Adjust dependencies/linting/docs/.gitignore and workflows for Python …

…3.9-3.13.

Fix off-by-one coefficient upper bound; remove helper function; updat…

…e version.

Update core/build/testing/publication dependency version locks in pac…

…kage file.

Update linting rules and use human-readable exceptions; update packag…

…e version.

Adjust README/configs and build/publish package dependencies; update …

…version.

Move source code into `src` directory; update README and docs config.