chore: set up pre-commit framework with general hooks

Add .pre-commit-config.yaml with pre-commit-hooks v5.0.0 (trailing
whitespace, end-of-file fixer, yaml/json checks, large file guard,
merge conflict detection). Add minimal pyproject.toml. Auto-fix
trailing whitespace and missing end-of-file newlines across the
codebase.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

README.md

@@ -986,9 +986,3 @@ If you use this project in your research or publication, please cite:
   version = {2.2.3}
 }
 ```
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