Address the rest of the clippy lints

[ribru17]

Commits are broken up by crate

[gemini-code-assist]

Summary of Changes

Hello @ribru17, 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 is dedicated to a comprehensive refactoring effort aimed at improving the overall code quality and adhering to idiomatic Rust patterns. By addressing numerous Clippy lints, the changes enhance code clarity, reduce potential pitfalls, and ensure a more robust and maintainable codebase. The modifications span across several modules, focusing on minor yet impactful adjustments to expressions, control flow, and data handling, without introducing new features or altering existing functionality.

Highlights

• Code Quality Improvements: Addressed a wide range of Clippy lints across multiple crates, enhancing code readability, maintainability, and adherence to Rust best practices.
• Idiomatic Rust Refactoring: Refactored several code patterns, including simplifying if let and match statements, using is_empty() instead of len() > 0, and replacing clone() with to_path_buf() for PathBuf arguments.
• Performance and Efficiency: Introduced minor optimizations such as using saturating_sub() for decrementing counts, first() instead of get(0) for collection access, and std::iter::repeat_n for creating repeated iterators.
• Dependency and Annotation Management: Removed unused dirs and serde imports, and added #[allow(clippy::mutable_key_type)], #[allow(clippy::module_inception)], and #[allow(clippy::too_many_arguments)] attributes where necessary to suppress specific Clippy warnings.

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[gemini-code-assist]

Code Review

This pull request addresses a number of clippy lints, which is a great effort towards improving code quality and idiomatic Rust. The changes are generally good, simplifying code and using more efficient patterns. I've found one potential issue where a loop seems to be re-processing an element it shouldn't. Please see my specific comment.

[CppCXY]

please resolve test fail