refactor(coverage): rename JavaSrcDirFinder to SrcDirFinder and add CLI options

- Rename `java_src_dirs` to `src_search_dirs` in Settings
- Rename `JavaSrcDirFinder` to `SrcDirFinder` (and rename file)
- Update user-facing output from "Discovered Java source directories" to "Source search directories"
- Add `--add-src-dir` CLI option to manually specify source directories (takes precedence over auto-discovered)
- Add `--remove-src-dir` CLI option to exclude directories from the search list
- Add warning when a file is found in multiple source directories

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

Author: brynary

qlty-cli/src/commands/coverage/publish.rs

@@ -14,7 +14,7 @@ use qlty_coverage::print::{print_report_as_json, print_report_as_text};
 use qlty_coverage::publish::{Plan, Planner, Processor, Reader, Report, Settings, Upload};
 use qlty_coverage::token::load_auth_token;
 use qlty_coverage::validate::{ValidationStatus, Validator};
-use qlty_coverage::{ExclusionStrategy, JavaSrcDirFinder};
+use qlty_coverage::{ExclusionStrategy, SrcDirFinder};
 use std::io::Write as _;
 use std::path::PathBuf;
 use std::time::Instant;
@@ -41,6 +41,15 @@ pub struct Publish {
     /// and use them to resolve file paths in coverage reports.
     pub discover_java_src_dirs: bool,
 
+    #[arg(long = "add-src-dir", hide = true)]
+    /// Add a source directory to search for files. Can be specified multiple times.
+    /// These directories take precedence over auto-discovered directories.
+    pub add_src_dirs: Vec<PathBuf>,
+
+    #[arg(long = "remove-src-dir", hide = true)]
+    /// Remove a source directory from the search list. Can be specified multiple times.
+    pub remove_src_dirs: Vec<PathBuf>,
+
     #[arg(long, hide = true)]
     pub output_dir: Option<PathBuf>,
 
@@ -256,24 +265,39 @@ impl Publish {
 
         let root = std::env::current_dir()?;
         let config = load_config();
-        let java_src_dirs = if self.discover_java_src_dirs {
+
+        let mut src_search_dirs = self.add_src_dirs.clone();
+        if self.discover_java_src_dirs {
             let exclusion_strategy = if config.exclude_patterns.is_empty() {
                 ExclusionStrategy::DefaultHeuristics
             } else {
                 ExclusionStrategy::UserDefined(config.exclude_patterns)
             };
-            let finder = JavaSrcDirFinder::new(root.clone(), exclusion_strategy);
-            finder.find()?
-        } else {
-            Vec::new()
-        };
+            let finder = SrcDirFinder::new(root.clone(), exclusion_strategy);
+            src_search_dirs.extend(finder.find()?);
+        }
+
+        for dir_to_remove in &self.remove_src_dirs {
+            if let Some(pos) = src_search_dirs.iter().position(|d| d == dir_to_remove) {
+                src_search_dirs.remove(pos);
+            } else {
+                tracing::warn!(
+                    "Directory '{}' not found in source search directories",
+                    dir_to_remove.display()
+                );
+                eprintln!(
+                    "WARNING: Directory '{}' not found in source search directories",
+                    dir_to_remove.display()
+                );
+            }
+        }
 
         Ok(Settings {
             add_prefix,
             dry_run: self.dry_run,
             discover_java_src_dirs: self.discover_java_src_dirs,
             root,
-            java_src_dirs,
+            src_search_dirs,
             incomplete,
             name: self.name.clone(),
             output_dir: self.output_dir.clone(),
@@ -320,13 +344,10 @@ impl Publish {
             return;
         }
 
-        if settings.discover_java_src_dirs
-            && !settings.java_src_dirs.is_empty()
-            && std::env::var("JACOCO_SOURCE_PATH").is_ok()
-        {
-            eprintln!("WARNING: Both --discover-java-src-dirs and JACOCO_SOURCE_PATH are set.");
+        if !settings.src_search_dirs.is_empty() && std::env::var("JACOCO_SOURCE_PATH").is_ok() {
+            eprintln!("WARNING: Both source search directories and JACOCO_SOURCE_PATH are set.");
             eprintln!("JACOCO_SOURCE_PATH applies during JaCoCo parsing.");
-            eprintln!("--discover-java-src-dirs applies to all formats during processing.\n");
+            eprintln!("Source search directories (--add-src-dir/--discover-java-src-dirs) apply to all formats during processing.\n");
         }
     }
 

qlty-cli/src/commands/coverage/utils.rs

@@ -108,15 +108,16 @@ pub fn print_settings(settings: &Settings) {
 
     eprintln!();
 
-    // Print discovered Java src dirs as a sub-section if --discover-java-src-dirs is enabled
-    if settings.discover_java_src_dirs {
-        eprintln!("    discover-java-src-dirs: true");
+    if settings.discover_java_src_dirs || !settings.src_search_dirs.is_empty() {
+        if settings.discover_java_src_dirs {
+            eprintln!("    discover-java-src-dirs: true");
+        }
         eprintln!();
-        eprintln!("    Discovered Java source directories:");
-        if settings.java_src_dirs.is_empty() {
+        eprintln!("    Source search directories:");
+        if settings.src_search_dirs.is_empty() {
             eprintln!("      (none found)");
         } else {
-            for dir in &settings.java_src_dirs {
+            for dir in &settings.src_search_dirs {
                 eprintln!("      {}", dir.display());
             }
         }

qlty-cli/tests/cmd/coverage/discover_java_src_dirs.stderr

@@ -12,7 +12,7 @@ https://qlty.sh/d/coverage
 
     discover-java-src-dirs: true
 
-    Discovered Java source directories:
+    Source search directories:
       src/main/java
 
  METADATA 

qlty-coverage/src/lib.rs

@@ -3,17 +3,17 @@ mod env;
 pub mod export;
 pub mod formats;
 pub mod git;
-mod java_src_dir_finder;
 pub mod parser;
 pub mod print;
 pub mod publish;
+mod src_dir_finder;
 pub mod token;
 pub mod transform;
 mod transformer;
 mod utils;
 pub mod validate;
 
-pub use java_src_dir_finder::{ExclusionStrategy, JavaSrcDirFinder};
+pub use src_dir_finder::{ExclusionStrategy, SrcDirFinder};
 
 #[macro_use]
 mod macros;

qlty-coverage/src/publish/planner.rs

@@ -115,10 +115,10 @@ impl Planner {
 
         // Add PrependSrcDir transformer if Java src dirs were discovered
         // This runs after path normalization so it receives clean relative paths
-        if !self.settings.java_src_dirs.is_empty() {
+        if !self.settings.src_search_dirs.is_empty() {
             transformers.push(Box::new(PrependSrcDir::new(
                 self.settings.root.clone(),
-                self.settings.java_src_dirs.clone(),
+                self.settings.src_search_dirs.clone(),
             )));
         }
 

qlty-coverage/src/publish/settings.rs

@@ -9,7 +9,7 @@ pub struct Settings {
     pub dry_run: bool,
     pub discover_java_src_dirs: bool,
     pub root: PathBuf,
-    pub java_src_dirs: Vec<PathBuf>,
+    pub src_search_dirs: Vec<PathBuf>,
     pub incomplete: bool,
     pub name: Option<String>,
     pub output_dir: Option<PathBuf>,