https://www.skills.sh/github/awesome-copilot/refactor and https://www.skills.sh/dietrichgebert/ponytail/ponytail
clean up stale issue plans, old testing artifacts, and any dead code

objective is a smaller and more logical codebase that is easier to understand, use, and maintain

[dantzert]

Low-priority packaging cleanup tasks (re: #33):

1. Stray root __init__.py. The repo root contains __init__.py with from .modpods import *. This makes the project directory itself importable as a package named after the repo, which confuses IDE/import resolution and packaging. It's only present so that import modpods resolves from an uninstalled checkout. With modpods properly declared in pyproject.toml (packages.find includes modpods*) this file is unnecessary and should be removed (install with pip install -e . instead).

2. Stale modpods.egg-info/requires.txt. It still lists 12 dependencies (pyswmm, pystorms, statsmodels, dill, …) that are not in pyproject.toml (which has 8 direct deps: numpy, pandas, scipy, matplotlib, control, pysindy, cvxpy, networkx). egg-info/ is a build artifact and should be regenerated (and gitignored) rather than hand-maintained or committed out of sync.