diff --git a/AGENTS.md b/AGENTS.md
new file mode 100644
index 0000000..165cfa6
--- /dev/null
+++ b/AGENTS.md
@@ -0,0 +1,25 @@
+# Repository Guidelines
+
+## Project Structure & Module Organization
+Core application code lives in `src/`. Use `src/main.js` for the Electron main process, `src/preload.js` for the preload bridge, and `src/renderer.js` plus `src/editor/`, `src/sidebar/`, `src/repl/`, and `src/utils/` for renderer-side features. Electron adapter code is in `src/adapters/electron/`. Reusable markdown/document templates live in `src/templates/`. Static assets and icons are in `assets/`. Tests are in `tests/`, and build output goes to `dist/`.
+
+## Build, Test, and Development Commands
+- `npm start`: launch the Electron app locally.
+- `npm test`: run the Jest suite once.
+- `npm run test:watch`: rerun tests during local development.
+- `npm run test:coverage`: generate coverage output.
+- `npm run lint` / `npm run lint:fix`: check or fix ESLint issues in `src` and `tests`.
+- `npm run format` / `npm run format:check`: apply or verify Prettier formatting.
+- `npm run build:linux`, `npm run build:win`, `npm run build:mac`: create platform packages with `electron-builder`.
+
+## Coding Style & Naming Conventions
+This repo uses Prettier and ESLint. Follow `.prettierrc`: 2-space indentation, single quotes, semicolons, trailing commas where valid in ES5, and a 100-character line width. Prefer `camelCase` for variables/functions, `PascalCase` for classes, and kebab-case for file names only when already established. Keep module boundaries clear: UI logic in renderer modules, OS/file-system work behind Electron IPC and adapters.
+
+## Testing Guidelines
+Tests use Jest with `jest-environment-jsdom`. Add new tests under `tests/` with `*.test.js` names, mirroring the feature area when possible, for example `tests/sidebar.test.js` or `tests/print-preview.test.js`. Update or add regression tests for renderer behavior, preload APIs, and utility helpers when fixing bugs. Run `npm test` before opening a PR; use `npm run test:coverage` for larger refactors.
+
+## Commit & Pull Request Guidelines
+Recent history follows Conventional Commit prefixes such as `feat:`, `fix:`, and `refactor:`. Keep subjects short and imperative, for example `fix: guard modal cleanup on close`. PRs should describe the user-visible change, note test coverage, link any related issue, and include screenshots or GIFs for UI changes.
+
+## Security & Configuration Tips
+Do not bypass preload boundaries or introduce direct `eval`/dynamic code paths; ESLint already treats these as errors. Export and conversion features depend on external tools such as Pandoc, FFmpeg, ImageMagick, and LibreOffice, so document any new runtime dependency in `README.md` and packaging config.
diff --git a/README.md b/README.md
index cca5841..19eae7e 100644
--- a/README.md
+++ b/README.md
@@ -162,4 +162,4 @@ Amit Haridas (amit.wh@gmail.com)
 
 ## Version
 
-v3.0.0
+v4.1.0
diff --git a/docs/THREAT_MODEL.md b/docs/THREAT_MODEL.md
index b903379..d80ae46 100644
--- a/docs/THREAT_MODEL.md
+++ b/docs/THREAT_MODEL.md
@@ -1,6 +1,6 @@
 # MarkdownConverter - STRIDE Threat Model Analysis
 
-**Version:** 4.0.0
+**Version:** 4.1.0
 **Date:** 2026-03-15
 **Methodology:** STRIDE + MITRE ATT&CK Mapping
 **Analyst:** Security Assessment Team
diff --git a/src/adapters/electron/fs.js b/src/adapters/electron/fs.js
index c865d09..955d09f 100644
--- a/src/adapters/electron/fs.js
+++ b/src/adapters/electron/fs.js
@@ -18,7 +18,7 @@ const electronFsAdapter = {
      * @returns {Promise<string>} File content
      */
     async readFile(path) {
-        return await window.electronAPI.readFile(path);
+        return await window.electronAPI.file.read(path);
     },
 
     /**
@@ -28,7 +28,7 @@ const electronFsAdapter = {
      * @returns {Promise<void>}
      */
     async writeFile(path, content) {
-        return await window.electronAPI.writeFile(path, content);
+        return await window.electronAPI.file.write(path, content);
     },
 
     /**
@@ -37,8 +37,7 @@ const electronFsAdapter = {
      * @returns {Promise<void>}
      */
     async deleteFile(path) {
-        // TODO: Add IPC channel for delete
-        throw new Error('deleteFile not implemented');
+        return await window.electronAPI.file.delete(path);
     },
 
     /**
@@ -47,8 +46,7 @@ const electronFsAdapter = {
      * @returns {Promise<void>}
      */
     async ensureDir(path) {
-        // TODO: Add IPC channel for ensureDir
-        throw new Error('ensureDir not implemented');
+        return await window.electronAPI.file.ensureDir(path);
     },
 
     /**
@@ -57,8 +55,18 @@ const electronFsAdapter = {
      * @returns {Promise<Array<import('../types').FileInfo>>}
      */
     async listDirectory(path) {
-        // TODO: Add IPC channel for listDirectory
-        throw new Error('listDirectory not implemented');
+        const result = await window.electronAPI.invoke('list-directory', path);
+        if (!result?.entries) {
+            return [];
+        }
+
+        return result.entries.map((entry) => ({
+            name: entry.name,
+            isDir: entry.isDirectory,
+            size: entry.size ?? 0,
+            modified: entry.modified ?? 0,
+            path: entry.path
+        }));
     },
 
     /**
@@ -67,8 +75,7 @@ const electronFsAdapter = {
      * @returns {Promise<boolean>}
      */
     async exists(path) {
-        // TODO: Add IPC channel for exists
-        throw new Error('exists not implemented');
+        return await window.electronAPI.file.exists(path);
     },
 
     /**
@@ -77,8 +84,7 @@ const electronFsAdapter = {
      * @returns {Promise<boolean>}
      */
     async isDirectory(path) {
-        // TODO: Add IPC channel for isDirectory
-        throw new Error('isDirectory not implemented');
+        return await window.electronAPI.file.isDirectory(path);
     },
 
     /**
@@ -88,8 +94,7 @@ const electronFsAdapter = {
      * @returns {Promise<void>}
      */
     async copy(source, dest) {
-        // TODO: Add IPC channel for copy
-        throw new Error('copy not implemented');
+        return await window.electronAPI.file.copy(source, dest);
     },
 
     /**
@@ -99,8 +104,7 @@ const electronFsAdapter = {
      * @returns {Promise<void>}
      */
     async move(source, dest) {
-        // TODO: Add IPC channel for move
-        throw new Error('move not implemented');
+        return await window.electronAPI.file.move(source, dest);
     }
 };
 
diff --git a/src/index.html b/src/index.html
index 6d40554..b8a717e 100644
--- a/src/index.html
+++ b/src/index.html
@@ -1275,6 +1275,8 @@
                         </div>
                     </div>
 
+                    <div id="pdf-status-message" class="info-message hidden" aria-live="polite"></div>
+
                     <!-- Progress indicator -->
                     <div id="pdf-progress" class="batch-progress hidden">
                         <div class="progress-bar">
@@ -1605,4 +1607,4 @@
     <script src="utils/ModalManager.js"></script>
     <script src="renderer.js"></script>
 </body>
-</html>
\ No newline at end of file
+</html>
diff --git a/src/main.js b/src/main.js
index f39b0f7..00d9874 100644
--- a/src/main.js
+++ b/src/main.js
@@ -124,6 +124,35 @@ function validatePath(filePath) {
   return { valid: true, resolved };
 }
 
+/**
+ * Resolves a path for operations where the target may not exist yet.
+ * Validates string shape and blocks obviously sensitive locations.
+ * @param {string} filePath
+ * @returns {{ valid: boolean, resolved: string, error?: string }}
+ */
+function resolveWritablePath(filePath) {
+  if (!filePath || typeof filePath !== 'string') {
+    return { valid: false, resolved: '', error: 'Invalid path' };
+  }
+
+  let resolved;
+  try {
+    resolved = path.normalize(path.resolve(filePath));
+  } catch (err) {
+    return { valid: false, resolved: '', error: 'Invalid path format' };
+  }
+
+  if (resolved.includes('\0')) {
+    return { valid: false, resolved: '', error: 'Null byte in path' };
+  }
+
+  if (!isPathAccessible(resolved)) {
+    return { valid: false, resolved, error: 'Path is not accessible' };
+  }
+
+  return { valid: true, resolved };
+}
+
 /**
  * Checks if a resolved path is within allowed directories
  * For an editor app, we allow access to all user-accessible paths
@@ -1000,7 +1029,7 @@ function showAboutDialog() {
 <body>
   <img src="${iconBase64}" class="logo" alt="MarkdownConverter">
   <h1>MarkdownConverter</h1>
-  <div class="version">Version 4.0.0</div>
+  <div class="version">Version 4.1.0</div>
 
   <div class="company">
     <span>by</span>
@@ -2793,9 +2822,13 @@ ipcMain.on('save-file', (event, { path, content }) => {
   currentFile = path;
 });
 
-ipcMain.on('save-current-file', (event, content) => {
-  if (currentFile) {
-    fs.writeFileSync(currentFile, content, 'utf-8');
+ipcMain.on('save-current-file', (event, payload) => {
+  const content = typeof payload === 'string' ? payload : payload?.content;
+  const targetFile = typeof payload === 'string' ? currentFile : payload?.filePath || currentFile;
+
+  if (targetFile) {
+    fs.writeFileSync(targetFile, content, 'utf-8');
+    currentFile = targetFile;
   } else {
     saveAsFile();
   }
@@ -4344,6 +4377,8 @@ ipcMain.handle('list-directory', async (event, dirPath) => {
       .map(e => ({
         name: e.name,
         isDirectory: e.isDirectory(),
+        size: e.isDirectory() ? 0 : fs.statSync(path.join(validation.resolved, e.name)).size,
+        modified: fs.statSync(path.join(validation.resolved, e.name)).mtimeMs,
         path: path.join(validation.resolved, e.name)
       }));
     return { path: validation.resolved, entries };
@@ -4353,6 +4388,103 @@ ipcMain.handle('list-directory', async (event, dirPath) => {
   }
 });
 
+ipcMain.handle('read-file', async (event, filePath) => {
+  const validation = validatePath(filePath);
+  if (!validation.valid || !isPathAccessible(validation.resolved)) {
+    throw new Error(validation.error || 'Invalid file path');
+  }
+
+  return fs.readFileSync(validation.resolved, 'utf-8');
+});
+
+ipcMain.handle('write-file', async (event, payload) => {
+  const validation = resolveWritablePath(payload?.path);
+  if (!validation.valid) {
+    throw new Error(validation.error || 'Invalid file path');
+  }
+
+  fs.mkdirSync(path.dirname(validation.resolved), { recursive: true });
+  fs.writeFileSync(validation.resolved, payload?.content ?? '', 'utf-8');
+  return { path: validation.resolved };
+});
+
+ipcMain.handle('delete-file', async (event, filePath) => {
+  const validation = validatePath(filePath);
+  if (!validation.valid || !isPathAccessible(validation.resolved)) {
+    throw new Error(validation.error || 'Invalid file path');
+  }
+
+  fs.rmSync(validation.resolved, { recursive: true, force: false });
+  return true;
+});
+
+ipcMain.handle('ensure-directory', async (event, dirPath) => {
+  const validation = resolveWritablePath(dirPath);
+  if (!validation.valid) {
+    throw new Error(validation.error || 'Invalid directory path');
+  }
+
+  fs.mkdirSync(validation.resolved, { recursive: true });
+  return validation.resolved;
+});
+
+ipcMain.handle('path-exists', async (event, filePath) => {
+  const validation = resolveWritablePath(filePath);
+  return validation.valid ? fs.existsSync(validation.resolved) : false;
+});
+
+ipcMain.handle('is-directory', async (event, filePath) => {
+  const validation = validatePath(filePath);
+  if (!validation.valid || !isPathAccessible(validation.resolved)) {
+    return false;
+  }
+
+  return fs.statSync(validation.resolved).isDirectory();
+});
+
+ipcMain.handle('copy-path', async (event, payload) => {
+  const sourceValidation = validatePath(payload?.source);
+  const destinationValidation = resolveWritablePath(payload?.destination);
+
+  if (!sourceValidation.valid || !isPathAccessible(sourceValidation.resolved)) {
+    throw new Error(sourceValidation.error || 'Invalid source path');
+  }
+  if (!destinationValidation.valid) {
+    throw new Error(destinationValidation.error || 'Invalid destination path');
+  }
+
+  fs.mkdirSync(path.dirname(destinationValidation.resolved), { recursive: true });
+  fs.cpSync(sourceValidation.resolved, destinationValidation.resolved, { recursive: true });
+  return { source: sourceValidation.resolved, destination: destinationValidation.resolved };
+});
+
+ipcMain.handle('move-path', async (event, payload) => {
+  const sourceValidation = validatePath(payload?.source);
+  const destinationValidation = resolveWritablePath(payload?.destination);
+
+  if (!sourceValidation.valid || !isPathAccessible(sourceValidation.resolved)) {
+    throw new Error(sourceValidation.error || 'Invalid source path');
+  }
+  if (!destinationValidation.valid) {
+    throw new Error(destinationValidation.error || 'Invalid destination path');
+  }
+
+  fs.mkdirSync(path.dirname(destinationValidation.resolved), { recursive: true });
+
+  try {
+    fs.renameSync(sourceValidation.resolved, destinationValidation.resolved);
+  } catch (error) {
+    if (error.code !== 'EXDEV') {
+      throw error;
+    }
+
+    fs.cpSync(sourceValidation.resolved, destinationValidation.resolved, { recursive: true });
+    fs.rmSync(sourceValidation.resolved, { recursive: true, force: false });
+  }
+
+  return { source: sourceValidation.resolved, destination: destinationValidation.resolved };
+});
+
 // Open a file by path (from explorer panel)
 ipcMain.on('open-file-path', (event, filePath) => {
   try {
@@ -4490,4 +4622,4 @@ ipcMain.handle('execute-code', async (event, { code, language }) => {
       });
     });
   });
-});
\ No newline at end of file
+});
diff --git a/src/preload.js b/src/preload.js
index 4087d8e..390d9d9 100644
--- a/src/preload.js
+++ b/src/preload.js
@@ -9,7 +9,7 @@
  * - All IPC channels are explicitly whitelisted
  * - Prevents XSS from escalating to full system access
  *
- * @version 4.0.0
+ * @version 4.1.0
  */
 
 const { contextBridge, ipcRenderer } = require('electron');
@@ -101,6 +101,14 @@ const ALLOWED_SEND_CHANNELS = [
 
   // File Explorer
   'list-directory',
+  'read-file',
+  'write-file',
+  'delete-file',
+  'ensure-directory',
+  'path-exists',
+  'is-directory',
+  'copy-path',
+  'move-path',
 
   // Git
   'git-status',
@@ -321,7 +329,15 @@ contextBridge.exposeInMainWorld('electronAPI', {
     setCurrent: (filePath) => ipcRenderer.send('set-current-file', filePath),
     saveRecent: (recentFiles) => ipcRenderer.send('save-recent-files', recentFiles),
     clearRecent: () => ipcRenderer.send('clear-recent-files'),
-    rendererReady: () => ipcRenderer.send('renderer-ready')
+    rendererReady: () => ipcRenderer.send('renderer-ready'),
+    read: (filePath) => ipcRenderer.invoke('read-file', filePath),
+    write: (filePath, content) => ipcRenderer.invoke('write-file', { path: filePath, content }),
+    delete: (filePath) => ipcRenderer.invoke('delete-file', filePath),
+    ensureDir: (dirPath) => ipcRenderer.invoke('ensure-directory', dirPath),
+    exists: (filePath) => ipcRenderer.invoke('path-exists', filePath),
+    isDirectory: (filePath) => ipcRenderer.invoke('is-directory', filePath),
+    copy: (source, destination) => ipcRenderer.invoke('copy-path', { source, destination }),
+    move: (source, destination) => ipcRenderer.invoke('move-path', { source, destination })
   },
 
   // Theme Operations
diff --git a/src/renderer.js b/src/renderer.js
index cc59c2b..60188d0 100644
--- a/src/renderer.js
+++ b/src/renderer.js
@@ -1,6 +1,6 @@
 /**
  * MarkdownConverter Renderer Process
- * @version 3.0.0
+ * @version 4.1.0
  */
 
 const { ipcRenderer } = require('electron');
@@ -31,6 +31,45 @@ function getZenMode() { if (!_ZenMode) _ZenMode = require('./zen-mode').ZenMode;
 let _showAnalyticsModal;
 function getShowAnalyticsModal() { if (!_showAnalyticsModal) _showAnalyticsModal = require('./analytics/analytics-panel').showAnalyticsModal; return _showAnalyticsModal; }
 
+function ensureToastContainer() {
+    let container = document.getElementById('app-toast-container');
+    if (!container) {
+        container = document.createElement('div');
+        container.id = 'app-toast-container';
+        container.className = 'app-toast-container';
+        document.body.appendChild(container);
+    }
+    return container;
+}
+
+function notifyUser(message, type = 'info', options = {}) {
+    if (!message) return;
+
+    const { duration = 3500 } = options;
+    const container = ensureToastContainer();
+    const toast = document.createElement('div');
+    toast.className = `app-toast app-toast-${type}`;
+    toast.setAttribute('role', type === 'warning' ? 'alert' : 'status');
+    toast.textContent = message;
+    container.appendChild(toast);
+
+    requestAnimationFrame(() => {
+        toast.classList.add('visible');
+    });
+
+    const dismiss = () => {
+        toast.classList.remove('visible');
+        setTimeout(() => toast.remove(), 180);
+    };
+
+    if (duration > 0) {
+        setTimeout(dismiss, duration);
+    }
+
+    toast.addEventListener('click', dismiss);
+    return toast;
+}
+
 // Configure marked with highlight extension
 marked.use(markedHighlight({
     highlight: function(code, lang) {
@@ -357,7 +396,7 @@ class TabManager {
         } catch (error) {
             console.error('Error loading PDF:', error);
             document.getElementById('status-text').textContent = 'Error loading PDF';
-            alert('Error loading PDF: ' + error.message);
+            notifyUser(`Error loading PDF: ${error.message}`, 'warning');
         }
     }
 
@@ -457,9 +496,7 @@ class TabManager {
 
         // Notify main process about current file for exports
         const tab = this.tabs.get(tabId);
-        if (tab?.filePath) {
-            ipcRenderer.send('set-current-file', tab.filePath);
-        }
+        ipcRenderer.send('set-current-file', tab?.filePath || null);
 
         // Refresh outline panel for new tab content
         if (outlinePanelContainer?._refreshOutline) outlinePanelContainer._refreshOutline();
@@ -1729,7 +1766,7 @@ document.addEventListener('DOMContentLoaded', () => {
         // Auto-save logic for all tabs
         tabManager.tabs.forEach(tab => {
             if (tab.isDirty && tab.filePath) {
-                ipcRenderer.send('save-current-file', tab.content);
+                ipcRenderer.send('save-current-file', { filePath: tab.filePath, content: tab.content });
             }
         });
     }, 30000);
@@ -1753,7 +1790,7 @@ ipcRenderer.on('file-save', () => {
     const currentContent = tabManager.getCurrentContent();
     const currentFilePath = tabManager.getCurrentFilePath();
     // send to main process which will save or trigger save-as dialog
-    ipcRenderer.send('save-current-file', currentContent);
+    ipcRenderer.send('save-current-file', { filePath: currentFilePath, content: currentContent });
 });
 
 ipcRenderer.on('get-content-for-save', (event, filePath) => {
@@ -1870,7 +1907,7 @@ function openPrintPreviewDialog() {
     const previewContent = document.getElementById(`preview-${activeTabId}`);
 
     if (!previewContent || !previewContent.innerHTML.trim()) {
-        alert('Nothing to print. Please create or open a document and ensure the preview is visible.');
+        notifyUser('Nothing to print. Create or open a document and keep the preview visible.', 'warning');
         return;
     }
 
@@ -2112,7 +2149,7 @@ function saveCurrentProfile() {
     // Select the newly created profile
     document.getElementById('export-profile-select').value = profileName;
 
-    alert(`Profile "${profileName}" saved successfully!`);
+    notifyUser(`Profile "${profileName}" saved successfully.`, 'success');
 }
 
 function loadProfile(profileName) {
@@ -2152,7 +2189,7 @@ function deleteSelectedProfile() {
     const profileName = select.value;
 
     if (!profileName) {
-        alert('Please select a profile to delete.');
+        notifyUser('Select a profile to delete.', 'warning');
         return;
     }
 
@@ -2161,7 +2198,7 @@ function deleteSelectedProfile() {
         saveExportProfiles();
         populateProfileDropdown();
         select.value = '';
-        alert(`Profile "${profileName}" deleted successfully!`);
+        notifyUser(`Profile "${profileName}" deleted successfully.`, 'success');
     }
 }
 
@@ -2855,7 +2892,8 @@ document.addEventListener('DOMContentLoaded', () => {
                 const includeSubfolders = document.getElementById('converter-batch-subfolders').checked;
 
                 if (!inputFolder || !outputFolder) {
-                    alert('Please select both input and output folders for batch conversion');
+                    document.getElementById('converter-progress').classList.remove('hidden');
+                    document.getElementById('converter-status').textContent = 'Select both input and output folders for batch conversion.';
                     return;
                 }
 
@@ -2877,7 +2915,8 @@ document.addEventListener('DOMContentLoaded', () => {
                 const filePath = converterFilePath;
 
                 if (!filePath) {
-                    alert('Please select a file to convert');
+                    document.getElementById('converter-progress').classList.remove('hidden');
+                    document.getElementById('converter-status').textContent = 'Select a file to convert.';
                     return;
                 }
 
@@ -3025,7 +3064,13 @@ function showPDFEditorDialog(operation, openedFilePath = null) {
 
 function hidePDFEditorDialog() {
     window.modals.pdfEditorModal.close();
+    clearPDFStatus();
     document.getElementById('pdf-progress').classList.add('hidden');
+    document.getElementById('pdf-progress-text').textContent = 'Processing...';
+    const progressFill = document.getElementById('pdf-progress-fill');
+    if (progressFill) {
+        progressFill.style.width = '0%';
+    }
     currentPDFOperation = null;
 }
 
@@ -3226,7 +3271,7 @@ document.addEventListener('DOMContentLoaded', () => {
         loadCurrentOrder.addEventListener('click', () => {
             const inputPath = document.getElementById('reorder-input-path').value;
             if (!inputPath) {
-                alert('Please select a PDF file first');
+                showPDFValidationMessage('Select a PDF file before loading the current page order.', '#reorder-input-path');
                 return;
             }
             // Request page count from main process
@@ -3243,7 +3288,7 @@ ipcRenderer.on('pdf-folder-selected', (event, { inputId, path }) => {
 // Handle PDF page count response
 ipcRenderer.on('pdf-page-count', (event, { count, error }) => {
     if (error) {
-        alert('Error reading PDF: ' + error);
+        showPDFStatus(`Error reading PDF: ${error}`, 'warning');
         return;
     }
 
@@ -3253,6 +3298,39 @@ ipcRenderer.on('pdf-page-count', (event, { count, error }) => {
     document.getElementById('reorder-pages').value = currentOrder;
 });
 
+function getPDFStatusElement() {
+    return document.getElementById('pdf-status-message');
+}
+
+function showPDFStatus(message, type = 'info') {
+    const status = getPDFStatusElement();
+    if (!status) return;
+
+    status.textContent = message;
+    status.classList.remove('hidden', 'info-message', 'warning-message', 'success-message');
+    status.classList.add(`${type}-message`);
+}
+
+function clearPDFStatus() {
+    const status = getPDFStatusElement();
+    if (!status) return;
+
+    status.textContent = '';
+    status.classList.remove('info-message', 'warning-message', 'success-message');
+    status.classList.add('hidden');
+}
+
+function showPDFValidationMessage(message, focusSelector = null) {
+    showPDFStatus(message, 'warning');
+
+    if (focusSelector) {
+        const field = document.querySelector(focusSelector);
+        if (field && typeof field.focus === 'function') {
+            field.focus();
+        }
+    }
+}
+
 // Process PDF Operation
 function processPDFOperation() {
     const operation = currentPDFOperation;
@@ -3262,13 +3340,13 @@ function processPDFOperation() {
         switch (operation) {
             case 'merge':
                 if (mergeFilePaths.length < 2) {
-                    alert('Please add at least 2 PDF files to merge');
+                    showPDFValidationMessage('Add at least 2 PDF files to merge first.', '#add-merge-file');
                     return;
                 }
                 operationData.inputFiles = mergeFilePaths;
                 operationData.outputPath = document.getElementById('merge-output-path').value.trim();
                 if (!operationData.outputPath) {
-                    alert('Please select an output file path');
+                    showPDFValidationMessage('Select an output file path.', '#merge-output-path');
                     return;
                 }
                 break;
@@ -3279,7 +3357,7 @@ function processPDFOperation() {
                 operationData.splitMode = document.getElementById('split-mode').value;
 
                 if (!operationData.inputPath || !operationData.outputFolder) {
-                    alert('Please select input file and output folder');
+                    showPDFValidationMessage('Select both an input PDF and an output folder.', '#split-input-path');
                     return;
                 }
 
@@ -3302,7 +3380,10 @@ function processPDFOperation() {
                 operationData.optimizeFonts = document.getElementById('compress-optimize-fonts').checked;
 
                 if (!operationData.inputPath || !operationData.outputPath) {
-                    alert('Please select input file' + (operationData.overwrite ? '' : ' and output file paths'));
+                    showPDFValidationMessage(
+                        'Select an input PDF' + (operationData.overwrite ? '.' : ' and an output file path.'),
+                        '#compress-input-path'
+                    );
                     return;
                 }
                 break;
@@ -3315,7 +3396,10 @@ function processPDFOperation() {
                 operationData.angle = parseInt(document.getElementById('rotate-angle').value);
 
                 if (!operationData.inputPath || !operationData.outputPath) {
-                    alert('Please select input file' + (operationData.overwrite ? '' : ' and output file'));
+                    showPDFValidationMessage(
+                        'Select an input PDF' + (operationData.overwrite ? '.' : ' and an output file path.'),
+                        '#rotate-input-path'
+                    );
                     return;
                 }
                 break;
@@ -3327,7 +3411,7 @@ function processPDFOperation() {
                 operationData.pages = document.getElementById('delete-pages').value.trim();
 
                 if (!operationData.inputPath || !operationData.outputPath || !operationData.pages) {
-                    alert('Please fill in all required fields');
+                    showPDFValidationMessage('Fill in the input file, output path, and pages to delete.', '#delete-input-path');
                     return;
                 }
                 break;
@@ -3339,7 +3423,7 @@ function processPDFOperation() {
                 operationData.newOrder = document.getElementById('reorder-pages').value.trim();
 
                 if (!operationData.inputPath || !operationData.outputPath || !operationData.newOrder) {
-                    alert('Please fill in all required fields');
+                    showPDFValidationMessage('Fill in the input file, output path, and new page order.', '#reorder-input-path');
                     return;
                 }
                 break;
@@ -3360,7 +3444,7 @@ function processPDFOperation() {
                 }
 
                 if (!operationData.inputPath || !operationData.outputPath || !operationData.text) {
-                    alert('Please fill in all required fields');
+                    showPDFValidationMessage('Fill in the input file, output path, and watermark text.', '#watermark-input-path');
                     return;
                 }
                 break;
@@ -3385,7 +3469,7 @@ function processPDFOperation() {
                 };
 
                 if (!operationData.inputPath || !operationData.outputPath || !operationData.userPassword) {
-                    alert('Please select file and enter a user password');
+                    showPDFValidationMessage('Select a file, output path, and user password.', '#encrypt-input-path');
                     return;
                 }
                 break;
@@ -3397,7 +3481,7 @@ function processPDFOperation() {
                 operationData.password = document.getElementById('decrypt-password').value;
 
                 if (!operationData.inputPath || !operationData.outputPath || !operationData.password) {
-                    alert('Please fill in all required fields');
+                    showPDFValidationMessage('Fill in the input file, output path, and password.', '#decrypt-input-path');
                     return;
                 }
                 break;
@@ -3421,21 +3505,26 @@ function processPDFOperation() {
                 };
 
                 if (!operationData.inputPath || !operationData.outputPath || !operationData.ownerPassword) {
-                    alert('Please fill in all required fields');
+                    showPDFValidationMessage('Fill in the input file, output path, and owner password.', '#permissions-input-path');
                     return;
                 }
                 break;
         }
 
+        clearPDFStatus();
         // Show progress
         document.getElementById('pdf-progress').classList.remove('hidden');
         document.getElementById('pdf-progress-text').textContent = 'Processing PDF...';
+        const progressFill = document.getElementById('pdf-progress-fill');
+        if (progressFill) {
+            progressFill.style.width = '10%';
+        }
 
         // Send to main process
         ipcRenderer.send('process-pdf-operation', operationData);
 
     } catch (error) {
-        alert('Error: ' + error.message);
+        showPDFStatus(`Error: ${error.message}`, 'warning');
         console.error('PDF operation error:', error);
     }
 }
@@ -3445,10 +3534,14 @@ ipcRenderer.on('pdf-operation-complete', (event, { success, error, message }) =>
     document.getElementById('pdf-progress').classList.add('hidden');
 
     if (success) {
-        alert(message || 'PDF operation completed successfully!');
-        hidePDFEditorDialog();
+        showPDFStatus(message || 'PDF operation completed successfully.', 'success');
+        setTimeout(() => {
+            if (window.modals?.pdfEditorModal?.isOpen()) {
+                hidePDFEditorDialog();
+            }
+        }, 800);
     } else {
-        alert('Error: ' + (error || 'PDF operation failed'));
+        showPDFStatus(`Error: ${error || 'PDF operation failed'}`, 'warning');
     }
 });
 
@@ -3780,13 +3873,13 @@ function insertGeneratedTable() {
     const table = document.getElementById('table-preview').textContent;
 
     if (!table) {
-        alert('Please generate a table preview first');
+        notifyUser('Generate a table preview first.', 'warning');
         return;
     }
 
     // Insert table using CodeMirror
     if (!tabManager) {
-        alert('No active editor found');
+        notifyUser('No active editor found.', 'warning');
         return;
     }
 
@@ -4254,13 +4347,13 @@ function insertASCIIArt() {
     const asciiArt = document.getElementById('ascii-preview').textContent;
 
     if (!asciiArt || asciiArt === 'Select a template from the buttons above') {
-        alert('Please generate ASCII art first');
+        notifyUser('Generate ASCII art first.', 'warning');
         return;
     }
 
     // Insert using CodeMirror
     if (!tabManager) {
-        alert('No active editor found');
+        notifyUser('No active editor found.', 'warning');
         return;
     }
 
@@ -4683,14 +4776,25 @@ document.addEventListener('DOMContentLoaded', () => {
 // ============================================
 
 ipcRenderer.on('show-image-tool', (event, tool) => {
-    alert(`Image ${tool} tool requires ImageMagick to be installed.\n\nPlease install ImageMagick from: https://imagemagick.org/\n\nThis feature will be available in a future update with built-in support.`);
+    notifyUser(
+        `Image ${tool} requires ImageMagick. Install it from imagemagick.org to enable this tool.`,
+        'info',
+        { duration: 5000 }
+    );
 });
 
 ipcRenderer.on('show-audio-tool', (event, tool) => {
-    alert(`Audio ${tool} tool requires FFmpeg to be installed.\n\nPlease install FFmpeg from: https://ffmpeg.org/\n\nThis feature will be available in a future update with built-in support.`);
+    notifyUser(
+        `Audio ${tool} requires FFmpeg. Install it from ffmpeg.org to enable this tool.`,
+        'info',
+        { duration: 5000 }
+    );
 });
 
 ipcRenderer.on('show-video-tool', (event, tool) => {
-    alert(`Video ${tool} tool requires FFmpeg to be installed.\n\nPlease install FFmpeg from: https://ffmpeg.org/\n\nThis feature will be available in a future update with built-in support.`);
+    notifyUser(
+        `Video ${tool} requires FFmpeg. Install it from ffmpeg.org to enable this tool.`,
+        'info',
+        { duration: 5000 }
+    );
 });
-
diff --git a/src/styles-concreteinfo.css b/src/styles-concreteinfo.css
index aa80553..7b584c7 100644
--- a/src/styles-concreteinfo.css
+++ b/src/styles-concreteinfo.css
@@ -1,7 +1,7 @@
 /**
  * ConcreteInfo Theme for MarkdownConverter
  * Based on logo palette: #464646, #9a9696, #e5461f, #e3e3e3, #0d0b09
- * Version: 3.0.0
+ * Version: 4.1.0
  */
 
 /* ============================================
diff --git a/src/styles.css b/src/styles.css
index 85fdfd0..c713715 100644
--- a/src/styles.css
+++ b/src/styles.css
@@ -522,6 +522,54 @@ body.dark .pdf-tab-container .pdf-controls {
     flex-shrink: 0;
 }
 
+.app-toast-container {
+    position: fixed;
+    top: 16px;
+    right: 16px;
+    display: flex;
+    flex-direction: column;
+    gap: 10px;
+    z-index: var(--z-toast, 500);
+    pointer-events: none;
+}
+
+.app-toast {
+    min-width: 260px;
+    max-width: 420px;
+    padding: 12px 14px;
+    border-radius: 8px;
+    box-shadow: 0 10px 24px rgba(0, 0, 0, 0.18);
+    color: #111827;
+    background: #ffffff;
+    border-left: 4px solid #3b82f6;
+    opacity: 0;
+    transform: translateY(-8px);
+    transition: opacity 0.18s ease, transform 0.18s ease;
+    pointer-events: auto;
+    cursor: pointer;
+    font-size: 13px;
+    line-height: 1.4;
+}
+
+.app-toast.visible {
+    opacity: 1;
+    transform: translateY(0);
+}
+
+.app-toast-info {
+    border-left-color: #2563eb;
+}
+
+.app-toast-success {
+    border-left-color: #059669;
+    background: #ecfdf5;
+}
+
+.app-toast-warning {
+    border-left-color: #d97706;
+    background: #fffbeb;
+}
+
 /* Dark theme adjustments for states */
 body[class*="dark"] .preview-error-message {
     color: #9ca3af;
diff --git a/src/styles/modal.css b/src/styles/modal.css
index 38fc52f..31e9fcf 100644
--- a/src/styles/modal.css
+++ b/src/styles/modal.css
@@ -1,7 +1,7 @@
 /**
  * Modal System Styles
  * Unified modal components with glassmorphism backdrop
- * @version 4.0.0
+ * @version 4.1.0
  */
 
 /* ============================================
diff --git a/src/utils/ModalManager.js b/src/utils/ModalManager.js
index b837fda..3dcd2a6 100644
--- a/src/utils/ModalManager.js
+++ b/src/utils/ModalManager.js
@@ -1,6 +1,6 @@
 /**
  * ModalManager - Unified modal system with accessibility support
- * @version 4.0.0
+ * @version 4.1.0
  */
 class ModalManager {
     #modal;
diff --git a/src/welcome.js b/src/welcome.js
index 8045727..ffb7b30 100644
--- a/src/welcome.js
+++ b/src/welcome.js
@@ -10,7 +10,7 @@ function createWelcomeContent(recentFiles = []) {
     <div class="welcome-container">
         <div class="welcome-hero">
             <h1 class="welcome-title">MarkdownConverter</h1>
-            <p class="welcome-version">Version 4.0.0</p>
+            <p class="welcome-version">Version 4.1.0</p>
             <p class="welcome-subtitle">Professional Markdown Editor & Universal Document Converter</p>
         </div>
 
@@ -45,7 +45,7 @@ function createWelcomeContent(recentFiles = []) {
             </div>
 
             <div class="welcome-section">
-                <h2>What's New in v4.0.0</h2>
+                <h2>What's New in v4.x</h2>
                 <ul class="welcome-features">
                     <li><strong>CodeMirror Editor</strong> — Syntax highlighting, code folding, multiple cursors</li>
                     <li><strong>Sidebar Panels</strong> — File Explorer, Git, Snippets, Templates</li>
diff --git a/tests/preload.test.js b/tests/preload.test.js
index 8fb3738..4f585bb 100644
--- a/tests/preload.test.js
+++ b/tests/preload.test.js
@@ -54,6 +54,14 @@ describe('Preload Security', () => {
       'save-pasted-image',
       'load-template',
       'list-directory',
+      'read-file',
+      'write-file',
+      'delete-file',
+      'ensure-directory',
+      'path-exists',
+      'is-directory',
+      'copy-path',
+      'move-path',
       'open-file-path',
       'git-status',
       'git-stage',
diff --git a/tests/setup.js b/tests/setup.js
index 7090e7a..9efc364 100644
--- a/tests/setup.js
+++ b/tests/setup.js
@@ -17,7 +17,15 @@ global.window.electronAPI = {
     setCurrent: jest.fn(),
     saveRecent: jest.fn(),
     clearRecent: jest.fn(),
-    rendererReady: jest.fn()
+    rendererReady: jest.fn(),
+    read: jest.fn(() => Promise.resolve('')),
+    write: jest.fn(() => Promise.resolve()),
+    delete: jest.fn(() => Promise.resolve()),
+    ensureDir: jest.fn(() => Promise.resolve()),
+    exists: jest.fn(() => Promise.resolve(false)),
+    isDirectory: jest.fn(() => Promise.resolve(false)),
+    copy: jest.fn(() => Promise.resolve()),
+    move: jest.fn(() => Promise.resolve())
   },
   theme: {
     get: jest.fn()