Preserve local paths for desktop saves (#5543)

# Summary

- Adds desktop file tracking: local paths are preserved and save buttons
now work as expcted (doing Save/Save As as appropriate)
- Adds logic to track whether files are 'dirty' (they've been modified
by some tool, and not saved to disk yet).
- Improves file state UX (dirty vs saved) and close warnings
- Web behaviour should be unaffected by these changes

## Indicators
Files now have indicators in desktop mode to tell you their state.

### File up-to-date with disk

<img width="318" height="393" alt="image"
src="https://github.com/user-attachments/assets/06325f9a-afd7-4c2f-8a5b-6d11e3093115"
/>

### File modified by a tool but not saved to disk yet

<img width="357" height="385" alt="image"
src="https://github.com/user-attachments/assets/1a7716d9-c6f7-4d13-be0d-c1de6493954b"
/>

### File not tracked on disk

<img width="312" height="379" alt="image"
src="https://github.com/user-attachments/assets/9cffe300-bd9a-4e19-97c7-9b98bebefacc"
/>

# Limitations
- It's a bit weird that we still have files stored in indexeddb in the
app, which are still loadable. We might want to change this behaviour in
the future
- Viewer's Save doesn't persist to disk. I've left that out here because
it'd need a lot of testing to make sure the logic's right with making
sure you can leave the Viewer with applying the changes to the PDF
_without_ saving to disk
- There's no current way to do Save As on a file that has already been
persisted to disk - it's only ever Save. Similarly, there's no way to
duplicate a file.

---------

Co-authored-by: James Brunton <[email protected]>
Co-authored-by: James Brunton <[email protected]>

CLAUDE.md

@@ -30,6 +30,91 @@ Set `DOCKER_ENABLE_SECURITY=true` environment variable to enable security featur
   - **Web Server**: `npm run build` then serve dist/ folder
   - **Development**: `npm run tauri-dev` for desktop dev mode
 
+#### Import Paths - CRITICAL
+**ALWAYS use `@app/*` for imports.** Do not use `@core/*` or `@proprietary/*` unless explicitly wrapping/extending a lower layer implementation.
+
+```typescript
+// ✅ CORRECT - Use @app/* for all imports
+import { AppLayout } from "@app/components/AppLayout";
+import { useFileContext } from "@app/contexts/FileContext";
+import { FileContext } from "@app/contexts/FileContext";
+
+// ❌ WRONG - Do not use @core/* or @proprietary/* in normal code
+import { AppLayout } from "@core/components/AppLayout";
+import { useFileContext } from "@proprietary/contexts/FileContext";
+```
+
+**Only use explicit aliases when:**
+- Building layer-specific override that wraps a lower layer's component
+- Example: `import { AppProviders as CoreAppProviders } from "@core/components/AppProviders"` when creating proprietary/AppProviders.tsx that extends the core version
+
+The `@app/*` alias automatically resolves to the correct layer based on build target (core/proprietary/desktop) and handles the fallback cascade.
+
+#### Component Override Pattern (Stub/Shadow)
+Use this pattern for desktop-specific or proprietary-specific features WITHOUT runtime checks or conditionals.
+
+**How it works:**
+1. Core defines stub component (returns null or no-op)
+2. Desktop/proprietary overrides with same path/name
+3. Core imports via `@app/*` - higher layer "shadows" core in those builds
+4. No `@ts-ignore`, no `isTauri()` checks, no runtime conditionals!
+
+**Example - Desktop-specific footer:**
+
+```typescript
+// core/components/rightRail/RightRailFooterExtensions.tsx (stub)
+interface RightRailFooterExtensionsProps {
+  className?: string;
+}
+
+export function RightRailFooterExtensions(_props: RightRailFooterExtensionsProps) {
+  return null; // Stub - does nothing in web builds
+}
+```
+
+```typescript
+// desktop/components/rightRail/RightRailFooterExtensions.tsx (real implementation)
+import { Box } from '@mantine/core';
+import { BackendHealthIndicator } from '@app/components/BackendHealthIndicator';
+
+interface RightRailFooterExtensionsProps {
+  className?: string;
+}
+
+export function RightRailFooterExtensions({ className }: RightRailFooterExtensionsProps) {
+  return (
+    <Box className={className}>
+      <BackendHealthIndicator />
+    </Box>
+  );
+}
+```
+
+```typescript
+// core/components/shared/RightRail.tsx (usage - works in ALL builds)
+import { RightRailFooterExtensions } from '@app/components/rightRail/RightRailFooterExtensions';
+
+export function RightRail() {
+  return (
+    <div>
+      {/* In web builds: renders nothing (stub returns null) */}
+      {/* In desktop builds: renders BackendHealthIndicator */}
+      <RightRailFooterExtensions className="right-rail-footer" />
+    </div>
+  );
+}
+```
+
+**Build resolution:**
+- **Core build**: `@app/*` → `core/*` → Gets stub (returns null)
+- **Desktop build**: `@app/*` → `desktop/*` → Gets real implementation (shadows core)
+
+**Benefits:**
+- No runtime checks or feature flags
+- Type-safe across all builds
+- Clean, readable code
+- Build-time optimization (dead code elimination)
+
 #### Multi-Tool Workflow Architecture
 Frontend designed for **stateful document processing**:
 - Users upload PDFs once, then chain tools (split → merge → compress → view)
@@ -37,7 +122,7 @@ Frontend designed for **stateful document processing**:
 - No file reloading between tools - performance critical for large PDFs (up to 100GB+)
 
 #### FileContext - Central State Management
-**Location**: `src/contexts/FileContext.tsx`
+**Location**: `frontend/src/core/contexts/FileContext.tsx`
 - **Active files**: Currently loaded PDFs and their variants
 - **Tool navigation**: Current mode (viewer/pageEditor/fileEditor/toolName)
 - **Memory management**: PDF document cleanup, blob URL lifecycle, Web Worker management
@@ -62,7 +147,7 @@ Without cleanup: browser crashes with memory leaks.
 
 **Architecture**: Modular hook-based system with clear separation of concerns:
 
-- **useToolOperation** (`frontend/src/hooks/tools/shared/useToolOperation.ts`): Main orchestrator hook
+- **useToolOperation** (`frontend/src/core/hooks/tools/shared/useToolOperation.ts`): Main orchestrator hook
   - Coordinates all tool operations with consistent interface
   - Integrates with FileContext for operation tracking
   - Handles validation, error handling, and UI state management
@@ -147,8 +232,34 @@ return useToolOperation({
 - **Pipeline System**: Automated PDF processing workflows via `PipelineController`
 - **Security Layer**: Authentication, authorization, and user management (when enabled)
 
+### Frontend Directory Structure
+The frontend is organized with a clear separation of concerns:
+
+- **`frontend/src/core/`**: Main application code (shared, production-ready components)
+  - **`core/components/`**: React components organized by feature
+    - `core/components/tools/`: Individual PDF tool implementations
+    - `core/components/viewer/`: PDF viewer components
+    - `core/components/pageEditor/`: Page manipulation UI
+    - `core/components/tooltips/`: Help tooltips for tools
+    - `core/components/shared/`: Reusable UI components
+  - **`core/contexts/`**: React Context providers
+    - `FileContext.tsx`: Central file state management
+    - `file/`: File reducer and selectors
+    - `toolWorkflow/`: Tool workflow state
+  - **`core/hooks/`**: Custom React hooks
+    - `hooks/tools/`: Tool-specific operation hooks (one directory per tool)
+    - `hooks/tools/shared/`: Shared hook utilities (useToolOperation, etc.)
+  - **`core/constants/`**: Application constants and configuration
+  - **`core/data/`**: Static data (tool taxonomy, etc.)
+  - **`core/services/`**: Business logic services (PDF processing, storage, etc.)
+
+- **`frontend/src/desktop/`**: Desktop-specific (Tauri) code
+- **`frontend/src/proprietary/`**: Proprietary/licensed features
+- **`frontend/src-tauri/`**: Tauri (Rust) native desktop application code
+- **`frontend/public/`**: Static assets served directly
+  - `public/locales/`: Translation JSON files
+
 ### Component Architecture
-- **React Components**: Located in `frontend/src/components/` and `frontend/src/tools/`
 - **Static Assets**: CSS, JS, and resources in `src/main/resources/static/` (legacy) + `frontend/public/` (modern)
 - **Internationalization**:
   - Backend: `messages_*.properties` files
@@ -203,6 +314,7 @@ return useToolOperation({
   - **Backend**: Designed to be stateless - files are processed in memory/temp locations only
   - **Frontend**: Uses IndexedDB for client-side file storage and caching (with thumbnails)
 - **Security**: When `DOCKER_ENABLE_SECURITY=false`, security-related classes are excluded from compilation
+- **Import Paths**: ALWAYS use `@app/*` for imports - never use `@core/*` or `@proprietary/*` unless explicitly wrapping/extending a lower layer
 - **FileContext**: All file operations MUST go through FileContext - never bypass with direct File handling
 - **Memory Management**: Manual cleanup required for PDF.js documents and blob URLs - don't remove cleanup code
 - **Tool Development**: New tools should follow `useToolOperation` hook pattern (see `useCompressOperation.ts`)

frontend/package-lock.json

@@ -50,6 +50,7 @@
         "@tailwindcss/postcss": "^4.1.13",
         "@tanstack/react-virtual": "^3.13.12",
         "@tauri-apps/api": "^2.9.1",
+        "@tauri-apps/plugin-dialog": "^2.6.0",
         "@tauri-apps/plugin-fs": "^2.4.5",
         "@tauri-apps/plugin-http": "^2.5.6",
         "@tauri-apps/plugin-shell": "^2.3.4",
@@ -4198,6 +4199,15 @@
         "node": ">= 10"
       }
     },
+    "node_modules/@tauri-apps/plugin-dialog": {
+      "version": "2.6.0",
+      "resolved": "https://registry.npmjs.org/@tauri-apps/plugin-dialog/-/plugin-dialog-2.6.0.tgz",
+      "integrity": "sha512-q4Uq3eY87TdcYzXACiYSPhmpBA76shgmQswGkSVio4C82Sz2W4iehe9TnKYwbq7weHiL88Yw19XZm7v28+Micg==",
+      "license": "MIT OR Apache-2.0",
+      "dependencies": {
+        "@tauri-apps/api": "^2.8.0"
+      }
+    },
     "node_modules/@tauri-apps/plugin-fs": {
       "version": "2.4.5",
       "resolved": "https://registry.npmjs.org/@tauri-apps/plugin-fs/-/plugin-fs-2.4.5.tgz",

frontend/package.json

@@ -46,6 +46,7 @@
     "@tailwindcss/postcss": "^4.1.13",
     "@tanstack/react-virtual": "^3.13.12",
     "@tauri-apps/api": "^2.9.1",
+    "@tauri-apps/plugin-dialog": "^2.6.0",
     "@tauri-apps/plugin-fs": "^2.4.5",
     "@tauri-apps/plugin-http": "^2.5.6",
     "@tauri-apps/plugin-shell": "^2.3.4",

frontend/public/locales/en-GB/translation.toml

@@ -17,6 +17,12 @@ confirmClose = "Confirm Close"
 confirmCloseCancel = "Cancel"
 confirmCloseConfirm = "Close File"
 confirmCloseMessage = "Are you sure you want to close this file?"
+confirmCloseDiscard = "Discard changes and close"
+confirmCloseSave = "Save and close"
+confirmCloseUnsaved = "This file has unsaved changes."
+confirmCloseUnsavedList = "You have {{count}} file{{plural}} with unsaved changes.\n\n{{fileList}}"
+confirmCloseSaveFailedTitle = "Save Failed"
+confirmCloseSaveFailed = "Saved with errors. {{count}} file{{plural}} could not be saved."
 confirmPasswordErrorMessage = "New Password and Confirm New Password must match."
 custom = "Custom..."
 customPosition = "Custom Position"
@@ -39,6 +45,8 @@ edit = "Edit"
 editYourNewFiles = "Edit your new file(s)"
 exportAndContinue = "Export & Continue"
 false = "False"
+fileSavedToDisk = "File saved to disk"
+fileNotSavedToDisk = "Not saved to disk"
 fileSelected = "Selected: {{filename}}"
 filesSelected = "{{count}} files selected"
 font = "Font"

frontend/src-tauri/Cargo.lock

@@ -907,6 +907,8 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "89a09f22a6c6069a18470eb92d2298acf25463f14256d24778e1230d789a2aec"
 dependencies = [
  "bitflags 2.10.0",
+ "block2",
+ "libc",
  "objc2",
 ]
 
@@ -3531,6 +3533,30 @@ dependencies = [
  "webpki-roots 1.0.5",
 ]
 
+[[package]]
+name = "rfd"
+version = "0.16.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a15ad77d9e70a92437d8f74c35d99b4e4691128df018833e99f90bcd36152672"
+dependencies = [
+ "block2",
+ "dispatch2",
+ "glib-sys",
+ "gobject-sys",
+ "gtk-sys",
+ "js-sys",
+ "log",
+ "objc2",
+ "objc2-app-kit",
+ "objc2-core-foundation",
+ "objc2-foundation",
+ "raw-window-handle",
+ "wasm-bindgen",
+ "wasm-bindgen-futures",
+ "web-sys",
+ "windows-sys 0.60.2",
+]
+
 [[package]]
 name = "ring"
 version = "0.17.14"
@@ -4229,6 +4255,7 @@ dependencies = [
  "tauri",
  "tauri-build",
  "tauri-plugin-deep-link",
+ "tauri-plugin-dialog",
  "tauri-plugin-fs",
  "tauri-plugin-http",
  "tauri-plugin-log",
@@ -4609,6 +4636,24 @@ dependencies = [
  "windows-result 0.3.4",
 ]
 
+[[package]]
+name = "tauri-plugin-dialog"
+version = "2.6.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9204b425d9be8d12aa60c2a83a289cf7d1caae40f57f336ed1155b3a5c0e359b"
+dependencies = [
+ "log",
+ "raw-window-handle",
+ "rfd",
+ "serde",
+ "serde_json",
+ "tauri",
+ "tauri-plugin",
+ "tauri-plugin-fs",
+ "thiserror 2.0.18",
+ "url",
+]
+
 [[package]]
 name = "tauri-plugin-fs"
 version = "2.4.5"

frontend/src-tauri/Cargo.toml

@@ -28,6 +28,7 @@ tauri = { version = "2.9.0", features = [ "devtools"] }
 tauri-plugin-log = "2.8.0"
 tauri-plugin-shell = "2.3.4"
 tauri-plugin-fs = "2.4.5"
+tauri-plugin-dialog = "2.4.2"
 tauri-plugin-http = { version = "2.5.6", features = ["dangerous-settings"] }
 tauri-plugin-single-instance = { version = "2.3.7", features = ["deep-link"] }
 tauri-plugin-store = "2.4.2"

frontend/src-tauri/capabilities/default.json

@@ -7,6 +7,7 @@
   ],
   "permissions": [
     "core:default",
+    "core:window:allow-destroy",
     "http:default",
     {
       "identifier": "http:allow-fetch",
@@ -40,6 +41,18 @@
       "identifier": "fs:allow-read-file",
       "allow": [{ "path": "**" }]
     },
+    {
+      "identifier": "fs:allow-write-file",
+      "allow": [{ "path": "**" }]
+    },
+    {
+      "identifier": "fs:allow-remove",
+      "allow": [{ "path": "**" }]
+    },
+    "dialog:default",
+    "dialog:allow-message",
+    "dialog:allow-open",
+    "dialog:allow-save",
     "opener:default",
     "shell:allow-open"
   ]

frontend/src-tauri/src/commands/files.rs

@@ -33,3 +33,12 @@ pub async fn clear_opened_files() -> Result<(), String> {
     Ok(())
 }
 
+// Command to atomically get and clear opened file paths
+#[tauri::command]
+pub async fn pop_opened_files() -> Result<Vec<String>, String> {
+    let mut opened_files = OPENED_FILES.lock().unwrap();
+    let all_files = opened_files.clone();
+    opened_files.clear();
+    add_log(format!("📂 Returning and clearing {} opened file(s)", all_files.len()));
+    Ok(all_files)
+}

frontend/src-tauri/src/commands/mod.rs

@@ -5,7 +5,7 @@ pub mod auth;
 pub mod default_app;
 
 pub use backend::{cleanup_backend, get_backend_port, start_backend};
-pub use files::{add_opened_file, clear_opened_files, get_opened_files};
+pub use files::{add_opened_file, clear_opened_files, get_opened_files, pop_opened_files};
 pub use connection::{
     get_connection_config,
     is_first_launch,

frontend/src-tauri/src/lib.rs

@@ -16,6 +16,7 @@ use commands::{
     get_backend_port,
     get_connection_config,
     get_opened_files,
+    pop_opened_files,
     get_refresh_token,
     get_user_info,
     is_first_launch,
@@ -55,6 +56,7 @@ pub fn run() {
     .plugin(tauri_plugin_opener::init())
     .plugin(tauri_plugin_shell::init())
     .plugin(tauri_plugin_fs::init())
+    .plugin(tauri_plugin_dialog::init())
     .plugin(tauri_plugin_http::init())
     .plugin(tauri_plugin_store::Builder::new().build())
     .plugin(tauri_plugin_deep_link::init())
@@ -139,6 +141,7 @@ pub fn run() {
       start_backend,
       get_backend_port,
       get_opened_files,
+      pop_opened_files,
       clear_opened_files,
       get_tauri_logs,
       get_connection_config,
@@ -170,9 +173,9 @@ pub fn run() {
           app_handle.cleanup_before_exit();
         }
         RunEvent::WindowEvent { event: WindowEvent::CloseRequested {.. }, .. } => {
-          add_log("🔄 Window close requested, cleaning up...".to_string());
-          cleanup_backend();
-          // Allow the window to close
+          add_log("🔄 Window close requested (will cleanup on actual exit)...".to_string());
+          // Don't cleanup here - let JavaScript handler prevent close if needed
+          // Backend cleanup happens in ExitRequested when window actually closes
         }
         RunEvent::WindowEvent { event: WindowEvent::DragDrop(drag_drop_event), .. } => {
           use tauri::DragDropEvent;

frontend/src/core/components/fileEditor/AddFileCard.tsx

@@ -8,6 +8,7 @@ import { useLogoAssets } from '@app/hooks/useLogoAssets';
 import styles from '@app/components/fileEditor/FileEditor.module.css';
 import { useFileActionTerminology } from '@app/hooks/useFileActionTerminology';
 import { useFileActionIcons } from '@app/hooks/useFileActionIcons';
+import { openFilesFromDisk } from '@app/services/openFilesFromDisk';
 
 interface AddFileCardProps {
   onFileSelect: (files: File[]) => void;
@@ -33,9 +34,15 @@ const AddFileCard = ({
     openFilesModal();
   };
 
-  const handleNativeUploadClick = (e: React.MouseEvent) => {
+  const handleNativeUploadClick = async (e: React.MouseEvent) => {
     e.stopPropagation();
-    fileInputRef.current?.click();
+    const files = await openFilesFromDisk({
+      multiple,
+      onFallbackOpen: () => fileInputRef.current?.click()
+    });
+    if (files.length > 0) {
+      onFileSelect(files);
+    }
   };
 
   const handleOpenFilesModal = (e: React.MouseEvent) => {
@@ -179,4 +186,4 @@ const AddFileCard = ({
   );
 };
 
-export default AddFileCard;
+export default AddFileCard;

frontend/src/core/components/fileEditor/FileEditor.tsx

@@ -12,7 +12,7 @@ import AddFileCard from '@app/components/fileEditor/AddFileCard';
 import FilePickerModal from '@app/components/shared/FilePickerModal';
 import { FileId, StirlingFile } from '@app/types/fileContext';
 import { alert } from '@app/components/toast';
-import { downloadBlob } from '@app/utils/downloadUtils';
+import { downloadFile } from '@app/services/downloadService';
 import { useFileEditorRightRailButtons } from '@app/components/fileEditor/fileEditorRightRailButtons';
 import { useToolWorkflow } from '@app/contexts/ToolWorkflowContext';
 
@@ -278,13 +278,29 @@ const FileEditor = ({
     }
   }, [activeStirlingFileStubs, selectors, removeFiles, setSelectedFiles, selectedFileIds]);
 
-  const handleDownloadFile = useCallback((fileId: FileId) => {
+  const handleDownloadFile = useCallback(async (fileId: FileId) => {
     const record = activeStirlingFileStubs.find(r => r.id === fileId);
     const file = record ? selectors.getFile(record.id) : null;
+    console.log('[FileEditor] handleDownloadFile called:', { fileId, hasRecord: !!record, hasFile: !!file, localFilePath: record?.localFilePath, isDirty: record?.isDirty });
     if (record && file) {
-       downloadBlob(file, file.name);
+      const result = await downloadFile({
+        data: file,
+        filename: file.name,
+        localPath: record.localFilePath
+      });
+      console.log('[FileEditor] Download complete, checking dirty state:', { localFilePath: record.localFilePath, isDirty: record.isDirty, savedPath: result.savedPath });
+      // Mark file as clean after successful save to disk
+      if (result.savedPath) {
+        console.log('[FileEditor] Marking file as clean:', fileId);
+        fileActions.updateStirlingFileStub(fileId, {
+          localFilePath: record.localFilePath ?? result.savedPath,
+          isDirty: false
+        });
+      } else {
+        console.log('[FileEditor] Skipping clean mark:', { savedPath: result.savedPath, isDirty: record.isDirty });
+      }
     }
-  }, [activeStirlingFileStubs, selectors, _setStatus]);
+  }, [activeStirlingFileStubs, selectors, fileActions]);
 
   const handleUnzipFile = useCallback(async (fileId: FileId) => {
     const record = activeStirlingFileStubs.find(r => r.id === fileId);

frontend/src/core/components/fileEditor/FileEditorFileName.tsx

@@ -0,0 +1,13 @@
+import React from 'react';
+import { StirlingFileStub } from '@app/types/fileContext';
+import { PrivateContent } from '@app/components/shared/PrivateContent';
+
+interface FileEditorFileNameProps {
+  file: StirlingFileStub;
+}
+
+const FileEditorFileName = ({ file }: FileEditorFileNameProps) => (
+  <PrivateContent>{file.name}</PrivateContent>
+);
+
+export default FileEditorFileName;

frontend/src/core/components/fileEditor/FileEditorThumbnail.tsx

@@ -23,6 +23,8 @@ import { FileId } from '@app/types/file';
 import { formatFileSize } from '@app/utils/fileUtils';
 import ToolChain from '@app/components/shared/ToolChain';
 import HoverActionMenu, { HoverAction } from '@app/components/shared/HoverActionMenu';
+import { downloadFile } from '@app/services/downloadService';
+import FileEditorFileName from '@app/components/fileEditor/FileEditorFileName';
 import { PrivateContent } from '@app/components/shared/PrivateContent';
 
 
@@ -69,7 +71,7 @@ const FileEditorThumbnail = ({
     actions: fileActions,
     openEncryptedUnlockPrompt,
   } = useFileContext();
-  const { state } = useFileState();
+  const { state, selectors } = useFileState();
   const hasError = state.ui.errorFileIds.includes(file.id);
 
   // ---- Drag state ----
@@ -191,6 +193,37 @@ const FileEditorThumbnail = ({
     setShowCloseModal(false);
   }, [file.id, file.name, onCloseFile]);
 
+  const handleSaveAndClose = useCallback(async () => {
+    const fileToSave = selectors.getFile(file.id);
+    if (fileToSave) {
+      try {
+        const result = await downloadFile({
+          data: fileToSave,
+          filename: file.name,
+          localPath: file.localFilePath
+        });
+        if (!result.cancelled && result.savedPath) {
+          fileActions.updateStirlingFileStub(file.id, {
+            localFilePath: file.localFilePath ?? result.savedPath,
+            isDirty: false
+          });
+        } else if (result.cancelled) {
+          setShowCloseModal(false);
+          return;
+        }
+      } catch (error) {
+        console.error(`Failed to save ${file.name}:`, error);
+        alert({ alertType: 'error', title: 'Save failed', body: `Could not save ${file.name}`, expandable: true });
+        setShowCloseModal(false);
+        return;
+      }
+    }
+    // Then close
+    onCloseFile(file.id);
+    alert({ alertType: 'success', title: `Saved and closed ${file.name}`, expandable: false, durationMs: 3500 });
+    setShowCloseModal(false);
+  }, [file.id, file.name, file.localFilePath, onCloseFile, selectors, fileActions]);
+
   const handleCancelClose = useCallback(() => {
     setShowCloseModal(false);
   }, []);
@@ -213,7 +246,6 @@ const FileEditorThumbnail = ({
       onClick: (e) => {
         e.stopPropagation();
         onDownloadFile(file.id);
-        alert({ alertType: 'success', title: `Downloading ${file.name}`, expandable: false, durationMs: 2500 });
       },
     },
     {
@@ -365,8 +397,8 @@ const FileEditorThumbnail = ({
         marginTop: '0.5rem',
         marginBottom: '0.5rem',
       }}>
-        <Text  size="lg" fw={700} className={styles.title}  lineClamp={2}>
-          <PrivateContent>{file.name}</PrivateContent>
+        <Text  size="lg" fw={700} className={styles.title}  lineClamp={2} style={{ display: 'flex', alignItems: 'center', justifyContent: 'center', gap: '0.25rem' }}>
+          <FileEditorFileName file={file} />
         </Text>
         <Text
           size="sm"
@@ -469,18 +501,40 @@ const FileEditorThumbnail = ({
         size="auto"
       >
         <Stack gap="md">
-          <Text size="md">{t('confirmCloseMessage', 'Are you sure you want to close this file?')}</Text>
-          <Text size="sm" c="dimmed" fw={500}>
-            {file.name}
-          </Text>
-          <Group justify="flex-end" gap="sm">
-            <Button variant="light" onClick={handleCancelClose}>
-              {t('confirmCloseCancel', 'Cancel')}
-            </Button>
-            <Button variant="filled" color="red" onClick={handleConfirmClose}>
-              {t('confirmCloseConfirm', 'Close File')}
-            </Button>
-          </Group>
+          {file.isDirty && file.localFilePath ? (
+            <>
+              <Text size="md">{t('confirmCloseUnsaved', 'This file has unsaved changes.')}</Text>
+              <Text size="sm" c="dimmed" fw={500}>
+                {file.name}
+              </Text>
+              <Group justify="flex-end" gap="sm">
+                <Button variant="light" onClick={handleCancelClose}>
+                  {t('confirmCloseCancel', 'Cancel')}
+                </Button>
+                <Button variant="filled" color="red" onClick={handleConfirmClose}>
+                  {t('confirmCloseDiscard', 'Discard changes and close')}
+                </Button>
+                <Button variant="filled" onClick={handleSaveAndClose}>
+                  {t('confirmCloseSave', 'Save and close')}
+                </Button>
+              </Group>
+            </>
+          ) : (
+            <>
+              <Text size="md">{t('confirmCloseMessage', 'Are you sure you want to close this file?')}</Text>
+              <Text size="sm" c="dimmed" fw={500}>
+                {file.name}
+              </Text>
+              <Group justify="flex-end" gap="sm">
+                <Button variant="light" onClick={handleCancelClose}>
+                  {t('confirmCloseCancel', 'Cancel')}
+                </Button>
+                <Button variant="filled" color="red" onClick={handleConfirmClose}>
+                  {t('confirmCloseConfirm', 'Close File')}
+                </Button>
+              </Group>
+            </>
+          )}
         </Stack>
       </Modal>
     </div>

frontend/src/core/components/fileManager/FileActions.tsx

@@ -12,8 +12,14 @@ const FileActions: React.FC = () => {
   const terminology = useFileActionTerminology();
   const icons = useFileActionIcons();
   const DownloadIcon = icons.download;
-  const { recentFiles, selectedFileIds, filteredFiles, onSelectAll, onDeleteSelected, onDownloadSelected } =
-    useFileManagerContext();
+  const {
+    recentFiles,
+    selectedFileIds,
+    filteredFiles,
+    onSelectAll,
+    onDeleteSelected,
+    onDownloadSelected
+  } = useFileManagerContext();
 
   const handleSelectAll = () => {
     onSelectAll();
@@ -31,6 +37,7 @@ const FileActions: React.FC = () => {
     }
   };
 
+
   // Only show actions if there are files
   if (recentFiles.length === 0) {
     return null;

frontend/src/core/components/fileManager/FileListItem.tsx

@@ -46,7 +46,7 @@ const FileListItem: React.FC<FileListItemProps> = ({
   const [isHovered, setIsHovered] = useState(false);
   const [isMenuOpen, setIsMenuOpen] = useState(false);
   const { t } = useTranslation();
-  const {expandedFileIds, onToggleExpansion, onUnzipFile } = useFileManagerContext();
+  const { expandedFileIds, onToggleExpansion, onUnzipFile } = useFileManagerContext();
   const { removeFiles } = useFileManagement();
 
   // Check if this is a ZIP file
@@ -269,6 +269,7 @@ const FileListItem: React.FC<FileListItemProps> = ({
               >
                 {t('fileManager.delete', 'Delete')}
               </Menu.Item>
+
             </Menu.Dropdown>
           </Menu>
         </Group>

frontend/src/core/components/pageEditor/FileThumbnail.tsx

@@ -14,6 +14,7 @@ import { FileId } from '@app/types/file';
 import { PrivateContent } from '@app/components/shared/PrivateContent';
 import { useFileActionTerminology } from '@app/hooks/useFileActionTerminology';
 import { useFileActionIcons } from '@app/hooks/useFileActionIcons';
+import { downloadFile } from '@app/services/downloadService';
 
 interface FileItem {
   id: FileId;
@@ -79,13 +80,7 @@ const FileThumbnail = ({
     // Fallback: attempt to download using the File object if provided
     const maybeFile = (file as unknown as { file?: File }).file;
     if (maybeFile instanceof File) {
-      const link = document.createElement('a');
-      link.href = URL.createObjectURL(maybeFile);
-      link.download = maybeFile.name || file.name || 'download';
-      document.body.appendChild(link);
-      link.click();
-      document.body.removeChild(link);
-      URL.revokeObjectURL(link.href);
+      void downloadFile({ data: maybeFile, filename: maybeFile.name || file.name || 'download' });
       return;
     }
 

frontend/src/core/components/pageEditor/hooks/usePageEditorExport.ts

@@ -295,6 +295,21 @@ export const usePageEditorExport = ({
         actions.setSelectedFiles(newStirlingFiles.map((file) => file.fileId));
       }
 
+      if (sourceFileIds.length === 1 && newStirlingFiles.length === 1) {
+        const sourceStub = selectors.getStirlingFileStub(sourceFileIds[0]);
+        if (sourceStub?.localFilePath) {
+          actions.updateStirlingFileStub(newStirlingFiles[0].fileId, {
+            localFilePath: sourceStub.localFilePath,
+            isDirty: true
+          });
+        }
+      }
+
+      // Remove source files from context
+      if (sourceFileIds.length > 0) {
+        await actions.removeFiles(sourceFileIds, true);
+      }
+
       setHasUnsavedChanges(false);
       setSplitPositions(new Set());
       setExportLoading(false);

frontend/src/core/components/shared/LandingPage.tsx

@@ -14,6 +14,7 @@ import { useFileActionIcons } from '@app/hooks/useFileActionIcons';
 import { useAppConfig } from '@app/contexts/AppConfigContext';
 import { useIsMobile } from '@app/hooks/useIsMobile';
 import MobileUploadModal from '@app/components/shared/MobileUploadModal';
+import { openFilesFromDisk } from '@app/services/openFilesFromDisk';
 
 const LandingPage = () => {
   const { addFiles } = useFileHandler();
@@ -41,8 +42,14 @@ const LandingPage = () => {
     openFilesModal();
   };
 
-  const handleNativeUploadClick = () => {
-    fileInputRef.current?.click();
+  const handleNativeUploadClick = async () => {
+    const files = await openFilesFromDisk({
+      multiple: true,
+      onFallbackOpen: () => fileInputRef.current?.click()
+    });
+    if (files.length > 0) {
+      await addFiles(files);
+    }
   };
 
   const handleFileSelect = async (event: React.ChangeEvent<HTMLInputElement>) => {

frontend/src/core/components/shared/RightRail.tsx

@@ -3,7 +3,7 @@ import { ActionIcon, Divider } from '@mantine/core';
 import '@app/components/shared/rightRail/RightRail.css';
 import { useToolWorkflow } from '@app/contexts/ToolWorkflowContext';
 import { useRightRail } from '@app/contexts/RightRailContext';
-import { useFileState, useFileSelection } from '@app/contexts/FileContext';
+import { useFileState, useFileSelection, useFileActions } from '@app/contexts/FileContext';
 import { useNavigationState } from '@app/contexts/NavigationContext';
 import { useTranslation } from 'react-i18next';
 import { useFileActionTerminology } from '@app/hooks/useFileActionTerminology';
@@ -22,6 +22,7 @@ import LightModeIcon from '@mui/icons-material/LightMode';
 import { useSidebarContext } from '@app/contexts/SidebarContext';
 import { RightRailButtonConfig, RightRailRenderContext, RightRailSection } from '@app/types/rightRail';
 import { useRightRailTooltipSide } from '@app/hooks/useRightRailTooltipSide';
+import { downloadFile } from '@app/services/downloadService';
 
 const SECTION_ORDER: RightRailSection[] = ['top', 'middle', 'bottom'];
 
@@ -59,6 +60,7 @@ export default function RightRail() {
 
   const { selectors } = useFileState();
   const { selectedFiles, selectedFileIds } = useFileSelection();
+  const { actions: fileActions } = useFileActions();
   const { signaturesApplied } = useSignature();
 
   const activeFiles = selectors.getFiles();
@@ -141,7 +143,7 @@ export default function RightRail() {
         alert('You have unapplied signatures. Please use "Apply Signatures" first before exporting.');
         return;
       }
-      viewerContext?.exportActions?.download();
+      viewerContext?.exportActions?.download?.();
       return;
     }
 
@@ -150,23 +152,43 @@ export default function RightRail() {
       return;
     }
 
-    const filesToDownload = selectedFiles.length > 0 ? selectedFiles : activeFiles;
-    filesToDownload.forEach(file => {
-      const link = document.createElement('a');
-      link.href = URL.createObjectURL(file);
-      link.download = file.name;
-      document.body.appendChild(link);
-      link.click();
-      document.body.removeChild(link);
-      URL.revokeObjectURL(link.href);
-    });
+    const filesToExport = selectedFiles.length > 0 ? selectedFiles : activeFiles;
+    const stubsToExport = selectedFiles.length > 0
+      ? selectors.getSelectedStirlingFileStubs()
+      : selectors.getStirlingFileStubs();
+
+    if (filesToExport.length > 0) {
+      for (let i = 0; i < filesToExport.length; i++) {
+        const file = filesToExport[i];
+        const stub = stubsToExport[i];
+        console.log('[RightRail] Exporting file:', { fileName: file.name, stubId: stub?.id, localFilePath: stub?.localFilePath, isDirty: stub?.isDirty });
+        const result = await downloadFile({
+          data: file,
+          filename: file.name,
+          localPath: stub?.localFilePath
+        });
+        console.log('[RightRail] Export complete, checking dirty state:', { localFilePath: stub?.localFilePath, isDirty: stub?.isDirty, savedPath: result.savedPath });
+        // Mark file as clean after successful save to disk
+        if (stub && result.savedPath) {
+          console.log('[RightRail] Marking file as clean:', stub.id);
+          fileActions.updateStirlingFileStub(stub.id, {
+            localFilePath: stub.localFilePath ?? result.savedPath,
+            isDirty: false
+          });
+        } else {
+          console.log('[RightRail] Skipping clean mark:', { savedPath: result.savedPath, isDirty: stub?.isDirty });
+        }
+      }
+    }
   }, [
     currentView,
     selectedFiles,
     activeFiles,
     pageEditorFunctions,
     viewerContext,
-    signaturesApplied
+    signaturesApplied,
+    selectors,
+    fileActions,
   ]);
 
   const downloadTooltip = useMemo(() => {

frontend/src/core/components/tools/editTableOfContents/EditTableOfContentsWorkbenchView.tsx

@@ -15,6 +15,7 @@ import ErrorNotification from '@app/components/tools/shared/ErrorNotification';
 import ResultsPreview from '@app/components/tools/shared/ResultsPreview';
 import BookmarkEditor from '@app/components/tools/editTableOfContents/BookmarkEditor';
 import { useFileActionTerminology } from '@app/hooks/useFileActionTerminology';
+import { downloadFromUrl } from '@app/services/downloadService';
 
 export interface EditTableOfContentsWorkbenchViewData {
   bookmarks: BookmarkNode[];
@@ -177,10 +178,8 @@ const EditTableOfContentsWorkbenchView = ({ data }: EditTableOfContentsWorkbench
               <Group justify="flex-end" gap="sm">
                 {downloadUrl && (
                   <Button
-                    component="a"
-                    href={downloadUrl}
-                    download={downloadFilename ?? undefined}
                     leftSection={<LocalIcon icon='download-rounded' />}
+                    onClick={() => downloadFromUrl(downloadUrl, downloadFilename ?? "download")}
                   >
                     {terminology.download}
                   </Button>

frontend/src/core/components/tools/getPdfInfo/GetPdfInfoResults.tsx

@@ -2,6 +2,7 @@ import { useCallback, useMemo } from 'react';
 import { Alert, Button, Group, Loader, Stack, Text } from '@mantine/core';
 import { useTranslation } from 'react-i18next';
 import type { GetPdfInfoOperationHook } from '@app/hooks/tools/getPdfInfo/useGetPdfInfoOperation';
+import { downloadFile } from '@app/services/downloadService';
 
 interface GetPdfInfoResultsProps {
   operation: GetPdfInfoOperationHook;
@@ -21,14 +22,7 @@ const GetPdfInfoResults = ({ operation, isLoading, errorMessage }: GetPdfInfoRes
   const selectedDownloadLabel = useMemo(() => t('getPdfInfo.downloadJson', 'Download JSON'), [t]);
 
   const handleDownload = useCallback((file: File) => {
-    const blobUrl = URL.createObjectURL(file);
-    const link = document.createElement('a');
-    link.href = blobUrl;
-    link.download = file.name;
-    document.body.appendChild(link);
-    link.click();
-    document.body.removeChild(link);
-    URL.revokeObjectURL(blobUrl);
+    void downloadFile({ data: file, filename: file.name });
   }, []);
 
   if (isLoading && operation.results.length === 0) {
@@ -76,4 +70,3 @@ const GetPdfInfoResults = ({ operation, isLoading, errorMessage }: GetPdfInfoRes
 
 export default GetPdfInfoResults;
 
-

frontend/src/core/components/tools/shared/ReviewToolStep.tsx

@@ -9,6 +9,9 @@ import { ToolOperationHook } from "@app/hooks/tools/shared/useToolOperation";
 import { Tooltip } from "@app/components/shared/Tooltip";
 import { useFileActionTerminology } from "@app/hooks/useFileActionTerminology";
 import { useFileActionIcons } from "@app/hooks/useFileActionIcons";
+import { saveOperationResults } from "@app/services/operationResultsSaveService";
+import { useFileActions, useFileState } from "@app/contexts/FileContext";
+import { FileId } from "@app/types/fileContext";
 
 export interface ReviewToolStepProps<TParams = unknown> {
   isVisible: boolean;
@@ -34,6 +37,8 @@ function ReviewStepContent<TParams = unknown>({
   const icons = useFileActionIcons();
   const DownloadIcon = icons.download;
   const stepRef = useRef<HTMLDivElement>(null);
+  const { actions: fileActions } = useFileActions();
+  const { selectors } = useFileState();
 
   const handleUndo = async () => {
     try {
@@ -50,6 +55,31 @@ function ReviewStepContent<TParams = unknown>({
       thumbnail: operation.thumbnails[index],
     })) || [];
 
+  const handleDownload = async () => {
+    if (!operation.downloadUrl) return;
+    try {
+      await saveOperationResults({
+        downloadUrl: operation.downloadUrl,
+        downloadFilename: operation.downloadFilename || "download",
+        downloadLocalPath: operation.downloadLocalPath,
+        outputFileIds: operation.outputFileIds,
+        getFile: (fileId) => selectors.getFile(fileId as FileId),
+        getStub: (fileId) => selectors.getStirlingFileStub(fileId as FileId),
+        markSaved: (fileId, savedPath) => {
+          const stub = selectors.getStirlingFileStub(fileId as FileId);
+          fileActions.updateStirlingFileStub(fileId as FileId, {
+            localFilePath: stub?.localFilePath ?? savedPath,
+            isDirty: false
+          });
+        }
+      });
+    } catch (error) {
+      const message = error instanceof Error ? error.message : String(error);
+      console.error("[ReviewToolStep] Failed to download file:", message);
+      alert(`Failed to download file: ${message}`);
+    }
+  };
+
   // Auto-scroll to bottom when content appears
   useEffect(() => {
     if (stepRef.current && (previewFiles.length > 0 || operation.downloadUrl || operation.errorMessage)) {
@@ -92,13 +122,11 @@ function ReviewStepContent<TParams = unknown>({
       )}
       {operation.downloadUrl && (
         <Button
-          component="a"
-          href={operation.downloadUrl}
-          download={operation.downloadFilename}
           leftSection={<DownloadIcon />}
           color="blue"
           fullWidth
           mb="md"
+          onClick={handleDownload}
         >
           {terminology.download}
         </Button>

frontend/src/core/components/tools/showJS/utils.ts

@@ -1,3 +1,5 @@
+import { downloadFromUrl } from "@app/services/downloadService";
+
 export type ShowJsTokenType = "kw" | "str" | "num" | "com" | "plain";
 export type ShowJsToken = { type: ShowJsTokenType; text: string };
 
@@ -372,11 +374,6 @@ export async function copyTextToClipboard(text: string, fallbackElement?: HTMLEl
   }
 }
 
-export function triggerDownload(url: string, filename: string): void {
-  const a = document.createElement("a");
-  a.href = url;
-  a.download = filename;
-  document.body.appendChild(a);
-  a.click();
-  document.body.removeChild(a);
+export async function triggerDownload(url: string, filename: string): Promise<void> {
+  await downloadFromUrl(url, filename);
 }

frontend/src/core/components/tools/validateSignature/ValidateSignatureResults.tsx

@@ -6,6 +6,7 @@ import type { ValidateSignatureOperationHook } from '@app/hooks/tools/validateSi
 import '@app/components/tools/validateSignature/reportView/styles.css';
 import FitText from '@app/components/shared/FitText';
 import { SuggestedToolsSection } from '@app/components/tools/shared/SuggestedToolsSection';
+import { downloadFile } from '@app/services/downloadService';
 
 interface ValidateSignatureResultsProps {
   operation: ValidateSignatureOperationHook;
@@ -80,14 +81,7 @@ const ValidateSignatureResults = ({
   ];
 
   const handleDownload = useCallback((file: File) => {
-    const blobUrl = URL.createObjectURL(file);
-    const link = document.createElement('a');
-    link.href = blobUrl;
-    link.download = file.name;
-    document.body.appendChild(link);
-    link.click();
-    document.body.removeChild(link);
-    URL.revokeObjectURL(blobUrl);
+    void downloadFile({ data: file, filename: file.name });
   }, []);
 
   // Show the big loader only while we're still waiting for the first results.

frontend/src/core/contexts/FileManagerContext.tsx

@@ -5,6 +5,11 @@ import { StirlingFileStub } from '@app/types/fileContext';
 import { downloadFiles } from '@app/utils/downloadUtils';
 import { FileId } from '@app/types/file';
 import { groupFilesByOriginal } from '@app/utils/fileHistoryUtils';
+import { openFilesFromDisk } from '@app/services/openFilesFromDisk';
+
+// Module-level storage for file path mappings (quickKey -> localFilePath)
+// Used to pass file paths from Tauri file dialog to FileContext
+export const pendingFilePathMappings = new Map<string, string>();
 
 // Type for the context value - now contains everything directly
 interface FileManagerContextValue {
@@ -121,6 +126,7 @@ export const FileManagerProvider: React.FC<FileManagerProviderProps> = ({
   const selectedFiles = selectedFileIds.length === 0 ? [] :
     displayFiles.filter(file => selectedFilesSet.has(file.id));
 
+
   const filteredFiles = !searchTerm ? displayFiles :
     displayFiles.filter(file =>
       file.name.toLowerCase().includes(searchTerm.toLowerCase())
@@ -135,9 +141,23 @@ export const FileManagerProvider: React.FC<FileManagerProviderProps> = ({
     }
   }, []);
 
-  const handleLocalFileClick = useCallback(() => {
-    fileInputRef.current?.click();
-  }, []);
+  const handleLocalFileClick = useCallback(async () => {
+    console.log('[FileManager] Opening file dialog...');
+
+    // Try native dialog first (desktop), falls back to empty array (web)
+    const files = await openFilesFromDisk({
+      multiple: true,
+      onFallbackOpen: () => fileInputRef.current?.click()
+    });
+
+    if (files.length > 0) {
+      console.log('[FileManager] Passing files to FileContext:', files.map(f => f.name));
+      onNewFilesSelect(files);
+
+      await refreshRecentFiles();
+      onClose();
+    }
+  }, [onNewFilesSelect, refreshRecentFiles, onClose]);
 
   const handleFileSelect = useCallback((file: StirlingFileStub, currentIndex: number, shiftKey?: boolean) => {
     const fileId = file.id;
@@ -434,7 +454,6 @@ export const FileManagerProvider: React.FC<FileManagerProviderProps> = ({
     }
   }, [selectedFileIds, handleFileRemoveById]);
 
-
   const handleDownloadSelected = useCallback(async () => {
     if (selectedFileIds.length === 0) return;
 

frontend/src/core/contexts/file/fileActions.ts

@@ -178,7 +178,7 @@ export function createChildStub(
   // Copy parent metadata but exclude processedFile to prevent stale data
   const { processedFile: _processedFile, ...parentMetadata } = parentStub;
 
-  return {
+  const childStub = {
     // Copy parent metadata (excluding processedFile)
     ...parentMetadata,
 
@@ -197,8 +197,24 @@ export function createChildStub(
     thumbnailUrl: thumbnail,
 
     // Set fresh processedFile metadata (no inheritance from parent)
-    processedFile: processedFileMetadata
+    processedFile: processedFileMetadata,
+
+    // Mark as dirty if parent has a localFilePath (modified file not yet saved to disk)
+    isDirty: parentStub.localFilePath ? true : undefined
   };
+
+  if (DEBUG) {
+    console.log('[createChildStub] Created child:', {
+      childId: newFileId,
+      parentId: parentStub.id,
+      parentLocalFilePath: parentStub.localFilePath,
+      childLocalFilePath: childStub.localFilePath,
+      childIsDirty: childStub.isDirty,
+      versionNumber: newVersionNumber
+    });
+  }
+
+  return childStub;
 }
 
 interface AddFileOptions {
@@ -311,6 +327,25 @@ export async function addFiles(
     // Create new filestub with minimal metadata; hydrate thumbnails/processedFile asynchronously
     const fileStub = createNewStirlingFileStub(file, fileId);
 
+    // Check for pending file path mapping from Tauri file dialog (desktop only)
+    try {
+      const { pendingFilePathMappings } = await import('@app/contexts/FileManagerContext');
+      console.log(`[FileActions] Checking for localFilePath mapping for quickKey: ${quickKey}`);
+      console.log(`[FileActions] Available mappings:`, Array.from(pendingFilePathMappings.keys()));
+      const localFilePath = pendingFilePathMappings.get(quickKey);
+      if (localFilePath) {
+        console.log(`[FileActions] ✓ Found localFilePath: ${localFilePath}`);
+        fileStub.localFilePath = localFilePath;
+        pendingFilePathMappings.delete(quickKey); // Clean up after use
+        console.log(`[FileActions] Applied localFilePath to file: ${file.name}`);
+      } else {
+        console.log(`[FileActions] ✗ No localFilePath found for this file`);
+      }
+    } catch (error) {
+      console.log('[FileActions] Could not check for localFilePath:', error);
+      // FileManagerContext may not be available in all contexts
+    }
+
     // Store insertion position if provided
     if (options.insertAfterPageId !== undefined) {
       fileStub.insertAfterPageId = options.insertAfterPageId;
@@ -558,11 +593,20 @@ export async function undoConsumeFiles(
       indexedDB
     );
 
+    // Mark restored files as dirty if they have localFilePath
+    // (they now differ from what's saved on disk)
+    const stubsWithDirtyMarked = inputStirlingFileStubs.map(stub => {
+      if (stub.localFilePath) {
+        return { ...stub, isDirty: true };
+      }
+      return stub;
+    });
+
     // Dispatch the undo action (only if everything else succeeded)
     dispatch({
       type: 'UNDO_CONSUME_FILES',
       payload: {
-        inputStirlingFileStubs,
+        inputStirlingFileStubs: stubsWithDirtyMarked,
         outputFileIds
       }
     });
@@ -697,5 +741,6 @@ export const createFileActions = (dispatch: React.Dispatch<FileContextAction>) =
   resetContext: () => dispatch({ type: 'RESET_CONTEXT' }),
   markFileError: (fileId: FileId) => dispatch({ type: 'MARK_FILE_ERROR', payload: { fileId } }),
   clearFileError: (fileId: FileId) => dispatch({ type: 'CLEAR_FILE_ERROR', payload: { fileId } }),
-  clearAllFileErrors: () => dispatch({ type: 'CLEAR_ALL_FILE_ERRORS' })
+  clearAllFileErrors: () => dispatch({ type: 'CLEAR_ALL_FILE_ERRORS' }),
+  updateStirlingFileStub: (fileId: FileId, updates: Partial<StirlingFileStub>) => dispatch({ type: 'UPDATE_FILE_RECORD', payload: { id: fileId, updates } })
 });

frontend/src/core/hooks/tools/shared/useToolOperation.ts

@@ -11,6 +11,7 @@ import { FILE_EVENTS } from '@app/services/errorUtils';
 import { getFilenameWithoutExtension } from '@app/utils/fileUtils';
 import { ResponseHandler } from '@app/utils/toolResponseProcessor';
 import { createChildStub, generateProcessedFileMetadata } from '@app/contexts/file/fileActions';
+import { createNewStirlingFileStub } from '@app/types/fileContext';
 import { ToolOperation } from '@app/types/file';
 import { ToolId } from '@app/types/toolId';
 import { ensureBackendReady } from '@app/services/backendReadinessGuard';
@@ -140,6 +141,8 @@ export interface ToolOperationHook<TParams = void> {
   isGeneratingThumbnails: boolean;
   downloadUrl: string | null;
   downloadFilename: string;
+  downloadLocalPath?: string | null;
+  outputFileIds?: string[] | null;
   isLoading: boolean;
   status: string;
   errorMessage: string | null;
@@ -375,7 +378,10 @@ export const useToolOperation = <TParams>(
         actions.setGeneratingThumbnails(false);
 
         actions.setThumbnails(thumbnails);
-        actions.setDownloadInfo(downloadInfo.url, downloadInfo.filename);
+        const downloadLocalPath =
+          validFiles.length === 1 && processedFiles.length === 1
+            ? selectors.getStirlingFileStub(validFiles[0].fileId)?.localFilePath ?? null
+            : null;
 
         // Replace input files with processed files (consumeFiles handles pinning)
         const inputFileIds: FileId[] = [];
@@ -390,6 +396,9 @@ export const useToolOperation = <TParams>(
             inputStirlingFileStubs.push(record);
           } else {
             console.warn(`No file stub found for file: ${file.name}`);
+            const fallbackStub = createNewStirlingFileStub(file, fileId);
+            inputFileIds.push(fileId);
+            inputStirlingFileStubs.push(fallbackStub);
           }
         }
 
@@ -437,6 +446,18 @@ export const useToolOperation = <TParams>(
         console.debug('[useToolOperation] Consuming files', { inputCount: inputFileIds.length, toConsume: toConsumeInputIds.length });
         const outputFileIds = await consumeFiles(toConsumeInputIds, outputStirlingFiles, outputStirlingFileStubs);
 
+        if (toConsumeInputIds.length === 1 && outputFileIds.length === 1) {
+          const inputStub = selectors.getStirlingFileStub(toConsumeInputIds[0]);
+          if (inputStub?.localFilePath) {
+            fileActions.updateStirlingFileStub(outputFileIds[0], {
+              localFilePath: inputStub.localFilePath
+            });
+          }
+        }
+
+        // Pass output file IDs to download info for marking clean after save
+        actions.setDownloadInfo(downloadInfo.url, downloadInfo.filename, downloadLocalPath, outputFileIds);
+
         // Store operation data for undo (only store what we need to avoid memory bloat)
         lastOperationRef.current = {
           inputFiles: extractFiles(validFiles), // Convert to File objects for undo
@@ -532,7 +553,6 @@ export const useToolOperation = <TParams>(
       // Undo the consume operation
       await undoConsumeFiles(inputFiles, inputStirlingFileStubs, outputFileIds);
 
-
       // Clear results and operation tracking
       resetResults();
       lastOperationRef.current = null;
@@ -565,6 +585,8 @@ export const useToolOperation = <TParams>(
     isGeneratingThumbnails: state.isGeneratingThumbnails,
     downloadUrl: state.downloadUrl,
     downloadFilename: state.downloadFilename,
+    downloadLocalPath: state.downloadLocalPath,
+    outputFileIds: state.outputFileIds,
     isLoading: state.isLoading,
     status: state.status,
     errorMessage: state.errorMessage,

frontend/src/core/hooks/tools/shared/useToolState.ts

@@ -12,6 +12,8 @@ export interface OperationState {
   isGeneratingThumbnails: boolean;
   downloadUrl: string | null;
   downloadFilename: string;
+  downloadLocalPath?: string | null;
+  outputFileIds?: string[] | null;
   isLoading: boolean;
   status: string;
   errorMessage: string | null;
@@ -23,7 +25,7 @@ type OperationAction =
   | { type: 'SET_FILES'; payload: File[] }
   | { type: 'SET_THUMBNAILS'; payload: string[] }
   | { type: 'SET_GENERATING_THUMBNAILS'; payload: boolean }
-  | { type: 'SET_DOWNLOAD_INFO'; payload: { url: string | null; filename: string } }
+  | { type: 'SET_DOWNLOAD_INFO'; payload: { url: string | null; filename: string; localPath?: string | null; outputFileIds?: string[] | null } }
   | { type: 'SET_STATUS'; payload: string }
   | { type: 'SET_ERROR'; payload: string | null }
   | { type: 'SET_PROGRESS'; payload: ProcessingProgress | null }
@@ -36,6 +38,8 @@ const initialState: OperationState = {
   isGeneratingThumbnails: false,
   downloadUrl: null,
   downloadFilename: '',
+  downloadLocalPath: null,
+  outputFileIds: null,
   isLoading: false,
   status: '',
   errorMessage: null,
@@ -53,10 +57,12 @@ const operationReducer = (state: OperationState, action: OperationAction): Opera
     case 'SET_GENERATING_THUMBNAILS':
       return { ...state, isGeneratingThumbnails: action.payload };
     case 'SET_DOWNLOAD_INFO':
-      return { 
-        ...state, 
-        downloadUrl: action.payload.url, 
-        downloadFilename: action.payload.filename 
+      return {
+        ...state,
+        downloadUrl: action.payload.url,
+        downloadFilename: action.payload.filename,
+        downloadLocalPath: action.payload.localPath ?? null,
+        outputFileIds: action.payload.outputFileIds ?? null
       };
     case 'SET_STATUS':
       return { ...state, status: action.payload };
@@ -97,8 +103,8 @@ export const useToolState = () => {
     dispatch({ type: 'SET_GENERATING_THUMBNAILS', payload: generating });
   }, []);
 
-  const setDownloadInfo = useCallback((url: string | null, filename: string) => {
-    dispatch({ type: 'SET_DOWNLOAD_INFO', payload: { url, filename } });
+  const setDownloadInfo = useCallback((url: string | null, filename: string, localPath?: string | null, outputFileIds?: string[] | null) => {
+    dispatch({ type: 'SET_DOWNLOAD_INFO', payload: { url, filename, localPath, outputFileIds } });
   }, []);
 
   const setStatus = useCallback((status: string) => {
@@ -136,4 +142,4 @@ export const useToolState = () => {
       clearError,
     },
   };
-};
+};

frontend/src/core/services/downloadService.ts

@@ -0,0 +1,40 @@
+export interface DownloadRequest {
+  data: Blob | File;
+  filename: string;
+  localPath?: string;
+}
+
+export interface DownloadResult {
+  savedPath?: string;
+  cancelled?: boolean;
+}
+
+export async function downloadFile(request: DownloadRequest): Promise<DownloadResult> {
+  const url = URL.createObjectURL(request.data);
+
+  const link = document.createElement("a");
+  link.href = url;
+  link.download = request.filename;
+  document.body.appendChild(link);
+  link.click();
+  document.body.removeChild(link);
+
+  URL.revokeObjectURL(url);
+
+  return { savedPath: request.localPath };
+}
+
+export async function downloadFromUrl(
+  url: string,
+  filename: string,
+  localPath?: string
+): Promise<DownloadResult> {
+  const link = document.createElement("a");
+  link.href = url;
+  link.download = filename;
+  document.body.appendChild(link);
+  link.click();
+  document.body.removeChild(link);
+
+  return { savedPath: localPath };
+}

frontend/src/core/services/fileDialogService.ts

@@ -0,0 +1,28 @@
+// Core stub - no-op implementation for web builds
+// Desktop overrides this with actual Tauri implementation
+
+export interface FileWithPath {
+  file: File;
+  path: string;
+  quickKey: string;
+}
+
+export interface FileDialogOptions {
+  multiple?: boolean;
+  filters?: Array<{
+    name: string;
+    extensions: string[];
+  }>;
+}
+
+/**
+ * Open native file dialog and read selected files
+ * Core stub - returns empty array (no native dialog in web)
+ * Desktop builds override this with actual Tauri implementation
+ */
+export async function openFileDialog(
+  _options?: FileDialogOptions
+): Promise<FileWithPath[]> {
+  // Web build: no native file dialog support
+  return [];
+}

frontend/src/core/services/localFileSaveService.ts

@@ -0,0 +1,48 @@
+// Core stub - no-op implementation for web builds
+// Desktop overrides this with actual Tauri implementation
+
+export interface SaveResult {
+  success: boolean;
+  error?: string;
+}
+
+export interface MultiFileSaveResult {
+  success: boolean;
+  savedCount: number;
+  cancelledByUser?: boolean;
+  error?: string;
+}
+
+/**
+ * Save file data to a local filesystem path
+ * Core stub - always returns failure
+ * Desktop builds override this with actual implementation
+ */
+export async function saveToLocalPath(
+  _data: Blob | File,
+  _filePath: string
+): Promise<SaveResult> {
+  return { success: false, error: "Local file save not available in web mode" };
+}
+
+/**
+ * Show native save dialog
+ * Core stub - always returns null
+ */
+export async function showSaveDialog(
+  _defaultFilename: string,
+  _defaultDirectory?: string
+): Promise<string | null> {
+  return null;
+}
+
+/**
+ * Prompt user to select folder and save multiple files
+ * Core stub - always returns failure
+ */
+export async function saveMultipleFilesWithPrompt(
+  _files: (Blob | File)[],
+  _defaultDirectory?: string
+): Promise<MultiFileSaveResult> {
+  return { success: false, savedCount: 0, error: "Multi-file save not available in web mode" };
+}

frontend/src/core/services/openFilesFromDisk.ts

@@ -0,0 +1,29 @@
+import { openFileDialog } from '@app/services/fileDialogService';
+import { pendingFilePathMappings } from '@app/contexts/FileManagerContext';
+import { getDocumentFileDialogFilter } from '@app/utils/fileDialogUtils';
+
+interface OpenFilesFromDiskOptions {
+  multiple?: boolean;
+  filters?: Array<{
+    name: string;
+    extensions: string[];
+  }>;
+  onFallbackOpen?: () => void;
+}
+
+export async function openFilesFromDisk(options: OpenFilesFromDiskOptions = {}): Promise<File[]> {
+  const filesWithPaths = await openFileDialog({
+    multiple: options.multiple ?? true,
+    filters: options.filters ?? getDocumentFileDialogFilter()
+  });
+
+  if (filesWithPaths.length > 0) {
+    for (const { quickKey, path } of filesWithPaths) {
+      pendingFilePathMappings.set(quickKey, path);
+    }
+    return filesWithPaths.map((entry) => entry.file);
+  }
+
+  options.onFallbackOpen?.();
+  return [];
+}

frontend/src/core/services/operationResultsSaveService.ts

@@ -0,0 +1,30 @@
+import type { FileId, StirlingFileStub } from '@app/types/fileContext';
+import { downloadFromUrl, DownloadResult } from '@app/services/downloadService';
+
+export interface OperationSaveContext {
+  downloadUrl: string | null;
+  downloadFilename: string;
+  downloadLocalPath?: string | null;
+  outputFileIds?: string[] | null;
+  getFile: (fileId: FileId) => File | undefined;
+  getStub: (fileId: FileId) => StirlingFileStub | undefined;
+  markSaved: (fileId: FileId, savedPath?: string) => void;
+}
+
+export async function saveOperationResults(context: OperationSaveContext): Promise<DownloadResult | null> {
+  if (!context.downloadUrl) return null;
+
+  const result = await downloadFromUrl(
+    context.downloadUrl,
+    context.downloadFilename || 'download',
+    context.downloadLocalPath || undefined
+  );
+
+  if (context.outputFileIds && result.savedPath) {
+    for (const fileId of context.outputFileIds) {
+      context.markSaved(fileId as FileId, result.savedPath);
+    }
+  }
+
+  return result;
+}

frontend/src/core/services/pdfExportService.ts

@@ -1,4 +1,5 @@
 import { PDFDocument as PDFLibDocument, degrees, PageSizes } from 'pdf-lib';
+import { downloadFile } from '@app/services/downloadService';
 import { PDFDocument, PDFPage } from '@app/types/pageEditor';
 
 export interface ExportOptions {
@@ -181,18 +182,7 @@ export class PDFExportService {
    * Download a single file
    */
   downloadFile(blob: Blob, filename: string): void {
-    const url = URL.createObjectURL(blob);
-    const link = document.createElement('a');
-    link.href = url;
-    link.download = filename;
-    link.style.display = 'none';
-
-    document.body.appendChild(link);
-    link.click();
-    document.body.removeChild(link);
-
-    // Clean up the URL after a short delay
-    setTimeout(() => URL.revokeObjectURL(url), 1000);
+    void downloadFile({ data: blob, filename });
   }
 
   /**

frontend/src/core/tests/convert/ConvertIntegration.test.tsx

@@ -192,7 +192,7 @@ describe('Convert Tool Integration Tests', () => {
       expect(result.current.downloadUrl).toBeTruthy();
       expect(result.current.downloadFilename).toBe('test.png');
       expect(result.current.isLoading).toBe(false);
-      expect(result.current.errorMessage).not.toBe(null);
+      expect(result.current.errorMessage).toBe(null);
     });
 
     test('should handle API error responses correctly', async () => {
@@ -478,7 +478,7 @@ describe('Convert Tool Integration Tests', () => {
       expect(result.current.downloadUrl).toBeTruthy();
       expect(result.current.downloadFilename).toBe('test.csv');
       expect(result.current.isLoading).toBe(false);
-      expect(result.current.errorMessage).not.toBe(null);
+      expect(result.current.errorMessage).toBe(null);
     });
 
     test('should handle complete unsupported conversion workflow', async () => {

frontend/src/core/tools/EditTableOfContents.tsx

@@ -1,5 +1,6 @@
 import { useCallback, useEffect, useMemo, useRef, useState } from 'react';
 import { useTranslation } from 'react-i18next';
+import { downloadFile } from '@app/services/downloadService';
 import MenuBookRoundedIcon from '@mui/icons-material/MenuBookRounded';
 import { alert } from '@app/components/toast';
 import { createToolFlow } from '@app/components/tools/shared/createToolFlow';
@@ -191,14 +192,7 @@ const EditTableOfContents = (props: BaseToolProps) => {
   const exportJsonCallback = () => {
     const data = JSON.stringify(serializeBookmarkNodes(base.params.parameters.bookmarks), null, 2);
     const blob = new Blob([data], { type: 'application/json' });
-    const url = URL.createObjectURL(blob);
-    const anchor = document.createElement('a');
-    anchor.href = url;
-    anchor.download = 'bookmarks.json';
-    document.body.appendChild(anchor);
-    anchor.click();
-    document.body.removeChild(anchor);
-    URL.revokeObjectURL(url);
+    void downloadFile({ data: blob, filename: 'bookmarks.json' });
     alert({
       title: t('editTableOfContents.messages.exported', 'JSON download ready'),
       alertType: 'success',

frontend/src/core/types/fileContext.ts

@@ -45,9 +45,11 @@ export interface StirlingFileStub extends BaseFileMetadata {
   quickKey?: string;             // Fast deduplication key: name|size|lastModified
   thumbnailUrl?: string;         // Generated thumbnail blob URL for visual display
   blobUrl?: string;             // File access blob URL for downloads/processing
+  localFilePath?: string;        // Original local filesystem path (desktop app only)
   processedFile?: ProcessedFileMetadata; // PDF page data and processing results
   insertAfterPageId?: string;   // Page ID after which this file should be inserted
   isPinned?: boolean;           // Protected from tool consumption (replace/remove)
+  isDirty?: boolean;            // Has unsaved changes (only for files with localFilePath)
   // Note: File object stored in provider ref, not in state
 }
 

frontend/src/core/utils/automationConverter.ts

@@ -4,6 +4,7 @@
 
 import { AutomationConfig } from '@app/types/automation';
 import { ToolRegistry } from '@app/data/toolsTaxonomy';
+import { downloadFile } from '@app/services/downloadService';
 import { ToolId } from '@app/types/toolId';
 
 /**
@@ -95,16 +96,5 @@ export function downloadFolderScanningConfig(
   const config = convertToFolderScanningConfig(automation, toolRegistry);
   const json = JSON.stringify(config, null, 2);
   const blob = new Blob([json], { type: 'application/json' });
-  const url = URL.createObjectURL(blob);
-
-  const a = document.createElement('a');
-  a.href = url;
-  a.download = `${automation.name}.json`;
-  a.style.display = 'none';
-
-  document.body.appendChild(a);
-  a.click();
-  document.body.removeChild(a);
-
-  URL.revokeObjectURL(url);
+  void downloadFile({ data: blob, filename: `${automation.name}.json` });
 }

frontend/src/core/utils/downloadUtils.ts

@@ -1,6 +1,7 @@
 import { StirlingFileStub } from '@app/types/fileContext';
 import { fileStorage } from '@app/services/fileStorage';
 import { zipFileService } from '@app/services/zipFileService';
+import { downloadFile } from '@app/services/downloadService';
 
 /**
  * Downloads a blob as a file using browser download API
@@ -8,17 +9,7 @@ import { zipFileService } from '@app/services/zipFileService';
  * @param filename - The filename for the download
  */
 export function downloadBlob(blob: Blob, filename: string): void {
-  const url = URL.createObjectURL(blob);
-
-  const link = document.createElement('a');
-  link.href = url;
-  link.download = filename;
-  document.body.appendChild(link);
-  link.click();
-  document.body.removeChild(link);
-
-  // Clean up the blob URL
-  URL.revokeObjectURL(url);
+  void downloadFile({ data: blob, filename });
 }
 
 /**
@@ -34,8 +25,11 @@ export async function downloadFileFromStorage(file: StirlingFileStub): Promise<v
     throw new Error(`File "${file.name}" not found in storage`);
   }
 
-  // StirlingFile is already a File object, just download it
-  downloadBlob(stirlingFile, stirlingFile.name);
+  await downloadFile({
+    data: stirlingFile,
+    filename: stirlingFile.name,
+    localPath: file.localFilePath
+  });
 }
 
 /**
@@ -80,7 +74,7 @@ export async function downloadFilesAsZip(files: StirlingFileStub[], zipFilename?
 
   // Create and download ZIP
   const { zipFile } = await zipFileService.createZipFromFiles(filesToZip, finalZipFilename);
-  downloadBlob(zipFile, finalZipFilename);
+  await downloadFile({ data: zipFile, filename: finalZipFilename });
 }
 
 /**
@@ -120,7 +114,7 @@ export async function downloadFiles(
  * @param filename - Optional custom filename
  */
 export function downloadFileObject(file: File, filename?: string): void {
-  downloadBlob(file, filename || file.name);
+  void downloadFile({ data: file, filename: filename || file.name });
 }
 
 /**
@@ -135,7 +129,7 @@ export function downloadTextAsFile(
   mimeType: string = 'text/plain'
 ): void {
   const blob = new Blob([content], { type: mimeType });
-  downloadBlob(blob, filename);
+  void downloadFile({ data: blob, filename });
 }
 
 /**

frontend/src/core/utils/fileDialogUtils.ts

@@ -0,0 +1,6 @@
+export function getDocumentFileDialogFilter() {
+  return [{
+    name: 'Documents',
+    extensions: ['pdf', 'jpg', 'jpeg', 'png', 'gif', 'tiff', 'bmp', 'html', 'zip']
+  }];
+}

frontend/src/desktop/components/AppProviders.tsx

@@ -2,6 +2,7 @@ import { ReactNode, useEffect, useState } from "react";
 import { AppProviders as ProprietaryAppProviders } from "@proprietary/components/AppProviders";
 import { DesktopConfigSync } from '@app/components/DesktopConfigSync';
 import { DesktopBannerInitializer } from '@app/components/DesktopBannerInitializer';
+import { SaveShortcutListener } from '@app/components/SaveShortcutListener';
 import { SetupWizard } from '@app/components/SetupWizard';
 import { useFirstLaunchCheck } from '@app/hooks/useFirstLaunchCheck';
 import { useBackendInitializer } from '@app/hooks/useBackendInitializer';
@@ -149,6 +150,7 @@ export function AppProviders({ children }: { children: ReactNode }) {
     >
       <DesktopConfigSync />
       <DesktopBannerInitializer />
+      <SaveShortcutListener />
       {children}
     </ProprietaryAppProviders>
   );

frontend/src/desktop/components/SaveShortcutListener.tsx

@@ -0,0 +1,14 @@
+import { useSaveShortcut } from '@app/hooks/useSaveShortcut';
+import { useExitWarning } from '@app/hooks/useExitWarning';
+
+/**
+ * Desktop-only component that sets up keyboard shortcuts and exit warnings
+ * - Ctrl/Cmd+S to save selected files
+ * - Warning on app exit if unsaved files
+ * Renders nothing, just sets up the listeners
+ */
+export function SaveShortcutListener() {
+  useSaveShortcut();
+  useExitWarning();
+  return null;
+}

frontend/src/desktop/components/fileEditor/FileEditorFileName.tsx

@@ -0,0 +1,66 @@
+import React from 'react';
+import { Tooltip } from '@mantine/core';
+import { useTranslation } from 'react-i18next';
+import { StirlingFileStub } from '@app/types/fileContext';
+import { PrivateContent } from '@app/components/shared/PrivateContent';
+
+interface FileEditorFileNameProps {
+  file: StirlingFileStub;
+}
+
+const FileEditorFileName = ({ file }: FileEditorFileNameProps) => {
+  const { t } = useTranslation();
+
+  return (
+    <>
+      <PrivateContent>{file.name}</PrivateContent>
+      {!file.localFilePath && (
+        <Tooltip label={t('fileNotSavedToDisk', 'Not saved to disk')}>
+          <span
+            style={{
+              display: 'inline-block',
+              width: '6px',
+              height: '6px',
+              borderRadius: '50%',
+              backgroundColor: 'var(--mantine-color-red-6)',
+              flexShrink: 0
+            }}
+            aria-label={t('fileNotSavedToDisk', 'Not saved to disk')}
+          />
+        </Tooltip>
+      )}
+      {file.localFilePath && file.isDirty && (
+        <Tooltip label={t('unsavedChanges', 'Unsaved changes')}>
+          <span
+            style={{
+              display: 'inline-block',
+              width: '6px',
+              height: '6px',
+              borderRadius: '50%',
+              backgroundColor: 'var(--mantine-color-yellow-6)',
+              flexShrink: 0
+            }}
+            aria-label={t('unsavedChanges', 'Unsaved changes')}
+          />
+        </Tooltip>
+      )}
+      {file.localFilePath && !file.isDirty && (
+        <Tooltip label={t('fileSavedToDisk', 'File saved to disk')}>
+          <span
+            style={{
+              display: 'inline-block',
+              width: '6px',
+              height: '6px',
+              borderRadius: '50%',
+              backgroundColor: 'var(--mantine-color-green-6)',
+              flexShrink: 0
+            }}
+            aria-label={t('fileSavedToDisk', 'File saved to disk')}
+          />
+        </Tooltip>
+      )}
+    </>
+  );
+};
+
+export default FileEditorFileName;

frontend/src/desktop/constants/connection.ts

@@ -6,9 +6,6 @@
 // The SaaS authentication server
 export const STIRLING_SAAS_URL: string = import.meta.env.VITE_SAAS_SERVER_URL || '';
 
-// SaaS signup URL for creating new cloud accounts
-export const STIRLING_SAAS_SIGNUP_URL: string = import.meta.env.VITE_SAAS_SIGNUP_URL || '';
-
 // Supabase publishable key from environment variable
 // Used for SaaS authentication
 export const SUPABASE_KEY: string = import.meta.env.VITE_SUPABASE_PUBLISHABLE_DEFAULT_KEY || 'sb_publishable_UHz2SVRF5mvdrPHWkRteyA_yNlZTkYb';

frontend/src/desktop/hooks/useAppInitialization.ts

@@ -2,6 +2,7 @@ import { useEffect, useState } from 'react';
 import { useOpenedFile } from '@app/hooks/useOpenedFile';
 import { fileOpenService } from '@app/services/fileOpenService';
 import { useFileManagement } from '@app/contexts/file/fileHooks';
+import { createQuickKey } from '@app/types/fileContext';
 
 /**
  * App initialization hook
@@ -11,10 +12,10 @@ import { useFileManagement } from '@app/contexts/file/fileHooks';
  */
 export function useAppInitialization(): void {
   // Get file management actions
-  const { addFiles } = useFileManagement();
+  const { addFiles, updateStirlingFileStub } = useFileManagement();
 
   // Handle files opened with app (Tauri mode)
-  const { openedFilePaths, loading: openedFileLoading } = useOpenedFile();
+  const { openedFilePaths, loading: openedFileLoading, consumeOpenedFilePaths } = useOpenedFile();
 
   // Load opened files and add directly to FileContext
   useEffect(() => {
@@ -23,29 +24,50 @@ export function useAppInitialization(): void {
     }
 
     const loadOpenedFiles = async () => {
+      const filePaths = consumeOpenedFilePaths();
+      if (filePaths.length === 0) {
+        return;
+      }
       try {
-        const filesArray: File[] = [];
+        const loadedFiles = (
+          await Promise.all(
+            filePaths.map(async (filePath) => {
+              try {
+                const fileData = await fileOpenService.readFileAsArrayBuffer(filePath);
+                if (!fileData) return null;
 
-        await Promise.all(
-          openedFilePaths.map(async (filePath) => {
-            try {
-              const fileData = await fileOpenService.readFileAsArrayBuffer(filePath);
-              if (fileData) {
                 const file = new File([fileData.arrayBuffer], fileData.fileName, {
                   type: 'application/pdf'
                 });
-                filesArray.push(file);
-                console.log('[Desktop] Loaded file:', fileData.fileName);
-              }
-            } catch (error) {
-              console.error('[Desktop] Failed to load file:', filePath, error);
-            }
-          })
-        );
 
-        if (filesArray.length > 0) {
-          await addFiles(filesArray);
-          console.log(`[Desktop] ${filesArray.length} opened file(s) added to FileContext`);
+                console.log('[Desktop] Loaded file:', fileData.fileName);
+
+                return {
+                  file,
+                  filePath,
+                  quickKey: createQuickKey(file),
+                };
+              } catch (error) {
+                console.error('[Desktop] Failed to load file:', filePath, error);
+                return null;
+              }
+            })
+          )
+        ).filter((entry): entry is { file: File; filePath: string; quickKey: string } => Boolean(entry));
+
+        if (loadedFiles.length > 0) {
+          const filesArray = loadedFiles.map(entry => entry.file);
+          const quickKeyToPath = new Map(loadedFiles.map(entry => [entry.quickKey, entry.filePath]));
+
+          const addedFiles = await addFiles(filesArray);
+          addedFiles.forEach(file => {
+            const localFilePath = quickKeyToPath.get(file.quickKey);
+            if (localFilePath) {
+              updateStirlingFileStub(file.fileId, { localFilePath });
+            }
+          });
+
+          console.log(`[Desktop] ${loadedFiles.length} opened file(s) added to FileContext`);
         }
       } catch (error) {
         console.error('[Desktop] Failed to load opened files:', error);
@@ -53,7 +75,7 @@ export function useAppInitialization(): void {
     };
 
     loadOpenedFiles();
-  }, [openedFilePaths, openedFileLoading, addFiles]);
+  }, [openedFilePaths, openedFileLoading, addFiles, updateStirlingFileStub, consumeOpenedFilePaths]);
 }
 
 export function useSetupCompletion(): (completed: boolean) => void {

frontend/src/desktop/hooks/useExitWarning.ts

@@ -0,0 +1,135 @@
+import { useEffect, useRef } from 'react';
+import { getCurrentWindow } from '@tauri-apps/api/window';
+import { message } from '@tauri-apps/plugin-dialog';
+import { useFileState, useFileActions } from '@app/contexts/FileContext';
+import { downloadFile } from '@app/services/downloadService';
+import type { StirlingFileStub } from '@app/types/fileContext';
+import { useTranslation } from 'react-i18next';
+
+export function useExitWarning() {
+  const { t } = useTranslation();
+  const { selectors } = useFileState();
+  const { actions: fileActions } = useFileActions();
+  const selectorsRef = useRef(selectors);
+  const isClosingRef = useRef(false);
+
+  selectorsRef.current = selectors;
+
+  useEffect(() => {
+    const appWindow = getCurrentWindow();
+
+    const handleCloseRequested = async (event: { preventDefault: () => void }) => {
+      event.preventDefault();
+
+      if (isClosingRef.current) {
+        return;
+      }
+
+      const allStubs = selectorsRef.current.getStirlingFileStubs();
+      const dirtyStubs = allStubs.filter(stub => stub.isDirty);
+
+      if (dirtyStubs.length > 0) {
+        const fileList = dirtyStubs.map(f => `• ${f.name}`).join('\n');
+        const saveLabel = t('confirmCloseSave', 'Save and close');
+        const discardLabel = t('confirmCloseDiscard', 'Discard changes and close');
+        const cancelLabel = t('confirmCloseCancel', 'Cancel');
+
+        const choice = await message(
+          t(
+            'confirmCloseUnsavedList',
+            'You have {{count}} file{{plural}} with unsaved changes.\n\n{{fileList}}',
+            { count: dirtyStubs.length, plural: dirtyStubs.length > 1 ? 's' : '', fileList }
+          ),
+          {
+            title: t('confirmCloseUnsaved', 'This file has unsaved changes.'),
+            kind: 'warning',
+            buttons: {
+              yes: saveLabel,
+              no: discardLabel,
+              cancel: cancelLabel,
+            },
+          }
+        );
+
+        if (choice === cancelLabel) {
+          return;
+        }
+
+        if (choice === saveLabel) {
+          const { failedCount, cancelled } = await saveDirtyFiles(dirtyStubs);
+          if (cancelled) {
+            return;
+          }
+          if (failedCount > 0) {
+            await message(
+              t(
+                'confirmCloseSaveFailed',
+                'Saved with errors. {{count}} file{{plural}} could not be saved.',
+                { count: failedCount, plural: failedCount > 1 ? 's' : '' }
+              ),
+              { title: t('confirmCloseSaveFailedTitle', 'Save Failed'), kind: 'error' }
+            );
+            return;
+          }
+        } else if (choice !== discardLabel) {
+          return;
+        }
+      }
+
+      isClosingRef.current = true;
+      try {
+        await appWindow.destroy();
+      } catch (error) {
+        console.error('[exit-warning] destroy failed', error);
+        isClosingRef.current = false;
+      }
+    };
+
+    const unlisten = appWindow.onCloseRequested(handleCloseRequested);
+    return () => {
+      unlisten.then(fn => {
+        fn();
+      });
+    };
+  }, [fileActions, t]);
+
+  const saveDirtyFiles = async (dirtyStubs: StirlingFileStub[]) => {
+    const filesById = new Map(selectorsRef.current.getFiles().map(file => [file.fileId, file]));
+    let failedCount = 0;
+    let cancelled = false;
+
+    for (const stub of dirtyStubs) {
+      const file = filesById.get(stub.id);
+      if (!file || !stub.localFilePath) {
+        if (!file) {
+          failedCount += 1;
+          continue;
+        }
+      }
+
+      try {
+        const result = await downloadFile({
+          data: file,
+          filename: file.name,
+          localPath: stub.localFilePath,
+        });
+
+        if (result.cancelled) {
+          cancelled = true;
+          break;
+        }
+
+        if (result.savedPath) {
+          fileActions.updateStirlingFileStub(stub.id, {
+            localFilePath: stub.localFilePath ?? result.savedPath,
+            isDirty: false
+          });
+        }
+      } catch {
+        failedCount += 1;
+      }
+    }
+
+    return { failedCount, cancelled };
+  };
+}

frontend/src/desktop/hooks/useOpenedFile.ts

@@ -1,10 +1,23 @@
-import { useState, useEffect } from 'react';
+import { useState, useEffect, useRef, useCallback } from 'react';
 import { fileOpenService } from '@app/services/fileOpenService';
 import { listen } from '@tauri-apps/api/event';
 
 export function useOpenedFile() {
   const [openedFilePaths, setOpenedFilePaths] = useState<string[]>([]);
   const [loading, setLoading] = useState(true);
+  const openedFilePathsRef = useRef<string[]>([]);
+
+  const clearOpenedFilePaths = useCallback(() => {
+    openedFilePathsRef.current = [];
+    setOpenedFilePaths([]);
+  }, []);
+
+  const consumeOpenedFilePaths = useCallback(() => {
+    const current = openedFilePathsRef.current;
+    openedFilePathsRef.current = [];
+    setOpenedFilePaths([]);
+    return current;
+  }, []);
 
   useEffect(() => {
     // Function to read and process files from storage
@@ -16,8 +29,8 @@ export function useOpenedFile() {
 
         if (filePaths.length > 0) {
           console.log(`✅ Found ${filePaths.length} file(s) in storage:`, filePaths);
+          openedFilePathsRef.current = filePaths;
           setOpenedFilePaths(filePaths);
-          await fileOpenService.clearOpenedFiles();
         }
       } catch (error) {
         console.error('❌ Failed to read files from storage:', error);
@@ -44,5 +57,5 @@ export function useOpenedFile() {
     };
   }, []);
 
-  return { openedFilePaths, loading };
+  return { openedFilePaths, loading, clearOpenedFilePaths, consumeOpenedFilePaths };
 }

frontend/src/desktop/hooks/useSaveShortcut.ts

@@ -0,0 +1,63 @@
+import { useEffect } from 'react';
+import { useFileState, useFileActions } from '@app/contexts/FileContext';
+import { downloadFile } from '@app/services/downloadService';
+
+/**
+ * Desktop-only keyboard shortcut: Ctrl/Cmd+S to save selected files
+ * Only saves files that have a localFilePath (came from disk)
+ * Matches Right Rail button behavior: saves selected files if any, otherwise all files
+ */
+export function useSaveShortcut() {
+  const { selectors, state } = useFileState();
+  const { actions: fileActions } = useFileActions();
+
+  useEffect(() => {
+    const handleKeyDown = async (event: KeyboardEvent) => {
+      // Check for Ctrl+S (Windows/Linux) or Cmd+S (Mac)
+      if ((event.ctrlKey || event.metaKey) && event.key === 's') {
+        event.preventDefault();
+
+        // Get selected files or all files if nothing selected
+        const selectedFileIds = state.ui.selectedFileIds;
+        const filesToSave = selectedFileIds.length > 0
+          ? selectors.getFiles(selectedFileIds)
+          : selectors.getFiles();
+        const stubsToSave = selectedFileIds.length > 0
+          ? selectors.getStirlingFileStubs(selectedFileIds)
+          : selectors.getStirlingFileStubs();
+
+        if (filesToSave.length === 0) {
+          return;
+        }
+
+        // Save files (Save As for files without localFilePath)
+        for (let i = 0; i < filesToSave.length; i++) {
+          const file = filesToSave[i];
+          const stub = stubsToSave[i];
+          if (!stub) continue;
+
+          try {
+            const result = await downloadFile({
+              data: file,
+              filename: file.name,
+              localPath: stub.localFilePath
+            });
+
+            // Mark file as clean after successful save
+            if (result.savedPath) {
+              fileActions.updateStirlingFileStub(stub.id, {
+                localFilePath: stub.localFilePath ?? result.savedPath,
+                isDirty: false
+              });
+            }
+          } catch (error) {
+            console.error(`Failed to save ${file.name}:`, error);
+          }
+        }
+      }
+    };
+
+    document.addEventListener('keydown', handleKeyDown);
+    return () => document.removeEventListener('keydown', handleKeyDown);
+  }, [selectors, state.ui.selectedFileIds, fileActions]);
+}

frontend/src/desktop/services/downloadService.ts

@@ -0,0 +1,39 @@
+import type { DownloadRequest, DownloadResult } from "@core/services/downloadService";
+import { saveToLocalPath, showSaveDialog } from "@app/services/localFileSaveService";
+
+export type { DownloadRequest, DownloadResult };
+
+export async function downloadFile(request: DownloadRequest): Promise<DownloadResult> {
+  if (request.localPath) {
+    const result = await saveToLocalPath(request.data, request.localPath);
+    if (!result.success) {
+      throw new Error(result.error || "Failed to save file");
+    }
+    return { savedPath: request.localPath };
+  }
+
+  const savePath = await showSaveDialog(request.filename);
+  if (!savePath) {
+    return { cancelled: true };
+  }
+
+  const result = await saveToLocalPath(request.data, savePath);
+  if (!result.success) {
+    throw new Error(result.error || "Failed to save file");
+  }
+
+  return { savedPath: savePath };
+}
+
+export async function downloadFromUrl(
+  url: string,
+  filename: string,
+  localPath?: string
+): Promise<DownloadResult> {
+  const response = await fetch(url);
+  if (!response.ok) {
+    throw new Error(`Download failed (${response.status})`);
+  }
+  const blob = await response.blob();
+  return downloadFile({ data: blob, filename, localPath });
+}

frontend/src/desktop/services/fileDialogService.ts

@@ -0,0 +1,60 @@
+// Desktop implementation - Tauri native file dialogs
+import type { FileWithPath, FileDialogOptions } from '@core/services/fileDialogService';
+import { createQuickKey } from '@app/types/fileContext';
+import { getDocumentFileDialogFilter } from '@app/utils/fileDialogUtils';
+
+export type { FileWithPath, FileDialogOptions };
+
+/**
+ * Open native file dialog and read selected files (Desktop/Tauri only)
+ */
+export async function openFileDialog(
+  options?: FileDialogOptions
+): Promise<FileWithPath[]> {
+  try {
+    const { open } = await import('@tauri-apps/plugin-dialog');
+    const { readFile } = await import('@tauri-apps/plugin-fs');
+
+    console.log('[FileDialog] Opening file dialog...');
+    const selectedPaths = await open({
+      multiple: options?.multiple ?? true,
+      filters: options?.filters ?? getDocumentFileDialogFilter()
+    });
+
+    if (!selectedPaths) {
+      console.log('[FileDialog] User cancelled');
+      return [];
+    }
+
+    const paths = Array.isArray(selectedPaths) ? selectedPaths : [selectedPaths];
+    console.log(`[FileDialog] Selected ${paths.length} file(s):`, paths);
+
+    const filesWithPaths: FileWithPath[] = [];
+
+    for (const filePath of paths) {
+      try {
+        console.log(`[FileDialog] Reading file: ${filePath}`);
+        const fileData = await readFile(filePath);
+        const fileName = filePath.split(/[/\\]/).pop() || 'document';
+        const file = new File([fileData], fileName, {
+          type: fileName.endsWith('.pdf') ? 'application/pdf' : undefined
+        });
+        const quickKey = createQuickKey(file);
+        console.log(`[FileDialog] Created File: ${fileName}, quickKey: ${quickKey}`);
+
+        filesWithPaths.push({
+          file,
+          path: filePath,
+          quickKey
+        });
+      } catch (error) {
+        console.error(`[FileDialog] Failed to read ${filePath}:`, error);
+      }
+    }
+
+    return filesWithPaths;
+  } catch (error) {
+    console.error('[FileDialog] Error:', error);
+    return [];
+  }
+}

frontend/src/desktop/services/fileOpenService.ts

@@ -10,9 +10,9 @@ export interface FileOpenService {
 class TauriFileOpenService implements FileOpenService {
   async getOpenedFiles(): Promise<string[]> {
     try {
-      console.log('🔍 Calling invoke(get_opened_files)...');
-      const result = await invoke<string[]>('get_opened_files');
-      console.log('🔍 invoke(get_opened_files) returned:', result);
+      console.log('🔍 Calling invoke(pop_opened_files)...');
+      const result = await invoke<string[]>('pop_opened_files');
+      console.log('🔍 invoke(pop_opened_files) returned:', result);
       return result;
     } catch (error) {
       console.error('❌ Failed to get opened files:', error);

frontend/src/desktop/services/localFileSaveService.ts

@@ -0,0 +1,123 @@
+import type { SaveResult, MultiFileSaveResult } from "@core/services/localFileSaveService";
+export type { SaveResult, MultiFileSaveResult };
+
+/**
+ * Save file data to a local filesystem path (Tauri desktop only)
+ *
+ * @param data - Blob or File to save
+ * @param filePath - Absolute path to save to
+ * @returns Result indicating success or failure with error message
+ */
+export async function saveToLocalPath(
+  data: Blob | File,
+  filePath: string
+): Promise<SaveResult> {
+  try {
+    const { writeFile } = await import("@tauri-apps/plugin-fs");
+    const arrayBuffer = await data.arrayBuffer();
+    await writeFile(filePath, new Uint8Array(arrayBuffer));
+    return { success: true };
+  } catch (error) {
+    const message = error instanceof Error ? error.message : String(error);
+    console.error('[LocalFileSave] Failed to save:', message);
+    return { success: false, error: message };
+  }
+}
+
+/**
+ * Show native save dialog and return selected path
+ *
+ * @param defaultFilename - Suggested filename
+ * @param defaultDirectory - Optional default directory
+ * @returns Selected file path or null if cancelled
+ */
+export async function showSaveDialog(
+  defaultFilename: string,
+  defaultDirectory?: string
+): Promise<string | null> {
+  try {
+    const { save } = await import("@tauri-apps/plugin-dialog");
+
+    const selectedPath = await save({
+      defaultPath: defaultDirectory ? `${defaultDirectory}/${defaultFilename}` : defaultFilename,
+      filters: [{
+        name: 'PDF',
+        extensions: ['pdf']
+      }],
+      title: 'Save As'
+    });
+
+    return selectedPath;
+  } catch (error) {
+    console.error('[SaveDialog] Failed to show dialog:', error);
+    return null;
+  }
+}
+
+/**
+ * Prompt user to select a folder and save multiple files there
+ *
+ * @param files - Array of files to save
+ * @param defaultDirectory - Optional default directory to open dialog in
+ * @returns Result with count of files saved
+ */
+export async function saveMultipleFilesWithPrompt(
+  files: (Blob | File)[],
+  defaultDirectory?: string
+): Promise<MultiFileSaveResult> {
+  try {
+    const { open } = await import("@tauri-apps/plugin-dialog");
+    const { writeFile } = await import("@tauri-apps/plugin-fs");
+    const { join } = await import("@tauri-apps/api/path");
+
+    // Prompt user to select folder
+    const selectedFolder = await open({
+      directory: true,
+      multiple: false,
+      defaultPath: defaultDirectory,
+      title: `Save ${files.length} file${files.length > 1 ? 's' : ''}`
+    });
+
+    // User cancelled
+    if (!selectedFolder) {
+      return { success: false, savedCount: 0, cancelledByUser: true };
+    }
+
+    // Save each file to the selected folder
+    let savedCount = 0;
+    const errors: string[] = [];
+
+    for (const file of files) {
+      try {
+        const fileName = file instanceof File ? file.name : `output_${savedCount + 1}.pdf`;
+        const filePath = await join(selectedFolder as string, fileName);
+        const arrayBuffer = await file.arrayBuffer();
+        await writeFile(filePath, new Uint8Array(arrayBuffer));
+        savedCount++;
+      } catch (error) {
+        const message = error instanceof Error ? error.message : String(error);
+        errors.push(`${file instanceof File ? file.name : 'file'}: ${message}`);
+      }
+    }
+
+    if (savedCount === files.length) {
+      return { success: true, savedCount };
+    } else if (savedCount > 0) {
+      return {
+        success: false,
+        savedCount,
+        error: `Saved ${savedCount}/${files.length} files. Errors: ${errors.join(', ')}`
+      };
+    } else {
+      return {
+        success: false,
+        savedCount: 0,
+        error: `Failed to save files: ${errors.join(', ')}`
+      };
+    }
+  } catch (error) {
+    const message = error instanceof Error ? error.message : String(error);
+    console.error('[LocalFileSave] Failed to save multiple files:', message);
+    return { success: false, savedCount: 0, error: message };
+  }
+}

frontend/src/desktop/services/operationResultsSaveService.ts

@@ -0,0 +1,42 @@
+import type { FileId } from '@app/types/fileContext';
+import type { OperationSaveContext } from '@core/services/operationResultsSaveService';
+import { downloadFile, downloadFromUrl, DownloadResult } from '@app/services/downloadService';
+
+export type { OperationSaveContext };
+
+export async function saveOperationResults(context: OperationSaveContext): Promise<DownloadResult | null> {
+  if (!context.downloadUrl) return null;
+
+  if (context.outputFileIds && context.outputFileIds.length > 0) {
+    for (const fileId of context.outputFileIds) {
+      const file = context.getFile(fileId as FileId);
+      const stub = context.getStub(fileId as FileId);
+      if (!file) continue;
+
+      const result = await downloadFile({
+        data: file,
+        filename: file.name,
+        localPath: stub?.localFilePath
+      });
+
+      if (result.savedPath) {
+        context.markSaved(fileId as FileId, result.savedPath);
+      }
+    }
+    return null;
+  }
+
+  const result = await downloadFromUrl(
+    context.downloadUrl,
+    context.downloadFilename || 'download',
+    context.downloadLocalPath || undefined
+  );
+
+  if (context.outputFileIds && result.savedPath) {
+    for (const fileId of context.outputFileIds) {
+      context.markSaved(fileId as FileId, result.savedPath);
+    }
+  }
+
+  return result;
+}

frontend/vite.config.ts

@@ -11,6 +11,22 @@ export default defineConfig(({ mode }) => {
     process.env.STIRLING_DESKTOP === 'true' ||
     process.env.VITE_DESKTOP === 'true';
 
+  // Validate required environment variables for desktop builds
+  if (isDesktopMode) {
+    const requiredEnvVars = [
+      'VITE_SAAS_SERVER_URL',
+      'VITE_SUPABASE_PUBLISHABLE_DEFAULT_KEY',
+    ];
+
+    const missingVars = requiredEnvVars.filter(varName => !process.env[varName]);
+
+    if (missingVars.length > 0) {
+      throw new Error(
+        `Desktop build failed: Missing required environment variables:\n${missingVars.map(v => `  - ${v}`).join('\n')}\n\nPlease set these variables before building the desktop app.`
+      );
+    }
+  }
+
   const baseProject = isProprietary ? './tsconfig.proprietary.vite.json' : './tsconfig.core.vite.json';
   const desktopProject = isProprietary ? './tsconfig.desktop.vite.json' : baseProject;
   const tsconfigProject = isDesktopMode ? desktopProject : baseProject;