fix: update ruff

[b-long]

Update ruff, require "PTH" (flake8-use-pathlib) and fix PTH violations. Also updated some README content.

[gemini-code-assist]

Summary of Changes

Hello @b-long, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request focuses on enhancing code quality and adherence to modern Python practices by updating the ruff linter to its latest version and refactoring file system interactions to utilize the pathlib module. It also includes minor cleanups such as removing unused code and updating documentation to accurately reflect changes in the project structure, ensuring a more robust and maintainable codebase.

Highlights

• Ruff Linter Update: The ruff linter has been updated from version v0.12.12 to v0.13.1 in the pre-commit configuration and the uv.lock file, ensuring the use of the latest linting features and fixes.
• Pathlib Adoption for File Operations: Numerous file operations previously using open() have been refactored to leverage Path.open() from the pathlib module. This change enhances readability, maintainability, and consistency in path handling across the codebase, and the PTH rule for pathlib has been enabled in pyproject.toml.
• Unused Variable Renaming: Several variables that were assigned but not subsequently used (e.g., manifest, size, kas_private_key) have been renamed with a leading underscore (e.g., _manifest, _size, _kas_private_key). This explicitly marks them as intentionally unused, aligning with Python's convention for ignoring variables and improving code clarity.
• Documentation and Example Cleanup: The README.md file has been cleaned up by removing a commented-out sdk.close() line from an example. Additionally, the otdf-python-proto/README.md has been updated to reflect the correct directory for generated protobuf and Connect RPC client files, changing from generated/ to src/otdf_python_proto/.

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[gemini-code-assist]

Code Review

This pull request updates ruff and applies several linting fixes, primarily related to using pathlib for file operations and marking unused variables. The changes are a good step towards modernizing the codebase and improving consistency. I've provided several suggestions to further simplify file I/O using pathlib's helper methods like read_text() and write_bytes(), which align with the direction of this PR. I also have a concern about removing sdk.close() from the README.md example, as it might encourage bad practices.

[b-long]

/gemini review

[gemini-code-assist]

Code Review

This pull request updates the ruff linter and applies its automated fixes across the codebase. The changes primarily involve using pathlib for file operations, removing unused imports, and marking unused variables, which improves code consistency and quality. I have one suggestion regarding the README.md file, where an important sdk.close() call was removed from an example. Restoring this call is crucial to demonstrate correct resource management.