Fix linter errors and spelling/grammar errors; add new linter rules

[zaz]

Checklist

• My pull request has a clear and explanatory title.
• My pull request passes the Linting test.
• I added appropriate unit tests and I made sure the code passes all unit tests. (refer to comment below)
• My PR follows PEP8 guidelines. (refer to comment below)
• My code is properly documented, using numpy docs conventions, and I made sure the documentation renders properly.
• I linked to issues and PRs that are relevant to this PR.

PR series: 303 #307 #308 #309

This PR is first in series of staged PRs designed to be merged in-order.
I prefer to get lint issues out of the way first to avoid ongoing nuisance when rebasing.

Description

All of the new linters added are just one line each in .pre-commit-config.yaml and require no new dependencies.

---

Note

Low Risk
Low risk: changes are primarily formatting/whitespace normalization and documentation/config cleanups, plus additional pre-commit hooks that may surface new lint failures but do not alter runtime behavior.

Overview
Linter tooling: Expands .pre-commit-config.yaml to run additional pre-commit-hooks checks (e.g., EOF fixing, trailing whitespace, AST/JSON/symlink checks) alongside existing Ruff and NumPy doc validation.

Repo hygiene: Normalizes formatting across many YAML/Markdown/RST/test files (trailing spaces, blank lines, missing final newlines) and makes small copy edits in README.md and docs; includes minor config housekeeping like ensuring uv.lock is ignored and tidying Codecov/GitHub Actions YAML formatting.

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"ensuring uv.lock is ignored". We just add a newline to the end of uv.lock because it's at the end of the file; no functional changes to the gitignore or anything else.

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