Add error handling with NyxError and refactor console output formatting

- Introduced `NyxError` and `NyxResult` for unified error handling across modules.
- Refactored `scan.rs`, `index.rs`, and `walk.rs` with improved error management and consistent formatting.
- Replaced existing error handling in `database.rs` with `NyxResult`.
- Improved database maintenance by integrating `vacuum` and `clear` methods into workflows.
- Added `dashmap` for efficient parallel diagnostics result aggregation in `scan_with_index_parallel`.
- Enhanced readability and formatting of console outputs in multiple modules.

src/utils/mod.rs

@@ -1,6 +1,7 @@
 pub mod project;
 pub mod config;
 pub(crate) mod query_cache;
+pub(crate) mod ext;
 
 // Re-export commonly used functions for convenience
 pub use project::{get_project_info};