Overwrite warning: confirm before replacing existing output files

Replaces the read-only fallback hack with proper UX:

Backend:
- New command 'check_output_conflicts': derives output paths from config
  (same logic as core pipeline) and returns which ones already exist.

Frontend:
- Before running, calls check_output_conflicts. If files exist, shows
  a native confirm dialog listing the filenames. User can cancel or
  proceed to overwrite. If the check fails (e.g. permission error),
  analysis proceeds anyway to let the core report the real error.

Author: Paururo

frontend/src/App.tsx

@@ -834,13 +834,31 @@ function App() {
                   <button
                     className={`run-button${justFinished ? " run-button--success" : ""}`}
                     disabled={running}
-                    onClick={() => {
+                    onClick={async () => {
                       if (!filesReady || samples.length === 0) {
                         setShowValidation(true);
                         return;
                       }
                       setShowValidation(false);
-                      (runnableCount > 0 ? handleRunAll : handleRerunAll)();
+
+                      // Check for existing output files before running
+                      if (runnableCount > 0) {
+                        try {
+                          const conflicts = await invoke<string[]>("check_output_conflicts", { config });
+                          if (conflicts.length > 0) {
+                            const names = conflicts.map((p) => p.split(/[\\/]/).pop()).join(", ");
+                            const ok = window.confirm(
+                              `The following output files already exist and will be overwritten:\n\n${names}\n\nContinue?`
+                            );
+                            if (!ok) return;
+                          }
+                        } catch {
+                          // If check fails, proceed anyway
+                        }
+                        handleRunAll();
+                      } else {
+                        handleRerunAll();
+                      }
                     }}
                   >
                     {justFinished ? (

src-tauri/src/commands.rs

@@ -136,28 +136,7 @@ pub fn run_analysis(
     app_handle: tauri::AppHandle,
     config: AnalysisConfig,
 ) -> Result<serde_json::Value, String> {
-    let mut args = config.into_args();
-
-    // If no explicit output dir, default to VCF's parent directory.
-    // If that's not writable (e.g., read-only volume, .dmg), fall back to ~/Desktop.
-    if args.output_dir.is_none() {
-        let vcf_dir = std::path::Path::new(&args.vcf_file)
-            .parent()
-            .unwrap_or(std::path::Path::new("."));
-        let test_file = vcf_dir.join(".get_mnv_write_test");
-        let writable = std::fs::write(&test_file, b"").is_ok();
-        if writable {
-            let _ = std::fs::remove_file(&test_file);
-        } else if let Ok(home) = std::env::var("HOME").or_else(|_| std::env::var("USERPROFILE")) {
-            let home_path = std::path::PathBuf::from(&home);
-            let desktop = home_path.join("Desktop");
-            if desktop.is_dir() {
-                args.output_dir = Some(desktop.to_string_lossy().into_owned());
-            } else {
-                args.output_dir = Some(home);
-            }
-        }
-    }
+    let args = config.into_args();
 
     let progress_callback = move |evt: get_mnv::pipeline::ProgressEvent| {
         let _ = app_handle.emit("analysis-progress", &evt);
@@ -169,6 +148,42 @@ pub fn run_analysis(
     serde_json::to_value(&summary).map_err(|e| format!("Failed to serialize summary: {}", e))
 }
 
+// ---------------------------------------------------------------------------
+// check_output_conflicts
+// ---------------------------------------------------------------------------
+
+/// Check if any output files already exist. Returns paths that would be overwritten.
+#[tauri::command]
+pub fn check_output_conflicts(config: AnalysisConfig) -> Vec<String> {
+    let vcf_path = std::path::Path::new(&config.vcf_file);
+
+    let base_name = vcf_path
+        .file_name()
+        .unwrap_or_default()
+        .to_string_lossy()
+        .replace(".vcf.gz", "")
+        .replace(".vcf", "");
+
+    let stem = config.output_prefix.as_deref().unwrap_or(&base_name);
+    let dir = config.output_dir.as_deref().map(std::path::Path::new)
+        .unwrap_or_else(|| vcf_path.parent().unwrap_or(std::path::Path::new(".")));
+    let base = dir.join(stem);
+
+    let mut paths = Vec::new();
+    if config.output_tsv.unwrap_or(true) {
+        paths.push(format!("{}.MNV.tsv", base.display()));
+    }
+    if config.output_vcf.unwrap_or(false) {
+        if config.vcf_gz.unwrap_or(false) {
+            paths.push(format!("{}.MNV.vcf.gz", base.display()));
+        } else {
+            paths.push(format!("{}.MNV.vcf", base.display()));
+        }
+    }
+
+    paths.into_iter().filter(|p| std::path::Path::new(p).exists()).collect()
+}
+
 // ---------------------------------------------------------------------------
 // ensure_fasta_index
 // ---------------------------------------------------------------------------

src-tauri/src/main.rs

@@ -4,8 +4,8 @@
 mod commands;
 
 use commands::{
-    ensure_fasta_index, get_bam_view, get_core_version, get_gff_features, read_tsv_file,
-    run_analysis, write_text_file,
+    check_output_conflicts, ensure_fasta_index, get_bam_view, get_core_version, get_gff_features,
+    read_tsv_file, run_analysis, write_text_file,
 };
 
 fn main() {
@@ -19,6 +19,7 @@ fn main() {
             get_core_version,
             get_gff_features,
             ensure_fasta_index,
+            check_output_conflicts,
             read_tsv_file,
             get_bam_view,
             write_text_file,