Refactor error handling with NyxResult and enhance debugging

- Replaced `Result` with `NyxResult` across the codebase for consistent error management.
- Enhanced `NyxError` with new variants and utility conversions for better flexibility.
- Added detailed `tracing::debug` logs in `file.rs` and `walk.rs` for improved traceability.
- Simplified conditionals and improved path handling in `file.rs`.
- Refined severity filtering logic in `scan.rs`.

src/commands/clean.rs

@@ -1,12 +1,13 @@
 use std::{env, fs};
 use console::style;
+use crate::errors::NyxResult;
 use crate::utils::get_project_info;
 
 pub fn handle(
     project: Option<String>,
     all: bool,
     config_dir: &std::path::Path,
-) -> Result<(), Box<dyn std::error::Error>> {
+) -> NyxResult<()> {
     if all {
         println!("{}", style("Cleaning all indexes...").cyan().bold());
         if config_dir.exists() {

src/commands/index.rs

@@ -10,12 +10,13 @@ use crate::utils::Config;
 use crate::utils::project::get_project_info;
 use crate::walk::spawn_senders;
 use rayon::prelude::*;
+use crate::errors::NyxResult;
 
 pub fn handle(
     action: IndexAction,
     database_dir: &std::path::Path,
     config: &Config,
-) -> Result<(), Box<dyn std::error::Error>> {
+) -> NyxResult<()> {
     match action {
         IndexAction::Build { path, force } => {
             let build_path = std::path::Path::new(&path).canonicalize()?;
@@ -57,13 +58,13 @@ pub fn build_index(
     project_path: &std::path::Path,
     db_path: &std::path::Path,
     config: &Config,
-) -> Result<(), Box<dyn std::error::Error>> {
+) -> NyxResult<()> {
     tracing::debug!("Building index for: {}", project_name);
     fs::File::create(db_path)?;
     
     let pool = Indexer::init(db_path)?;
     {
-        let idx = Indexer::from_pool(project_name, &pool).unwrap();
+        let idx = Indexer::from_pool(project_name, &pool)?;
         idx.clear()?;
     }
 
@@ -73,9 +74,9 @@ pub fn build_index(
     let paths: Vec<_> = rx.into_iter().flatten().collect();
     
     paths.into_par_iter().try_for_each(|path| -> Result<(), Box<dyn std::error::Error + Send + Sync>> {
-        let issues = crate::commands::scan::run_rules_on_file(&path, config).unwrap();
-        let mut idx = Indexer::from_pool(project_name, &pool).unwrap();
-        let file_id = idx.upsert_file(&path).unwrap();
+        let issues = crate::commands::scan::run_rules_on_file(&path, config)?;
+        let mut idx = Indexer::from_pool(project_name, &pool)?;
+        let file_id = idx.upsert_file(&path)?;
 
         let rows: Vec<IssueRow> = issues.iter().map(|d| IssueRow {
             rule_id: d.id.as_ref(),
@@ -88,9 +89,9 @@ pub fn build_index(
             col:  d.col  as i64,
         }).collect();
         
-        idx.replace_issues(file_id, rows).unwrap();
+        idx.replace_issues(file_id, rows)?;
         Ok(())
-    }).unwrap();
+    })?;
     
     {
         let idx = Indexer::from_pool(project_name, &pool)?;

src/commands/list.rs

@@ -2,11 +2,12 @@ use std::fs;
 use bytesize::ByteSize;
 use chrono::{DateTime, Local};
 use console::style;
+use crate::errors::NyxResult;
 
 pub fn handle(
     verbose: bool,
     database_dir: &std::path::Path,
-) -> Result<(), Box<dyn std::error::Error>> {
+) -> NyxResult<()> {
     println!("{}", style("Indexed projects").blue().bold().underlined());
 
     if !database_dir.exists() {

src/commands/mod.rs

@@ -5,6 +5,7 @@ pub mod clean;
 
 use crate::cli::Commands;
 use std::path::Path;
+use crate::errors::NyxResult;
 use crate::patterns::Severity;
 use crate::utils::config::Config;
 
@@ -12,7 +13,7 @@ pub fn handle_command(
     command: Commands,
     database_dir: &Path,
     config: &mut Config
-) -> Result<(), Box<dyn std::error::Error>> {
+) -> NyxResult<()> {
     match command {
         Commands::Scan { path, no_index, rebuild_index, format, high_only } => {
             if high_only { config.scanner.min_severity = Severity::High };

src/commands/scan.rs

@@ -33,7 +33,7 @@ pub fn handle(
     format: String,
     database_dir: &Path,
     config: &Config,
-) -> Result<(), Box<dyn std::error::Error>> {
+) -> NyxResult<()> {
     let scan_path = Path::new(path).canonicalize()?;
     let (project_name, db_path) = get_project_info(&scan_path, database_dir)?;
 
@@ -87,7 +87,7 @@ pub fn handle(
 fn scan_filesystem(
     root: &Path,
     cfg: &Config,
-) ->Result<Vec<Diag>, Box<dyn std::error::Error>> {
+) -> NyxResult<Vec<Diag>> {
     let rx = spawn_senders(root, cfg);
     let acc = Mutex::new(Vec::new());
 
@@ -95,10 +95,10 @@ fn scan_filesystem(
       .flatten()
       .par_bridge()        
       .try_for_each(|path| {
-          let mut local = run_rules_on_file(&path, cfg).unwrap();  
+          let mut local = run_rules_on_file(&path, cfg)?;  
           acc.lock().unwrap().append(&mut local);
           Ok::<(), DynError>(())        
-      }).unwrap();
+      })?;
     
     Ok(acc.into_inner()?)
 }
@@ -126,7 +126,7 @@ pub fn scan_with_index_parallel(
 
               let mut diags = if needs_scan {
                   let d = run_rules_on_file(&path, cfg).unwrap_or_default();
-                  let file_id = idx.upsert_file(&path).unwrap();
+                  let file_id = idx.upsert_file(&path).unwrap_or_default();
                   idx.replace_issues(
                       file_id,
                       d.iter().map(|d| IssueRow {