diff --git a/assets/linked-workspace-guide.md b/assets/linked-workspace-guide.md
new file mode 100644
index 00000000..2e868c26
--- /dev/null
+++ b/assets/linked-workspace-guide.md
@@ -0,0 +1,35 @@
+# Welcome to Linked Workspace
+
+Linked Workspace lets you edit Markdown files where they already live on your computer.
+
+## Link a file or folder
+
+Use **Link Markdown files** or **Link a Markdown folder** in the Explorer toolbar or the New menu. A linked folder includes Markdown files in its subfolders.
+
+Linked documents use a file-with-arrow icon; linked folders use a folder-with-arrow icon. Hover over a linked document to see its original path.
+
+## Drafts and saving
+
+Editing automatically stores a recovery draft inside the application's **Linked Workspace** storage folder. It does **not** automatically overwrite your original file.
+
+- **Ctrl+S** or **Save** updates the original linked file.
+- **Save As** creates a new external file and a separate link. The previous document and original remain unchanged.
+- Saving a Vault document externally keeps its independent Vault copy and activates the new linked document.
+
+## Independent Vault copies
+
+**Convert to Workspace copy** turns a linked draft into an independent Vault document without changing the original. You can also drag a linked document into the Vault or one of its folders.
+
+Reopening the original creates or activates its link; it never replaces the independent Vault copy.
+
+## External changes and rescanning
+
+The application checks linked sources for external changes. If your local draft conflicts with a changed original, it keeps the draft and shows a warning.
+
+**Rescan folder** discovers new files and restores links previously removed or converted, if the originals still exist. Re-linking the same folder does the same. Automatic background refreshes respect removed links instead of restoring them.
+
+## Closing and removing
+
+Closing a tab keeps its document in the workspace. **Remove linked file** or **Remove linked folder** removes links from the application, not the originals from disk.
+
+This guide is an internal, editable document, not a link to an external file. You can delete it without deleting any source file; it will not reappear on every launch.
diff --git a/assets/lucide-icons.css b/assets/lucide-icons.css
index 9d216ce9..79318c61 100644
--- a/assets/lucide-icons.css
+++ b/assets/lucide-icons.css
@@ -3,6 +3,9 @@
  * Source: https://lucide.dev/ • ISC License
  * Only icons used by Markdown Viewer are embedded with a 1.5px stroke. No runtime JavaScript or webfont is loaded.
  */
+.lucide-file-symlink { --lucide-icon: url("data:image/svg+xml;base64,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"); }
+.lucide-folder-symlink { --lucide-icon: url("data:image/svg+xml;base64,PCEtLSBAbGljZW5zZSBsdWNpZGUtc3RhdGljIHYxLjI1LjAgLSBJU0MgLS0+PHN2ZyBjbGFzcz0ibHVjaWRlIGx1Y2lkZS1mb2xkZXItc3ltbGluayIgeG1sbnM9Imh0dHA6Ly93d3cudzMub3JnLzIwMDAvc3ZnIiB3aWR0aD0iMjQiIGhlaWdodD0iMjQiIHZpZXdCb3g9IjAgMCAyNCAyNCIgZmlsbD0ibm9uZSIgc3Ryb2tlPSJibGFjayIgc3Ryb2tlLXdpZHRoPSIxLjUiIHN0cm9rZS1saW5lY2FwPSJyb3VuZCIgc3Ryb2tlLWxpbmVqb2luPSJyb3VuZCI+PHBhdGggZD0iTTIgOS4zNVY1YTIgMiAwIDAgMSAyLTJoMy45YTIgMiAwIDAgMSAxLjY5LjlsLjgxIDEuMmEyIDIgMCAwIDAgMS42Ny45SDIwYTIgMiAwIDAgMSAyIDJ2MTBhMiAyIDAgMCAxLTIgMkg0YTIgMiAwIDAgMS0yLTJ2LTNhMiAyIDAgMCAxIDItMmg3Ii8+PHBhdGggZD0ibTggMTYgMy0zLTMtMyIvPjwvc3ZnPg=="); }
+
 .lucide {
   display: inline-block;
   width: 1em;
diff --git a/desktop-app/README.md b/desktop-app/README.md
index a0a78103..b4c9cac7 100644
--- a/desktop-app/README.md
+++ b/desktop-app/README.md
@@ -34,6 +34,15 @@ Desktop-only files:
 - Document metadata loads at startup; Markdown content loads only when a document is opened and is kept in a bounded in-memory cache.
 - Native Markdown/HTML save and Markdown open flows use Neutralino dialogs and filesystem APIs.
 - A Markdown file passed as a launch argument is loaded into the editor.
+- Files opened from disk can remain linked to their original path. Workspace (Vault) copies are separate documents; converting a linked file to a copy leaves its source untouched.
+- Linked files keep an app-local draft, but write to the original only on Ctrl+S. Reopening the same path selects its existing document rather than making another copy.
+- **Link a Markdown folder** adds its Markdown files under Linked Workspace, alongside Workspace (Vault) and Secret Workspace. Nested folders can be expanded independently; source paths appear on hover. Files added or changed outside the app are detected while the desktop app is running; a locally edited draft is not silently overwritten by an external change.
+- Linked recovery drafts are stored separately under `Markdown Viewer Vault/Linked Workspace`; normal copies remain under `Markdown Viewer Vault/Workspace`. Existing linked drafts migrate safely. The default Linked Workspace guide is editable and is not recreated after intentional deletion.
+- Converted Vault copies stay independent even when the original is reopened. Explicit **Rescan folder** or re-adding the folder restores removed links without replacing those copies; background scans respect removals.
+- Linked context menus offer **Save** and **Save As**. Save updates the current source; Save As creates a separate external file and link. Vault Save As (or Ctrl+S) preserves the Vault document and focuses the external linked copy. Dialogs propose the document title and add `.md` when no extension is given. Ctrl+S also works with non-Latin keyboard layouts; Ctrl+Shift+S retains scroll-sync behavior.
+- Dragging a linked document onto the Vault root or a Vault folder converts it into an independent copy there. The original is unchanged. Secret Workspace and reverse Vault-to-linked drops are not supported. Ordinary Vault moves use the existing HTML drag-and-drop behavior.
+- Native linked controls and Save/Save As actions are desktop-only. Browser/Docker users retain normal stored documents and Markdown downloads. Desktop workflows are validated on Windows; macOS/Linux have not been manually verified. No custom Neutralino runtime is required by this feature.
+- Removing a link removes the app's reference, not the original file or folder. Native file drops are not covered by the linked-file flow in this build.
 - The app asks before closing the window.
 - Prepared desktop resources load dynamic libraries from local `/libs/...` paths after setup.
 - Private mode pauses document-state persistence for the current page session without deleting the vault, shows an active incognito status, and resets on reload or exit. **Reset workspace** permanently deletes documents, folders, review data, settings, Secret Workspace records, history, trash, and recovery journals after confirmation.
@@ -81,7 +90,7 @@ Seven self-contained executables are written to `desktop-app/dist/markdown-viewe
 | Token security | One-time |
 | Logging | Disabled |
 
-Native APIs are intentionally allowlisted: app exit, open/save dialogs, message boxes, external URL/folder open, tray setup, scoped file and folder operations, path lookup, and storage get/set/remove. Command execution is not part of the default allowlist.
+Native APIs are intentionally allowlisted: app exit, open/save/folder dialogs, message boxes, external URL/folder open, tray setup, scoped file and folder operations, filesystem watchers, path lookup, and storage get/set/remove. Command execution is not part of the default allowlist.
 
 ## Local Renderer Security
 
diff --git a/desktop-app/neutralino.config.json b/desktop-app/neutralino.config.json
index 7239f796..3dcc68e5 100644
--- a/desktop-app/neutralino.config.json
+++ b/desktop-app/neutralino.config.json
@@ -18,6 +18,7 @@
   "nativeAllowList": [
     "app.exit",
     "os.showOpenDialog",
+    "os.showFolderDialog",
     "os.showSaveDialog",
     "os.showMessageBox",
     "os.getPath",
@@ -34,6 +35,9 @@
     "filesystem.copy",
     "filesystem.move",
     "filesystem.remove",
+    "filesystem.createWatcher",
+    "filesystem.removeWatcher",
+    "filesystem.getWatchers",
     "storage.setData",
     "storage.getData",
     "storage.getKeys",
diff --git a/desktop-app/resources/index.html b/desktop-app/resources/index.html
index 3cfcbe2b..66e172f3 100644
--- a/desktop-app/resources/index.html
+++ b/desktop-app/resources/index.html
@@ -72,7 +72,9 @@ <h1 class="h4 mb-0">Markdown Viewer<span class="visually-hidden"> - Online Markd
                         </button>
                         <ul class="dropdown-menu app-command-menu header-command-menu header-new-menu" aria-labelledby="importDropdown">
                             <li><a class="dropdown-item app-menu-item" href="#" id="header-new-document"><i class="lucide lucide-file-plus-2" aria-hidden="true"></i><span class="app-menu-label">New document</span></a></li>
-                            <li><a class="dropdown-item app-menu-item" href="#" id="import-from-file"><i class="lucide lucide-upload" aria-hidden="true"></i><span class="app-menu-label">From files</span></a></li>
+                            <li><a class="dropdown-item app-menu-item" href="#" id="import-from-file"><i class="lucide lucide-files" aria-hidden="true"></i><span class="app-menu-label">From files</span></a></li>
+                            <li class="desktop-linked-command" hidden><a class="dropdown-item app-menu-item" href="#" id="link-from-file"><i class="lucide lucide-file-symlink" aria-hidden="true"></i><span class="app-menu-label">Link files…</span></a></li>
+                            <li class="desktop-linked-command" hidden><a class="dropdown-item app-menu-item" href="#" id="link-from-folder"><i class="lucide lucide-folder-symlink" aria-hidden="true"></i><span class="app-menu-label">Link folder…</span></a></li>
                             <li><a class="dropdown-item app-menu-item" href="#" id="import-from-github"><i class="bi bi-github" aria-hidden="true"></i><span class="app-menu-label">From GitHub</span></a></li>
                         </ul>
                     </div>
@@ -346,6 +348,12 @@ <h2 id="document-sidebar-title">Explorer</h2>
                 <button id="sidebar-new-folder" class="document-sidebar-icon-btn" type="button" aria-label="Create a folder" title="New folder">
                   <i class="lucide lucide-folder-plus" aria-hidden="true"></i>
                 </button>
+                <button id="sidebar-link-files" class="document-sidebar-icon-btn desktop-linked-command" type="button" aria-label="Link Markdown files" title="Link Markdown files" hidden>
+                  <i class="lucide lucide-file-symlink" aria-hidden="true"></i>
+                </button>
+                <button id="sidebar-link-folder" class="document-sidebar-icon-btn desktop-linked-command" type="button" aria-label="Link a Markdown folder" title="Link a Markdown folder" hidden>
+                    <i class="lucide lucide-folder-symlink" aria-hidden="true"></i>
+                </button>
                 <button id="sidebar-trash-button" class="document-sidebar-icon-btn" type="button" aria-label="Open Trash" title="Trash">
                   <i class="lucide lucide-trash-2" aria-hidden="true"></i>
                 </button>
diff --git a/desktop-app/resources/js/main.js b/desktop-app/resources/js/main.js
index 7e92a51d..8833c71b 100644
--- a/desktop-app/resources/js/main.js
+++ b/desktop-app/resources/js/main.js
@@ -131,6 +131,14 @@ if (isNeutralinoRuntime()) {
     // TODO: Fix https://github.com/neutralinojs/neutralinojs/issues/615
     setTray();
   }
+
+  window.addEventListener('markdown-viewer:ready', function() {
+    if (typeof window.NL_START_LINKED_MONITORING === 'function') {
+      window.NL_START_LINKED_MONITORING().catch(function(error) {
+        console.warn('Linked source monitoring initialization failed:', error);
+      });
+    }
+  }, { once: true });
 }
 
 // Open file passed as command-line argument (e.g. when double-clicking a .md file)
@@ -146,12 +154,13 @@ if (isNeutralinoRuntime()) {
     
     window.NL_INITIAL_FILE_CONTENT = {
       name: fileName,
-      content: content
+      content: content,
+      sourcePath: filePath
     };
 
     // Callback hook in case script.js loaded first
     if (window.NL_IMPORT_EXTERNAL_FILE) {
-      window.NL_IMPORT_EXTERNAL_FILE(content, fileName);
+      window.NL_IMPORT_EXTERNAL_FILE(content, fileName, filePath);
     }
   } catch (e) {
     console.warn('Could not open initial file:', e);
diff --git a/desktop-app/resources/js/script.js b/desktop-app/resources/js/script.js
index 0484e8c7..f3f2ccf7 100644
--- a/desktop-app/resources/js/script.js
+++ b/desktop-app/resources/js/script.js
@@ -3,6 +3,7 @@ document.addEventListener("DOMContentLoaded", async function () {
   const PRIVATE_MODE_KEY = 'markdownViewerPrivateMode';
   const APP_VERSION = '3.10.3';
   const RELEASE_NOTES_TAB_KIND = 'release-notes';
+  const LINKED_WORKSPACE_GUIDE_KIND = 'linked-workspace-guide';
   const RELEASE_NOTES_LAST_VERSION_KEY = 'markdownViewerLastVersion';
   const RELEASE_NOTES_PENDING_VERSION_KEY = 'markdownViewerPendingReleaseNotesVersion';
   const RELEASE_NOTES_PENDING_MODE_KEY = 'markdownViewerPendingReleaseNotesMode';
@@ -44,6 +45,20 @@ document.addEventListener("DOMContentLoaded", async function () {
     );
   }
 
+  function hasDesktopFileAccess() {
+    return Boolean(typeof Neutralino !== 'undefined' && typeof NL_PORT !== 'undefined' &&
+      Neutralino.filesystem && typeof Neutralino.filesystem.readFile === 'function' &&
+      typeof Neutralino.filesystem.writeFile === 'function' && Neutralino.os);
+  }
+
+  function isLinkedDocument(tab) {
+    return Boolean(hasDesktopFileAccess() && tab && tab.sourcePath);
+  }
+
+  function isLinkedWorkspaceDocument(tab) {
+    return hasDesktopFileAccess() && Boolean(tab && (tab.sourcePath || tab.kind === LINKED_WORKSPACE_GUIDE_KIND));
+  }
+
   const workspaceStorage = typeof window.MarkdownWorkspaceStorage === 'function'
     ? new window.MarkdownWorkspaceStorage()
     : null;
@@ -361,6 +376,8 @@ document.addEventListener("DOMContentLoaded", async function () {
   const themeSwitchIcon = document.getElementById("theme-switch-icon");
   const directionToggle = document.getElementById("direction-toggle");
   const importFromFileButton = document.getElementById("import-from-file");
+  const linkFromFileButton = document.getElementById("link-from-file");
+  const linkFromFolderButton = document.getElementById("link-from-folder");
   const importFromGithubButton = document.getElementById("import-from-github");
   const fileInput = document.getElementById("file-input");
   const exportDropdown = document.getElementById("exportDropdown");
@@ -4207,7 +4224,7 @@ document.addEventListener("DOMContentLoaded", async function () {
   const UNTITLED_COUNTER_KEY = 'markdownViewerUntitledCounter';
   const DOCUMENT_ORGANIZATION_KEY = 'markdownViewerDocumentOrganization';
   const SECRET_WORKSPACE_STORAGE_KEY = 'markdownViewerSecretWorkspace';
-  const DOCUMENT_ORGANIZATION_VERSION = 3;
+  const DOCUMENT_ORGANIZATION_VERSION = 4;
   const SECRET_WORKSPACE_VERSION = 2;
   const SECRET_KDF_ITERATIONS = 250000;
   const DEFAULT_WORKSPACE_ID = 'workspace_default';
@@ -4235,6 +4252,9 @@ document.addEventListener("DOMContentLoaded", async function () {
   let documentTreeDragExpandRow = null;
   let documentTreeAutoScrollFrame = null;
   let documentTreeAutoScrollSpeed = 0;
+  const linkedSourceWatchers = new Map();
+  const linkedSourceRefreshTimers = new Map();
+  let linkedSourceMonitoringReady = false;
   let secretWorkspaceKey = null;
   let secretWorkspaceSalt = null;
   let secretWorkspaceIterations = SECRET_KDF_ITERATIONS;
@@ -4277,7 +4297,7 @@ document.addEventListener("DOMContentLoaded", async function () {
       workspaces: [
         {
           id: DEFAULT_WORKSPACE_ID,
-          name: 'Workspace',
+          name: hasDesktopFileAccess() ? 'Workspace (Vault)' : 'Workspace',
           expanded: true,
           createdAt: 0
         },
@@ -4289,8 +4309,10 @@ document.addEventListener("DOMContentLoaded", async function () {
         }
       ],
       folders: [],
+      linkedLocations: [],
       ui: {
         filter: 'all',
+        linkedWorkspaceExpanded: true,
         collapsed: false,
         width: 288,
         lastWorkspaceId: DEFAULT_WORKSPACE_ID,
@@ -4349,6 +4371,30 @@ document.addEventListener("DOMContentLoaded", async function () {
       }
     });
 
+    const seenLinkedLocationIds = new Set();
+    const linkedLocations = (Array.isArray(source.linkedLocations) ? source.linkedLocations : []).map(function(location) {
+      if (!location || typeof location !== 'object') return null;
+      const id = String(location.id || '').slice(0, 120);
+      const path = String(location.path || '').trim();
+      if (!id || !path || seenLinkedLocationIds.has(id)) return null;
+      seenLinkedLocationIds.add(id);
+      return {
+        id: id,
+        path: path,
+        name: String(location.name || '').trim().slice(0, 160) || path.split(/[/\\]/).filter(Boolean).pop() || 'Linked folder',
+        expanded: location.expanded !== false,
+        collapsedFolderPaths: Array.from(new Set((Array.isArray(location.collapsedFolderPaths) ? location.collapsedFolderPaths : [])
+          .map(function(item) { return String(item || '').replace(/\\/g, '/').replace(/^\/+/, ''); })
+          .filter(Boolean))),
+        excludedPaths: Array.from(new Set((Array.isArray(location.excludedPaths) ? location.excludedPaths : [])
+          .map(function(item) { return String(item || '').replace(/\\/g, '/').replace(/^\/+/, ''); })
+          .filter(Boolean))),
+        createdAt: Number.isFinite(Number(location.createdAt)) ? Number(location.createdAt) : Date.now(),
+        lastScanAt: Number.isFinite(Number(location.lastScanAt)) ? Number(location.lastScanAt) : 0,
+        unavailable: location.unavailable === true
+      };
+    }).filter(Boolean);
+
     const ui = source.ui && typeof source.ui === 'object' ? source.ui : {};
     const allowedFilters = new Set(['all', 'recent', 'favorites']);
     const width = Number(ui.width);
@@ -4360,8 +4406,11 @@ document.addEventListener("DOMContentLoaded", async function () {
       version: DOCUMENT_ORGANIZATION_VERSION,
       workspaces: workspaces,
       folders: folders,
+      linkedLocations: linkedLocations,
       ui: {
         filter: allowedFilters.has(ui.filter) ? ui.filter : 'all',
+        linkedWorkspaceExpanded: ui.linkedWorkspaceExpanded !== false,
+        linkedGuideInitialized: ui.linkedGuideInitialized === true,
         collapsed: ui.collapsed === true,
         width: Number.isFinite(width) ? Math.max(SIDEBAR_MIN_WIDTH, Math.min(SIDEBAR_MAX_WIDTH, width)) : 288,
         lastWorkspaceId: lastWorkspaceId,
@@ -4417,6 +4466,19 @@ document.addEventListener("DOMContentLoaded", async function () {
       folders: documentOrganization.folders.filter(function(folder) {
         return folder.workspaceId !== SECRET_WORKSPACE_ID;
       }),
+      linkedLocations: (documentOrganization.linkedLocations || []).map(function(location) {
+        return {
+          id: location.id,
+          path: location.path,
+          name: location.name,
+          expanded: location.expanded !== false,
+          collapsedFolderPaths: Array.isArray(location.collapsedFolderPaths) ? location.collapsedFolderPaths.slice() : [],
+          excludedPaths: Array.isArray(location.excludedPaths) ? location.excludedPaths.slice() : [],
+          createdAt: location.createdAt,
+          lastScanAt: location.lastScanAt || 0,
+          unavailable: location.unavailable === true
+        };
+      }),
       ui: Object.assign({}, documentOrganization.ui, {
         lastWorkspaceId: documentOrganization.ui.lastWorkspaceId === SECRET_WORKSPACE_ID && !secretWorkspaceKey
           ? DEFAULT_WORKSPACE_ID
@@ -5715,6 +5777,30 @@ document.addEventListener("DOMContentLoaded", async function () {
     document.querySelectorAll('.document-menu-dropdown').forEach(function(menu) { menu.remove(); });
   }
 
+  let linkedBackgroundUIRefreshPending = false;
+
+  function linkedSidebarState() {
+    return JSON.stringify([
+      tabs.filter(function(tab) { return tab.sourcePath; }).map(function(tab) {
+        return [tab.id, tab.title, tab.sourcePath, Boolean(tab.sourceMissing), Boolean(tab.sourceConflict),
+          tab.workspaceId, tab.folderId, tab.linkedRootId, tab.sourceRelativePath, tab.isOpen, tab.favorite];
+      }),
+      (documentOrganization.linkedLocations || []).map(function(location) {
+        return [location.id, location.name, location.path, Boolean(location.unavailable)];
+      })
+    ]);
+  }
+
+  function requestLinkedBackgroundUIRefresh() {
+    if (document.querySelector('.document-menu-dropdown.open, .tab-menu-dropdown.open, [data-tab-context-menu="true"]')) {
+      linkedBackgroundUIRefreshPending = true;
+      return;
+    }
+    linkedBackgroundUIRefreshPending = false;
+    renderTabBar(tabs, activeTabId);
+    renderDocumentSidebar();
+  }
+
   function closeDocumentSidebarMenus() {
     document.querySelectorAll('.document-menu-btn.open').forEach(function(button) {
       button.classList.remove('open');
@@ -5722,6 +5808,7 @@ document.addEventListener("DOMContentLoaded", async function () {
     });
     document.querySelectorAll('.document-menu-dropdown.open').forEach(function(menu) { menu.classList.remove('open'); });
     document.querySelectorAll('.document-menu-context').forEach(function(menu) { menu.remove(); });
+    if (linkedBackgroundUIRefreshPending) queueMicrotask(requestLinkedBackgroundUIRefresh);
   }
 
   function openDocumentMenu(button, menu, position, returnFocus, options) {
@@ -5849,11 +5936,35 @@ document.addEventListener("DOMContentLoaded", async function () {
   }
 
   function getDocumentMenuActions(tab) {
+    if (tab && tab.kind === LINKED_WORKSPACE_GUIDE_KIND) {
+      return [
+        { id: 'open', icon: 'lucide-file-text', label: 'Open', run: function() { openSidebarDocument(tab.id); } },
+        { id: 'favorite', icon: tab.favorite ? 'lucide-star-filled' : 'lucide-star', label: tab.favorite ? 'Remove from Favorites' : 'Add to Favorites', run: function() { toggleDocumentFavorite(tab.id); } },
+        { id: 'download', icon: 'lucide-download', label: 'Download Markdown', run: function() { downloadTabMarkdown(tab.id); } },
+        { id: 'delete', icon: 'lucide-trash-2', label: 'Delete', danger: true, run: function() { deleteTab(tab.id); } }
+      ];
+    }
+    if (isLinkedDocument(tab) && !isTemporaryDocument(tab)) {
+      const linkedActions = [
+        { id: 'open', icon: 'lucide-file-symlink', label: 'Open', run: function() { openSidebarDocument(tab.id); } },
+        { id: 'save', icon: 'lucide-download', label: 'Save', run: function() { void nativeSaveMarkdown({ tabId: tab.id, useLinkedSource: true }); } },
+        { id: 'save-as', icon: 'lucide-file-plus-2', label: 'Save As…', run: function() { void nativeSaveMarkdown({ tabId: tab.id, createLinked: true }); } },
+        { id: 'reload-source', icon: 'lucide-refresh-cw', label: 'Reload from disk', run: function() { void reloadLinkedDocument(tab.id, { force: true }); } },
+        { id: 'reveal-source', icon: 'lucide-folder-symlink', label: 'Open containing folder', run: function() { void revealLinkedSource(tab); } },
+        { separator: true },
+        { id: 'convert-vault', icon: 'lucide-files', label: 'Convert to Workspace copy', run: function() { void convertLinkedDocumentToVault(tab.id); } },
+        { id: 'remove-link', icon: 'lucide-x', label: 'Remove linked file', danger: true, run: function() { void removeLinkedDocument(tab.id); } }
+      ];
+      return linkedActions;
+    }
     const actions = [
       { id: 'open', icon: 'lucide-file-text', label: 'Open', run: function() { openSidebarDocument(tab.id); } }, {
       id: 'rename', icon: 'lucide-square-pen', label: 'Rename', run: function() { renameTab(tab.id); }
     }];
     if (!isTemporaryDocument(tab)) {
+      if (hasDesktopFileAccess() && tab.workspaceId !== SECRET_WORKSPACE_ID) {
+        actions.push({ id: 'save-as', icon: 'lucide-file-plus-2', label: 'Save As…', run: function() { void nativeSaveMarkdown({ tabId: tab.id, createLinked: true }); } });
+      }
       actions.push({ id: 'duplicate', icon: 'lucide-files', label: 'Duplicate', run: function() { duplicateTab(tab.id); } });
       actions.push({
         id: 'favorite',
@@ -5929,6 +6040,10 @@ document.addEventListener("DOMContentLoaded", async function () {
       const workspace = getWorkspaceById(id);
       return workspace ? getWorkspaceMenuActions(workspace) : [];
     }
+    if (type === 'linked-location') {
+      const location = (documentOrganization.linkedLocations || []).find(function(item) { return item.id === id; });
+      return location ? getLinkedLocationMenuActions(location) : [];
+    }
     return [];
   }
 
@@ -6054,6 +6169,10 @@ document.addEventListener("DOMContentLoaded", async function () {
         },
         { separator: true }
       );
+      if (getSelectedDocuments().some(function(tab) { return tab.kind === LINKED_WORKSPACE_GUIDE_KIND; })) {
+        const moveIndex = actions.findIndex(function(action) { return action.id === 'move-selected'; });
+        if (moveIndex >= 0) actions.splice(moveIndex, 1);
+      }
     }
     actions.push({
       id: 'delete-selected',
@@ -6203,8 +6322,7 @@ document.addEventListener("DOMContentLoaded", async function () {
       if (cut) replaceDocumentSurfaceSelection(context, '');
       showAppToast(cut ? 'Selection cut to clipboard.' : 'Selection copied to clipboard.', {
         tone: 'success',
-        title: cut ? 'Cut' : 'Copied',
-        icon: cut ? 'lucide-square-pen' : 'lucide-copy'
+        title: cut ? 'Cut' : 'Copied'
       });
     } catch (error) {
       showAppToast('Clipboard access failed: ' + error.message, { tone: 'error', title: 'Clipboard unavailable' });
@@ -6262,6 +6380,7 @@ document.addEventListener("DOMContentLoaded", async function () {
     const shouldAnnounce = !options || options.announce !== false;
     const tab = tabs.find(function(item) { return item.id === tabId; });
     if (!tab || isTemporaryDocument(tab)) return false;
+    if (tab.kind === LINKED_WORKSPACE_GUIDE_KIND) return false;
     if (workspaceId === SECRET_WORKSPACE_ID && !isSecretWorkspaceUnlocked()) {
       withUnlockedSecretWorkspace(function() {
         moveDocumentToLocation(tabId, workspaceId, folderId, options);
@@ -6517,7 +6636,7 @@ document.addEventListener("DOMContentLoaded", async function () {
           dragOverlay.setAttribute('aria-hidden', 'true');
         }
         const importFiles = function() {
-          handleIncomingDroppedFiles(files, { location: location });
+          handleIncomingDroppedFiles(files, { location: location, source: 'drop' });
         };
         if (location.workspaceId === SECRET_WORKSPACE_ID && !isSecretWorkspaceUnlocked()) {
           withUnlockedSecretWorkspace(importFiles);
@@ -6527,11 +6646,19 @@ document.addEventListener("DOMContentLoaded", async function () {
         return;
       }
       const tabIds = getDraggedSidebarDocumentIds(event.dataTransfer);
-      if (tabIds.length > 1) moveDocumentsToLocation(tabIds, location.workspaceId, location.folderId || null);
-      else if (tabIds.length === 1) moveDocumentToLocation(tabIds[0], location.workspaceId, location.folderId || null);
+      void dropSidebarDocuments(tabIds, location);
     });
   }
 
+  async function dropSidebarDocuments(tabIds, location) {
+    const documents = tabIds.map(function(id) { return tabs.find(function(tab) { return tab.id === id; }); }).filter(Boolean);
+    if (documents.some(isLinkedDocument) && location.workspaceId !== DEFAULT_WORKSPACE_ID) return;
+    for (const tab of documents) {
+      if (isLinkedDocument(tab)) await convertLinkedDocumentToVault(tab.id, location);
+      else await moveDocumentToLocation(tab.id, location.workspaceId, location.folderId || null);
+    }
+  }
+
   function createDocumentTreeRow(options) {
     const row = document.createElement('div');
     row.className = 'document-tree-row';
@@ -6550,6 +6677,7 @@ document.addEventListener("DOMContentLoaded", async function () {
     if (options.favorite) row.classList.add('is-favorite');
     if (options.temporary) row.classList.add('document-tree-temporary');
     if (options.locked) row.classList.add('is-secret-locked');
+    if (options.currentLocation) row.classList.add('is-current-location');
     if (typeof options.expanded === 'boolean') row.setAttribute('aria-expanded', options.expanded ? 'true' : 'false');
     row.setAttribute('aria-label', options.ariaLabel || options.label);
 
@@ -6580,7 +6708,7 @@ document.addEventListener("DOMContentLoaded", async function () {
     main.type = 'button';
     main.className = 'document-tree-main';
     main.setAttribute('tabindex', '-1');
-    main.title = options.label;
+    main.title = options.hoverTitle || options.label;
     const icon = document.createElement('i');
     icon.className = 'lucide ' + options.icon;
     icon.setAttribute('aria-hidden', 'true');
@@ -6625,7 +6753,7 @@ document.addEventListener("DOMContentLoaded", async function () {
       if (event.target.closest('input, select, textarea, a')) return;
       openDocumentTreeContextMenu(row, event);
     });
-    if (options.documentId && !options.temporary) {
+    if (options.documentId && !options.temporary && !options.disableDrag) {
       row.draggable = true;
       row.addEventListener('dragstart', function(event) {
         const rowSelectionKey = getDocumentTreeSelectionKey('document', options.documentId);
@@ -6671,9 +6799,11 @@ document.addEventListener("DOMContentLoaded", async function () {
       type: 'document',
       id: tab.id,
       documentId: tab.id,
+      disableDrag: tab.kind === LINKED_WORKSPACE_GUIDE_KIND,
       label: tab.title || 'Untitled',
-      ariaLabel: (tab.id === activeTabId ? 'Active document, ' : 'Document, ') + (tab.title || 'Untitled') + (tab.favorite ? ', favorite' : ''),
-      icon: 'lucide-file-text',
+      hoverTitle: isLinkedDocument(tab) ? tab.sourcePath : tab.title || 'Untitled',
+      ariaLabel: (tab.id === activeTabId ? 'Active document, ' : 'Document, ') + (tab.title || 'Untitled') + (isLinkedDocument(tab) ? ', linked file' : '') + (tab.favorite ? ', favorite' : ''),
+      icon: isLinkedDocument(tab) ? 'lucide-file-symlink' : 'lucide-file-text',
       depth: depth,
       favorite: tab.favorite === true,
       temporary: isTemporaryDocument(tab),
@@ -6683,6 +6813,12 @@ document.addEventListener("DOMContentLoaded", async function () {
         openSidebarDocument(tab.id);
       }
     });
+    if (isLinkedDocument(tab)) {
+      row.classList.add('is-linked-document');
+      row.title = tab.sourcePath;
+    }
+    if (isLinkedDocument(tab) && tab.sourceMissing) row.classList.add('is-source-missing');
+    if (isLinkedDocument(tab) && tab.sourceConflict) row.classList.add('is-source-conflict');
     container.appendChild(row);
     if (consumesRenderBudget) {
       documentSidebarRenderBudget.remaining = Math.max(0, documentSidebarRenderBudget.remaining - 1);
@@ -6691,6 +6827,8 @@ document.addEventListener("DOMContentLoaded", async function () {
   }
 
   function getDocumentLocationLabel(tab) {
+    if (hasDesktopFileAccess() && tab && tab.kind === LINKED_WORKSPACE_GUIDE_KIND) return 'Linked Workspace';
+    if (isLinkedDocument(tab)) return 'Linked · ' + tab.sourcePath;
     const workspace = getWorkspaceById(tab.workspaceId);
     const folder = getFolderById(tab.folderId);
     if (folder && workspace) return workspace.name + ' / ' + getFolderPath(folder.id);
@@ -6699,10 +6837,19 @@ document.addEventListener("DOMContentLoaded", async function () {
 
   function getDocumentTabHoverTitle(tab) {
     const title = tab && tab.title ? tab.title : 'Untitled';
+    if (isLinkedDocument(tab)) return title + ' — Linked file: ' + tab.sourcePath;
     const folder = tab ? getFolderById(tab.folderId) : null;
     return folder ? getFolderPath(folder.id) + ' / ' + title : title;
   }
 
+  if (hasDesktopFileAccess()) {
+    document.querySelectorAll('.desktop-linked-command').forEach(function(element) {
+      element.hidden = false;
+    });
+    const importLabel = document.querySelector('#import-from-file .app-menu-label');
+    if (importLabel) importLabel.textContent = 'Import copies';
+  }
+
   function documentMatchesSidebarSearch(tab) {
     if (!documentSidebarSearch) return true;
     const haystack = ((tab.title || '') + ' ' + getDocumentLocationLabel(tab)).toLocaleLowerCase();
@@ -6726,7 +6873,150 @@ document.addEventListener("DOMContentLoaded", async function () {
     }
     let renderedDocuments = 0;
     documents.forEach(function(tab) {
-      if (appendDocumentTreeItem(tree, tab, 0, getDocumentLocationLabel(tab))) renderedDocuments++;
+      const meta = isLinkedDocument(tab) ? getLinkedDocumentMeta(tab) : getDocumentLocationLabel(tab);
+      if (appendDocumentTreeItem(tree, tab, 0, meta)) renderedDocuments++;
+    });
+    return renderedDocuments;
+  }
+
+  function getLinkedDocumentMeta(tab) {
+    if (tab.sourceMissing) return 'Missing source';
+    if (tab.sourceConflict) return 'Conflict';
+    return '';
+  }
+
+  function getLinkedLocationMenuActions(location) {
+    return [
+      { id: 'rescan', icon: 'lucide-refresh-cw', label: 'Rescan folder', run: function() { void reconcileLinkedLocation(location.id, { notify: true, restoreExcluded: true }); } },
+      { id: 'reveal', icon: 'lucide-folder-symlink', label: 'Open folder', run: function() { void Neutralino.os.open(location.path); } },
+      { id: 'unlink', icon: 'lucide-x', label: 'Remove linked folder', danger: true, run: function() { void removeLinkedLocation(location.id); } }
+    ];
+  }
+
+  function renderLinkedLocationsTree(tree) {
+    if (!hasDesktopFileAccess()) return 0;
+    const linkedTabs = tabs.filter(function(tab) {
+      return !isTemporaryDocument(tab) && isLinkedWorkspaceDocument(tab);
+    });
+    const locations = Array.isArray(documentOrganization.linkedLocations) ? documentOrganization.linkedLocations : [];
+    let renderedDocuments = 0;
+    const activeDocument = tabs.find(function(tab) { return tab.id === activeTabId; });
+    const workspaceExpanded = documentSidebarSearch ? true : documentOrganization.ui.linkedWorkspaceExpanded !== false;
+    const toggleWorkspace = function() {
+      documentOrganization.ui.linkedWorkspaceExpanded = !workspaceExpanded;
+      saveDocumentOrganization();
+      renderDocumentSidebar();
+    };
+    tree.appendChild(createDocumentTreeRow({
+      type: 'linked-workspace',
+      id: 'linked-workspace',
+      label: 'Linked Workspace',
+      ariaLabel: 'Linked Workspace, original files remain on disk',
+      icon: 'lucide-link-2',
+      depth: 0,
+      expanded: workspaceExpanded,
+      currentLocation: isLinkedWorkspaceDocument(activeDocument),
+      meta: String(linkedTabs.length),
+      onToggle: toggleWorkspace,
+      onActivate: toggleWorkspace
+    }));
+    const workspaceGroup = document.createElement('div');
+    workspaceGroup.className = 'document-tree-group document-tree-group--workspace';
+    workspaceGroup.setAttribute('role', 'group');
+    workspaceGroup.hidden = !workspaceExpanded;
+    tree.appendChild(workspaceGroup);
+
+    const individualTabs = linkedTabs.filter(function(tab) { return !tab.linkedRootId; })
+      .filter(documentMatchesSidebarSearch)
+      .sort(function(left, right) { return (left.title || '').localeCompare(right.title || ''); });
+    individualTabs.forEach(function(tab) {
+      if (appendDocumentTreeItem(workspaceGroup, tab, 1, getLinkedDocumentMeta(tab))) renderedDocuments++;
+    });
+
+    locations.slice().sort(function(left, right) {
+      return (left.name || '').localeCompare(right.name || '');
+    }).forEach(function(location) {
+      const locationTabs = linkedTabs.filter(function(tab) { return tab.linkedRootId === location.id; });
+      const matchingTabs = locationTabs.filter(documentMatchesSidebarSearch);
+      const locationMatches = !documentSidebarSearch || (location.name + ' ' + location.path).toLocaleLowerCase().includes(documentSidebarSearch.toLocaleLowerCase());
+      if (documentSidebarSearch && !locationMatches && !matchingTabs.length) return;
+      const expanded = documentSidebarSearch ? true : location.expanded !== false;
+      const toggleLocation = function() {
+        location.expanded = !expanded;
+        saveDocumentOrganization();
+        renderDocumentSidebar();
+      };
+      const rootRow = createDocumentTreeRow({
+        type: 'linked-location',
+        id: location.id,
+        label: location.name,
+        ariaLabel: 'Linked folder, ' + location.path + (location.unavailable ? ', unavailable' : ''),
+        icon: location.unavailable ? 'lucide-triangle-alert' : 'lucide-folder-symlink',
+        depth: 1,
+        currentLocation: Boolean(activeDocument && activeDocument.linkedRootId === location.id),
+        expanded: expanded,
+        meta: location.unavailable ? 'Unavailable' : String(locationTabs.length),
+        menuActions: getLinkedLocationMenuActions(location),
+        onToggle: toggleLocation,
+        onActivate: toggleLocation
+      });
+      workspaceGroup.appendChild(rootRow);
+
+      const rootGroup = document.createElement('div');
+      rootGroup.className = 'document-tree-group document-tree-group--folder';
+      rootGroup.setAttribute('role', 'group');
+      rootGroup.hidden = !expanded;
+      const rootNode = { folders: new Map(), documents: [] };
+      matchingTabs.forEach(function(tab) {
+        const parts = String(tab.sourceRelativePath || '').replace(/\\/g, '/').split('/').filter(Boolean);
+        if (parts.length) parts.pop();
+        let node = rootNode;
+        parts.forEach(function(part) {
+          if (!node.folders.has(part)) node.folders.set(part, { folders: new Map(), documents: [] });
+          node = node.folders.get(part);
+        });
+        node.documents.push(tab);
+      });
+      const appendVirtualNode = function(node, container, depth, pathParts) {
+        Array.from(node.folders.entries()).sort(function(left, right) { return left[0].localeCompare(right[0]); }).forEach(function(entry) {
+          const folderName = entry[0];
+          const child = entry[1];
+          const folderPath = pathParts.concat(folderName).join('/');
+          const collapsedPaths = location.collapsedFolderPaths || [];
+          const folderExpanded = documentSidebarSearch ? true : !collapsedPaths.includes(folderPath);
+          const toggleFolder = function() {
+            const nextCollapsed = new Set(location.collapsedFolderPaths || []);
+            if (folderExpanded) nextCollapsed.add(folderPath);
+            else nextCollapsed.delete(folderPath);
+            location.collapsedFolderPaths = Array.from(nextCollapsed);
+            saveDocumentOrganization();
+            renderDocumentSidebar();
+          };
+          const row = createDocumentTreeRow({
+            type: 'linked-virtual-folder',
+            id: location.id + ':' + folderPath,
+            label: folderName,
+            icon: 'lucide-folder-symlink',
+            depth: depth,
+            expanded: folderExpanded,
+            meta: '',
+            onToggle: toggleFolder,
+            onActivate: toggleFolder
+          });
+          container.appendChild(row);
+          const childGroup = document.createElement('div');
+          childGroup.className = 'document-tree-group document-tree-group--folder';
+          childGroup.setAttribute('role', 'group');
+          childGroup.hidden = !folderExpanded;
+          appendVirtualNode(child, childGroup, depth + 1, pathParts.concat(folderName));
+          container.appendChild(childGroup);
+        });
+        node.documents.sort(function(left, right) { return (left.title || '').localeCompare(right.title || ''); }).forEach(function(tab) {
+          if (appendDocumentTreeItem(container, tab, depth, getLinkedDocumentMeta(tab))) renderedDocuments++;
+        });
+      };
+      appendVirtualNode(rootNode, rootGroup, 2, []);
+      workspaceGroup.appendChild(rootGroup);
     });
     return renderedDocuments;
   }
@@ -6750,9 +7040,10 @@ document.addEventListener("DOMContentLoaded", async function () {
 
     documentOrganization.workspaces.forEach(function(workspace) {
       const isSecretWorkspace = workspace.id === SECRET_WORKSPACE_ID;
+      if (isSecretWorkspace) renderedDocuments += renderLinkedLocationsTree(tree);
       const secretLocked = isSecretWorkspace && !isSecretWorkspaceUnlocked();
       const workspaceDocuments = tabs.filter(function(tab) {
-        return !isTemporaryDocument(tab) && tab.workspaceId === workspace.id;
+        return !isTemporaryDocument(tab) && !isLinkedWorkspaceDocument(tab) && tab.workspaceId === workspace.id;
       });
       const folders = documentOrganization.folders.filter(function(folder) { return folder.workspaceId === workspace.id; });
       const matchingDocuments = workspaceDocuments.filter(documentMatchesSidebarSearch);
@@ -6783,6 +7074,7 @@ document.addEventListener("DOMContentLoaded", async function () {
           ? (secretLocked ? 'lucide-shield' : 'lucide-shield-check')
           : (expanded ? 'lucide-folder-open' : 'lucide-folder'),
         depth: 0,
+        currentLocation: tabs.some(function(tab) { return tab.id === activeTabId && !isLinkedWorkspaceDocument(tab) && tab.workspaceId === workspace.id; }),
         expanded: expanded,
         meta: secretLocked ? 'Locked' : String(workspaceDocuments.length),
         locked: secretLocked,
@@ -6960,6 +7252,8 @@ document.addEventListener("DOMContentLoaded", async function () {
       : (preferredWorkspace ? preferredWorkspace.name : 'Workspace');
     const newDocumentButton = document.getElementById('sidebar-new-document');
     const newFolderButton = document.getElementById('sidebar-new-folder');
+    const linkFilesButton = document.getElementById('sidebar-link-files');
+    const linkFolderButton = document.getElementById('sidebar-link-folder');
     const collapseAllButton = document.getElementById('document-sidebar-collapse-all');
     if (newDocumentButton) {
       newDocumentButton.title = 'New Markdown file in ' + preferredLocationLabel;
@@ -7060,11 +7354,38 @@ document.addEventListener("DOMContentLoaded", async function () {
     const unlockedWorkspaceIds = new Set(documentOrganization.workspaces.filter(function(workspace) {
       return workspace.id !== SECRET_WORKSPACE_ID || isSecretWorkspaceUnlocked();
     }).map(function(workspace) { return workspace.id; }));
-    return documentOrganization.workspaces.filter(function(workspace) {
+    const items = documentOrganization.workspaces.filter(function(workspace) {
       return unlockedWorkspaceIds.has(workspace.id);
     }).concat(documentOrganization.folders.filter(function(folder) {
       return unlockedWorkspaceIds.has(folder.workspaceId);
     }));
+    if (hasDesktopFileAccess()) {
+      items.push({
+        get expanded() { return documentOrganization.ui.linkedWorkspaceExpanded !== false; },
+        set expanded(value) { documentOrganization.ui.linkedWorkspaceExpanded = value; }
+      });
+      (documentOrganization.linkedLocations || []).forEach(function(location) {
+        items.push(location);
+        const folderPaths = new Set(location.collapsedFolderPaths || []);
+        tabs.filter(function(tab) { return tab.sourcePath && tab.linkedRootId === location.id; }).forEach(function(tab) {
+          const parts = normalizeLinkedRelativePath(tab.sourceRelativePath).split('/').filter(Boolean);
+          parts.pop();
+          parts.forEach(function(_, index) { folderPaths.add(parts.slice(0, index + 1).join('/')); });
+        });
+        folderPaths.forEach(function(folderPath) {
+          items.push({
+            get expanded() { return !(location.collapsedFolderPaths || []).includes(folderPath); },
+            set expanded(value) {
+              const collapsed = new Set(location.collapsedFolderPaths || []);
+              if (value) collapsed.delete(folderPath);
+              else collapsed.add(folderPath);
+              location.collapsedFolderPaths = Array.from(collapsed);
+            }
+          });
+        });
+      });
+    }
+    return items;
   }
 
   function updateTreeExpansionButton(button, willExpand, label, enabled) {
@@ -7229,6 +7550,8 @@ document.addEventListener("DOMContentLoaded", async function () {
     const collapseAllButton = document.getElementById('document-sidebar-collapse-all');
     const newDocumentButton = document.getElementById('sidebar-new-document');
     const newFolderButton = document.getElementById('sidebar-new-folder');
+    const linkFilesButton = document.getElementById('sidebar-link-files');
+    const linkFolderButton = document.getElementById('sidebar-link-folder');
     const trashButton = document.getElementById('sidebar-trash-button');
     const search = document.getElementById('document-sidebar-search');
     const clearSearch = document.getElementById('document-sidebar-search-clear');
@@ -7240,6 +7563,8 @@ document.addEventListener("DOMContentLoaded", async function () {
     if (closeButton) closeButton.addEventListener('click', toggleDocumentSidebarCollapsed);
     if (backdrop) backdrop.addEventListener('click', closeDocumentSidebarOnMobile);
     if (collapseAllButton) collapseAllButton.addEventListener('click', toggleDocumentTreeExpansion);
+    if (linkFilesButton) linkFilesButton.addEventListener('click', function() { void nativeLinkMarkdownFiles(); });
+    if (linkFolderButton) linkFolderButton.addEventListener('click', function() { void nativeLinkMarkdownFolder(); });
     if (newDocumentButton) newDocumentButton.addEventListener('click', function() {
       const location = getPreferredDocumentLocation();
       newTab('', null, location);
@@ -10866,9 +11191,16 @@ document.addEventListener("DOMContentLoaded", async function () {
     if (!saveStatus || !saveStatusIcon || !saveStatusText) return;
     const requestedState = state === 'saving' || state === 'error' ? state : 'saved';
     const nextState = isPrivateStorageMode() && requestedState !== 'error' ? 'private' : requestedState;
+    let activeDocument = null;
+    try {
+      activeDocument = tabs.find(function(tab) { return tab.id === activeTabId; });
+    } catch (_) {
+      // Startup calls this before the workspace tab state is initialized.
+    }
+    const linkedSourcePath = isLinkedDocument(activeDocument) ? activeDocument.sourcePath : '';
     const presentation = {
       saving: { icon: 'lucide lucide-refresh-cw', text: 'Saving...' },
-      saved: { icon: 'lucide lucide-check', text: 'All changes saved' },
+      saved: { icon: 'lucide lucide-check', text: linkedSourcePath ? 'Draft saved · Ctrl+S updates original' : 'All changes saved' },
       private: { icon: 'lucide lucide-hat-glasses', text: 'Private mode is on' },
       error: { icon: 'lucide lucide-circle-alert', text: 'Changes not saved' }
     }[nextState];
@@ -10877,6 +11209,8 @@ document.addEventListener("DOMContentLoaded", async function () {
     saveStatus.dataset.state = nextState;
     if (nextState === 'private') {
       saveStatus.title = 'Private mode is on. Session changes are not saved.';
+    } else if (nextState === 'saved' && linkedSourcePath) {
+      saveStatus.title = 'Workspace recovery copy saved. Press Ctrl+S to update ' + linkedSourcePath;
     } else {
       saveStatus.removeAttribute('title');
     }
@@ -11097,6 +11431,487 @@ document.addEventListener("DOMContentLoaded", async function () {
     return tab;
   }
 
+  function normalizeLinkedSourcePath(sourcePath) {
+    const value = String(sourcePath || '').trim();
+    if (!value) return '';
+    const normalized = value.replace(/\//g, '\\').replace(/\\+$/g, '');
+    return /^[a-z]:\\/i.test(normalized) ? normalized.toLocaleLowerCase('en-US') : normalized;
+  }
+
+  function findTabBySourcePath(sourcePath) {
+    const pathKey = normalizeLinkedSourcePath(sourcePath);
+    if (!pathKey) return null;
+    return tabs.find(function(tab) {
+      return normalizeLinkedSourcePath(tab && tab.sourcePath) === pathKey;
+    }) || null;
+  }
+
+  async function hashLinkedSourceContent(content) {
+    if (!window.crypto || !window.crypto.subtle || typeof TextEncoder === 'undefined') return '';
+    const bytes = new TextEncoder().encode(String(content == null ? '' : content));
+    const digest = new Uint8Array(await window.crypto.subtle.digest('SHA-256', bytes));
+    return Array.from(digest).map(function(byte) { return byte.toString(16).padStart(2, '0'); }).join('');
+  }
+
+  async function openLinkedMarkdownDocument(content, title, sourcePath, options) {
+    if (!hasDesktopFileAccess()) return null;
+    const settings = options || {};
+    const normalizedPath = String(sourcePath || '').trim();
+    const incomingContent = String(content == null ? '' : content);
+    const incomingHash = await hashLinkedSourceContent(incomingContent);
+    let tab = findTabBySourcePath(normalizedPath);
+    let contentRefreshed = false;
+
+    // Only a matching source path identifies a linked document. A Vault copy
+    // remains independent even when its title and content match the original.
+
+    if (tab) {
+      await ensureTabContent(tab);
+      const draftHash = await hashLinkedSourceContent(tab.content);
+      const hasLocalDraft = Boolean(tab.sourceContentHash && draftHash && draftHash !== tab.sourceContentHash);
+      if (!hasLocalDraft && tab.content !== incomingContent) {
+        tab.content = incomingContent;
+        tab.contentLoaded = true;
+        tab._persistedContent = undefined;
+        contentRefreshed = true;
+      } else if (incomingHash && incomingHash !== tab.sourceContentHash) {
+        showAppToast('The file changed outside Markdown Viewer. Your workspace draft was kept; press Ctrl+S only if you want to overwrite the disk file.', {
+          tone: 'info',
+          title: 'External change detected'
+        });
+      }
+      tab.sourcePath = normalizedPath || tab.sourcePath;
+      if (!hasLocalDraft) tab.sourceContentHash = incomingHash;
+      tab.sourceMissing = false;
+      tab.sourceConflict = hasLocalDraft && Boolean(incomingHash && incomingHash !== tab.sourceContentHash);
+      tab.title = title || tab.title;
+      if (settings.open !== false) tab.isOpen = true;
+      if (settings.open !== false) tab.lastOpenedAt = Date.now();
+    } else {
+      tab = createTab(incomingContent, title || 'Untitled', 'split', { workspaceId: DEFAULT_WORKSPACE_ID, folderId: null });
+      tab.sourcePath = normalizedPath;
+      tab.sourceContentHash = incomingHash;
+      tab.sourceMissing = false;
+      tab.sourceConflict = false;
+      tab.isOpen = settings.open === false ? false : true;
+      tabs.push(tab);
+    }
+
+    tab.sourceKind = 'linked';
+    if (settings.linkedRootId) tab.linkedRootId = String(settings.linkedRootId);
+    if (settings.sourceRelativePath) tab.sourceRelativePath = String(settings.sourceRelativePath).replace(/\\/g, '/').replace(/^\/+/, '');
+
+    if (settings.open !== false) selectedDocumentId = tab.id;
+    saveTabsToStorage(tabs, [tab.id]);
+    if (settings.open === false) {
+      if (tab.id === activeTabId && contentRefreshed) {
+        markdownEditor.value = tab.content;
+        renderMarkdown();
+      }
+      if (!settings.deferUI) {
+        renderTabBar(tabs, activeTabId);
+        renderDocumentSidebar();
+      }
+    } else if (settings.activate === false) {
+      activeTabId = tab.id;
+      saveActiveTabId(tab.id);
+    } else {
+      if (tab.id === activeTabId) {
+        if (contentRefreshed) {
+          markdownEditor.value = tab.content;
+          renderMarkdown();
+        }
+        renderTabBar(tabs, activeTabId);
+        renderDocumentSidebar();
+      } else {
+        await switchTab(tab.id);
+      }
+      if (settings.notify !== false) showAppToast('Linked to ' + tab.sourcePath + '. Press Ctrl+S to save changes to the original file.', {
+        tone: 'info',
+        title: 'Linked Markdown file'
+      });
+    }
+    return tab;
+  }
+
+  function getNativePathName(filePath) {
+    return String(filePath || '').replace(/[\\/]+$/, '').split(/[\\/]/).pop() || '';
+  }
+
+  function getNativeParentPath(filePath) {
+    const value = String(filePath || '').replace(/[\\/]+$/, '');
+    const separator = Math.max(value.lastIndexOf('\\'), value.lastIndexOf('/'));
+    return separator > 2 ? value.slice(0, separator) : value.slice(0, separator + 1);
+  }
+
+  function getLinkedLocation(locationId) {
+    return (documentOrganization.linkedLocations || []).find(function(location) { return location.id === locationId; }) || null;
+  }
+
+  function normalizeLinkedRelativePath(value) {
+    return String(value || '').replace(/\\/g, '/').replace(/^\/+/, '');
+  }
+
+  async function collectMarkdownFilesFromFolder(rootPath) {
+    const files = [];
+    const ignoredDirectories = new Set(['.git', 'node_modules']);
+    async function visit(folderPath, relativePrefix) {
+      if (files.length >= 5000) throw new Error('This folder contains more than 5,000 Markdown files. Link a smaller folder instead.');
+      const entries = await Neutralino.filesystem.readDirectory(folderPath);
+      for (const entry of entries) {
+        if (!entry || !entry.entry || entry.entry === '.' || entry.entry === '..') continue;
+        const childPath = await Neutralino.filesystem.getJoinedPath(folderPath, entry.entry);
+        const relativePath = normalizeLinkedRelativePath(relativePrefix ? relativePrefix + '/' + entry.entry : entry.entry);
+        if (entry.type === 'DIRECTORY') {
+          if (!ignoredDirectories.has(String(entry.entry).toLowerCase())) await visit(childPath, relativePath);
+        } else if (entry.type === 'FILE' && /\.(md|markdown)$/i.test(entry.entry)) {
+          files.push({ path: childPath, relativePath: relativePath });
+        }
+      }
+    }
+    await visit(rootPath, '');
+    return files;
+  }
+
+  async function reloadLinkedDocument(tabId, options) {
+    const tab = tabs.find(function(item) { return item.id === tabId; });
+    if (!isLinkedDocument(tab)) return false;
+    const settings = options || {};
+    const previousSidebarState = linkedSidebarState();
+    function refreshUI() {
+      if (settings.background) {
+        if (previousSidebarState !== linkedSidebarState()) requestLinkedBackgroundUIRefresh();
+      } else renderDocumentSidebar();
+    }
+    let diskContent;
+    try {
+      diskContent = await Neutralino.filesystem.readFile(tab.sourcePath);
+    } catch (_) {
+      tab.sourceMissing = true;
+      tab.sourceConflict = false;
+      saveTabsToStorage(tabs, [tab.id]);
+      refreshUI();
+      return false;
+    }
+    await ensureTabContent(tab);
+    const diskHash = await hashLinkedSourceContent(diskContent);
+    const draftHash = await hashLinkedSourceContent(tab.content);
+    const hasLocalDraft = Boolean(tab.sourceContentHash && draftHash && draftHash !== tab.sourceContentHash);
+    const hasExternalChange = Boolean(tab.sourceContentHash && diskHash && diskHash !== tab.sourceContentHash);
+    if (hasLocalDraft && hasExternalChange && !settings.force) {
+      tab.sourceConflict = true;
+      tab.sourceMissing = false;
+      saveTabsToStorage(tabs, [tab.id]);
+      refreshUI();
+      showAppToast('The original changed on disk while a local draft exists. The draft was kept.', { tone: 'info', title: 'Linked file conflict' });
+      return false;
+    }
+    if (hasLocalDraft && settings.force) {
+      const replaceDraft = window.confirm('Discard the current workspace draft and reload this linked file from disk?\n\n' + tab.sourcePath);
+      if (!replaceDraft) return false;
+    }
+    if (!hasExternalChange && !tab.sourceMissing && !settings.force) return true;
+    tab.content = String(diskContent == null ? '' : diskContent);
+    tab.contentLoaded = true;
+    tab._persistedContent = undefined;
+    tab.sourceContentHash = diskHash;
+    tab.sourceMissing = false;
+    tab.sourceConflict = false;
+    tab.lastEditedAt = Date.now();
+    saveTabsToStorage(tabs, [tab.id]);
+    if (tab.id === activeTabId) {
+      markdownEditor.value = tab.content;
+      renderMarkdown();
+    }
+    if (!settings.background) renderTabBar(tabs, activeTabId);
+    refreshUI();
+    return true;
+  }
+
+  async function reconcileLinkedLocation(locationId, options) {
+    const location = getLinkedLocation(locationId);
+    if (!location) return 0;
+    const settings = options || {};
+    const previousSidebarState = linkedSidebarState();
+    function refreshUI() {
+      if (settings.background) {
+        if (previousSidebarState !== linkedSidebarState()) requestLinkedBackgroundUIRefresh();
+      } else {
+        renderTabBar(tabs, activeTabId);
+        renderDocumentSidebar();
+      }
+    }
+    let files;
+    try {
+      files = await collectMarkdownFilesFromFolder(location.path);
+      location.unavailable = false;
+    } catch (error) {
+      location.unavailable = true;
+      saveDocumentOrganization();
+      refreshUI();
+      if (settings.notify) showAppToast('The linked folder is unavailable: ' + location.path, { tone: 'error', title: 'Folder scan failed' });
+      return 0;
+    }
+    // Explicit rescans/re-linking restore removed links; background refreshes
+    // continue respecting exclusions. Only reset after a successful folder scan.
+    if (settings.restoreExcluded) location.excludedPaths = [];
+    const excluded = new Set((location.excludedPaths || []).map(normalizeLinkedRelativePath));
+    const discoveredPaths = new Set();
+    let added = 0;
+    for (const file of files) {
+      if (excluded.has(file.relativePath)) continue;
+      discoveredPaths.add(normalizeLinkedSourcePath(file.path));
+      let existing = findTabBySourcePath(file.path);
+      try {
+        const content = await Neutralino.filesystem.readFile(file.path);
+        await openLinkedMarkdownDocument(content, getNativePathName(file.path).replace(/\.(md|markdown)$/i, ''), file.path, {
+          activate: false,
+          open: false,
+          deferUI: true,
+          linkedRootId: location.id,
+          sourceRelativePath: file.relativePath
+        });
+        if (!existing) added++;
+      } catch (error) {
+        console.warn('Could not read linked Markdown file:', file.path, error);
+      }
+    }
+    tabs.filter(function(tab) { return tab.linkedRootId === location.id; }).forEach(function(tab) {
+      if (!discoveredPaths.has(normalizeLinkedSourcePath(tab.sourcePath))) tab.sourceMissing = true;
+    });
+    location.lastScanAt = Date.now();
+    saveDocumentOrganization();
+    saveTabsToStorage(tabs);
+    refreshUI();
+    if (settings.notify) showAppToast('Linked folder scanned. ' + added + ' new Markdown file' + (added === 1 ? '' : 's') + ' found.', { tone: 'success', title: location.name });
+    return added;
+  }
+
+  async function addLinkedFolderPath(folderPath, options) {
+    if (!hasDesktopFileAccess()) return null;
+    const normalized = normalizeLinkedSourcePath(folderPath);
+    let location = (documentOrganization.linkedLocations || []).find(function(item) {
+      return normalizeLinkedSourcePath(item.path) === normalized;
+    });
+    if (!location) {
+      location = {
+        id: createDocumentEntityId('linked'),
+        path: String(folderPath),
+        name: getNativePathName(folderPath) || 'Linked folder',
+        expanded: true,
+        excludedPaths: [],
+        createdAt: Date.now(),
+        lastScanAt: 0,
+        unavailable: false
+      };
+      documentOrganization.linkedLocations.push(location);
+      saveDocumentOrganization();
+    }
+    await reconcileLinkedLocation(location.id, { notify: !(options && options.silent), restoreExcluded: true });
+    await refreshLinkedSourceMonitoring();
+    return location;
+  }
+
+  async function addLinkedFilePath(filePath, options) {
+    if (!/\.(md|markdown)$/i.test(filePath)) return null;
+    const content = await Neutralino.filesystem.readFile(filePath);
+    const tab = await openLinkedMarkdownDocument(content, getNativePathName(filePath).replace(/\.(md|markdown)$/i, ''), filePath, {
+      activate: options && options.activate === true,
+      open: options && options.open === true
+    });
+    await refreshLinkedSourceMonitoring();
+    return tab;
+  }
+
+  async function nativeLinkMarkdownFiles() {
+    if (!hasDesktopFileAccess()) return 0;
+    try {
+      const paths = await Neutralino.os.showOpenDialog('Link Markdown files', {
+        filters: [{ name: 'Markdown files (*.md, *.markdown)', extensions: ['md', 'markdown'] }],
+        multiSelections: true
+      });
+      if (!paths || !paths.length) return 0;
+      let count = 0;
+      for (const filePath of paths) {
+        if (await addLinkedFilePath(filePath, { open: false })) count++;
+      }
+      showAppToast(count + ' file' + (count === 1 ? '' : 's') + ' linked. Originals remain on disk.', { tone: 'success', title: 'Linked files' });
+      return count;
+    } catch (error) {
+      console.warn('Could not link Markdown files:', error);
+      showAppToast(error.message || 'The selected files could not be linked.', { tone: 'error', title: 'Link failed' });
+      return 0;
+    }
+  }
+
+  async function nativeLinkMarkdownFolder() {
+    if (!hasDesktopFileAccess()) return;
+    try {
+      const folderPath = await Neutralino.os.showFolderDialog('Link Markdown folder');
+      if (folderPath) await addLinkedFolderPath(folderPath);
+    } catch (error) {
+      console.warn('Could not link Markdown folder:', error);
+      showAppToast(error.message || 'The selected folder could not be linked.', { tone: 'error', title: 'Link failed' });
+    }
+  }
+
+  async function revealLinkedSource(tab) {
+    if (!isLinkedDocument(tab)) return;
+    await Neutralino.os.open(getNativeParentPath(tab.sourcePath));
+  }
+
+  async function convertLinkedDocumentToVault(tabId, destination) {
+    const tab = tabs.find(function(item) { return item.id === tabId; });
+    if (!isLinkedDocument(tab)) return;
+    await ensureTabContent(tab);
+    const previous = Object.assign({}, tab);
+    const sourcePath = tab.sourcePath;
+    const location = tab.linkedRootId ? getLinkedLocation(tab.linkedRootId) : null;
+    const previousExcluded = location ? (location.excludedPaths || []).slice() : null;
+    if (location && tab.sourceRelativePath) {
+      location.excludedPaths = Array.from(new Set((location.excludedPaths || []).concat(normalizeLinkedRelativePath(tab.sourceRelativePath))));
+      saveDocumentOrganization();
+    }
+    delete tab.sourcePath;
+    delete tab.sourceContentHash;
+    delete tab.sourceKind;
+    delete tab.linkedRootId;
+    delete tab.sourceRelativePath;
+    delete tab.sourceMissing;
+    delete tab.sourceConflict;
+    setDocumentLocation(tab, DEFAULT_WORKSPACE_ID, destination && destination.folderId || null);
+    tab.isOpen = true;
+    try {
+      if (!(await _flushTabsToStorage(tabs, { changedIds: [tab.id] }))) throw new Error('Workspace copy could not be saved.');
+    } catch (error) {
+      Object.keys(tab).forEach(function(key) { delete tab[key]; });
+      Object.assign(tab, previous);
+      if (location) location.excludedPaths = previousExcluded;
+      saveDocumentOrganization();
+      renderDocumentSidebar();
+      showAppToast(error.message, { tone: 'error', title: 'Conversion failed' });
+      return false;
+    }
+    renderTabBar(tabs, activeTabId);
+    renderDocumentSidebar();
+    await refreshLinkedSourceMonitoring();
+    showAppToast('A separate Vault copy was created. The original file was left unchanged at ' + sourcePath, {
+      tone: 'success',
+      icon: 'lucide-check',
+      title: 'Converted to Workspace copy'
+    });
+    return true;
+  }
+
+  async function removeLinkedDocument(tabId) {
+    const tab = tabs.find(function(item) { return item.id === tabId; });
+    if (!tab || !tab.sourcePath) return;
+    const location = tab.linkedRootId ? getLinkedLocation(tab.linkedRootId) : null;
+    if (location && tab.sourceRelativePath) {
+      location.excludedPaths = Array.from(new Set((location.excludedPaths || []).concat(normalizeLinkedRelativePath(tab.sourceRelativePath))));
+      saveDocumentOrganization();
+    }
+    await deleteTab(tab.id);
+    await refreshLinkedSourceMonitoring();
+    showAppToast('Link removed. The original file remains on disk.', { tone: 'success', title: 'Linked file closed' });
+  }
+
+  async function removeLinkedLocation(locationId) {
+    const location = getLinkedLocation(locationId);
+    if (!location) return;
+    const linkedTabs = tabs.filter(function(tab) { return tab.linkedRootId === locationId; });
+    const confirmed = await showAppToastConfirmation(
+      'Remove this linked folder and ' + linkedTabs.length + ' file link' + (linkedTabs.length === 1 ? '' : 's') + '? Original files remain on disk.',
+      { title: 'Remove linked folder', confirmLabel: 'Remove link', dedupeKey: 'remove-linked-folder:' + location.id }
+    );
+    if (!confirmed) return;
+    documentOrganization.linkedLocations = documentOrganization.linkedLocations.filter(function(item) { return item.id !== locationId; });
+    saveDocumentOrganization();
+    for (const tab of linkedTabs.slice()) await deleteTab(tab.id);
+    await refreshLinkedSourceMonitoring();
+    renderDocumentSidebar();
+    showAppToast('Linked folder removed. Original files remain on disk.', { tone: 'success', title: 'Folder unlinked' });
+  }
+
+  async function stopLinkedSourceMonitoring() {
+    const watchers = Array.from(linkedSourceWatchers.values());
+    linkedSourceWatchers.clear();
+    for (const watcher of watchers) {
+      try { await Neutralino.filesystem.removeWatcher(watcher.id); } catch (_) {}
+    }
+  }
+
+  async function refreshLinkedSourceMonitoring() {
+    if (!linkedSourceMonitoringReady || !hasDesktopFileAccess() || !Neutralino.filesystem.createWatcher) return;
+    await stopLinkedSourceMonitoring();
+    const targets = [];
+    (documentOrganization.linkedLocations || []).forEach(function(location) {
+      targets.push({ key: 'folder:' + location.id, path: location.path, locationId: location.id });
+      const watchedDirectories = new Set([normalizeLinkedSourcePath(location.path)]);
+      tabs.filter(function(tab) { return tab.linkedRootId === location.id && tab.sourcePath; }).forEach(function(tab) {
+        const parentPath = getNativeParentPath(tab.sourcePath);
+        const normalizedParent = normalizeLinkedSourcePath(parentPath);
+        if (watchedDirectories.has(normalizedParent)) return;
+        watchedDirectories.add(normalizedParent);
+        targets.push({ key: 'folder:' + location.id + ':' + normalizedParent, path: parentPath, locationId: location.id });
+      });
+    });
+    const seenParents = new Set();
+    tabs.filter(function(tab) { return tab.sourcePath && !tab.linkedRootId; }).forEach(function(tab) {
+      const parentPath = getNativeParentPath(tab.sourcePath);
+      const key = normalizeLinkedSourcePath(parentPath);
+      if (!seenParents.has(key)) {
+        seenParents.add(key);
+        targets.push({ key: 'files:' + key, path: parentPath, individual: true });
+      }
+    });
+    for (const target of targets) {
+      try {
+        const watcherId = await Neutralino.filesystem.createWatcher(target.path);
+        linkedSourceWatchers.set(target.key, Object.assign({ id: watcherId }, target));
+      } catch (error) {
+        console.warn('Could not watch linked location:', target.path, error);
+      }
+    }
+  }
+
+  function scheduleLinkedWatcherRefresh(watcher) {
+    if (!watcher) return;
+    const key = watcher.locationId ? 'location:' + watcher.locationId : watcher.key;
+    clearTimeout(linkedSourceRefreshTimers.get(key));
+    linkedSourceRefreshTimers.set(key, setTimeout(async function() {
+      linkedSourceRefreshTimers.delete(key);
+      if (watcher.locationId) {
+        await reconcileLinkedLocation(watcher.locationId, { background: true });
+        await refreshLinkedSourceMonitoring();
+      }
+      else {
+        for (const tab of tabs.filter(function(item) { return item.sourcePath && !item.linkedRootId && normalizeLinkedSourcePath(getNativeParentPath(item.sourcePath)) === normalizeLinkedSourcePath(watcher.path); })) {
+          await reloadLinkedDocument(tab.id, { background: true });
+        }
+      }
+    }, 350));
+  }
+
+  async function initializeLinkedSourceMonitoring() {
+    if (linkedSourceMonitoringReady || !hasDesktopFileAccess()) return;
+    linkedSourceMonitoringReady = true;
+    if (Neutralino.events && typeof Neutralino.events.on === 'function') {
+      await Neutralino.events.on('watchFile', function(event) {
+        const watcher = Array.from(linkedSourceWatchers.values()).find(function(item) { return item.id === event.detail.id; });
+        scheduleLinkedWatcherRefresh(watcher);
+      });
+      await Neutralino.events.on('windowFocus', function() {
+        Array.from(linkedSourceWatchers.values()).forEach(scheduleLinkedWatcherRefresh);
+      });
+    }
+    await refreshLinkedSourceMonitoring();
+  }
+
+  window.NL_START_LINKED_MONITORING = function() {
+    return initializeLinkedSourceMonitoring();
+  };
+
   function isTabOpen(tab) {
     return Boolean(tab && tab.isOpen !== false);
   }
@@ -11628,7 +12443,7 @@ document.addEventListener("DOMContentLoaded", async function () {
         fileIcon.setAttribute('aria-hidden', 'true');
       } else {
         fileIcon = document.createElement('i');
-        fileIcon.className = 'lucide ' + (splitPartner ? 'lucide-columns-2' : 'lucide-file-text') + ' tab-file-icon';
+        fileIcon.className = 'lucide ' + (splitPartner ? 'lucide-columns-2' : (isLinkedDocument(tab) ? 'lucide-file-symlink' : 'lucide-file-text')) + ' tab-file-icon';
         fileIcon.setAttribute('aria-hidden', 'true');
       }
 
@@ -12545,14 +13360,9 @@ document.addEventListener("DOMContentLoaded", async function () {
     const content = typeof tab.content === 'string' ? tab.content : '';
     const filename = getSafeDocumentFilename(tab.title, "md", "document.md");
 
-    if (typeof Neutralino !== 'undefined') {
+    if (hasDesktopFileAccess()) {
       try {
-        const result = await Neutralino.os.showSaveDialog("Save Markdown File", {
-          filters: [
-            { name: "Markdown files (*.md)", extensions: ["md", "markdown"] },
-            { name: "All files (*.*)", extensions: ["*"] }
-          ]
-        });
+        const result = await chooseMarkdownSavePath(tab);
         if (result) {
           await Neutralino.filesystem.writeFile(result, content);
         }
@@ -12735,21 +13545,47 @@ document.addEventListener("DOMContentLoaded", async function () {
     const hadExistingWorkspace = tabs.length > 0;
     activeTabId = loadActiveTabId();
 
-    // Check if Neutralino passed an initial file via command line (early load)
-    if (window.NL_INITIAL_FILE_CONTENT) {
-      const initialFile = window.NL_INITIAL_FILE_CONTENT;
-      const tab = createTab(initialFile.content, initialFile.name);
+    // Seed the default Vault document before opening an initial linked file.
+    // File-association launches must not skip the Welcome on a fresh workspace.
+    if (!hadExistingWorkspace) {
+      const tab = createTab(sampleMarkdown, 'Welcome to Markdown', 'split', {
+        workspaceId: DEFAULT_WORKSPACE_ID,
+        folderId: null
+      });
       tabs.push(tab);
       activeTabId = tab.id;
       saveTabsToStorage(tabs);
       saveActiveTabId(activeTabId);
+    }
+
+    // Seed a real, editable internal guide once, including existing installations.
+    // It has no external source path and must never be watched or written back.
+    if (hasDesktopFileAccess() && !documentOrganization.ui.linkedGuideInitialized) {
+      if (!tabs.some(function(tab) { return tab.kind === LINKED_WORKSPACE_GUIDE_KIND; })) {
+        const response = await fetch('assets/linked-workspace-guide.md');
+        if (!response.ok) throw new Error('Unable to load the Linked Workspace guide.');
+        const guide = createTab(await response.text(), 'Welcome to Linked Workspace', 'preview', {
+          workspaceId: DEFAULT_WORKSPACE_ID, folderId: null
+        });
+        guide.kind = LINKED_WORKSPACE_GUIDE_KIND;
+        guide.isOpen = false;
+        tabs.push(guide);
+        if (!(await _flushTabsToStorage(tabs, { changedIds: [guide.id] }))) throw new Error('Unable to save the Linked Workspace guide.');
+      }
+      documentOrganization.ui.linkedGuideInitialized = true;
+      saveDocumentOrganization();
+    }
+
+    // Check if Neutralino passed an initial file via command line (early load)
+    if (window.NL_INITIAL_FILE_CONTENT) {
+      const initialFile = window.NL_INITIAL_FILE_CONTENT;
+      await openLinkedMarkdownDocument(
+        initialFile.content,
+        initialFile.name,
+        initialFile.sourcePath,
+        { activate: false }
+      );
       delete window.NL_INITIAL_FILE_CONTENT;
-    } else if (tabs.length === 0) {
-      const tab = createTab(sampleMarkdown, 'Welcome to Markdown');
-      tabs.push(tab);
-      activeTabId = tab.id;
-      saveTabsToStorage(tabs);
-      saveActiveTabId(activeTabId);
     } else if (!tabs.find(function(t) { return t.id === activeTabId && isTabOpen(t) && !t.storageCorruption; })) {
       const firstOpenTab = getOpenTabs().find(function(tab) { return !tab.storageCorruption; });
       activeTabId = firstOpenTab ? firstOpenTab.id : null;
@@ -12854,14 +13690,9 @@ document.addEventListener("DOMContentLoaded", async function () {
   }
 
   // Late-load callback hook for Neutralino command-line files
-  window.NL_IMPORT_EXTERNAL_FILE = function(content, name) {
+  window.NL_IMPORT_EXTERNAL_FILE = async function(content, name, sourcePath) {
     if (typeof tabs === 'undefined') return;
-    const existing = tabs.find(function(t) { return t.title === name && t.content === content; });
-    if (existing) {
-      switchTab(existing.id);
-      return;
-    }
-    newTab(content, name);
+    await openLinkedMarkdownDocument(content, name, sourcePath, { activate: true });
   };
 
   function showPreviewSkeleton() {
@@ -14881,7 +15712,7 @@ ${selector} .arrowheadPath {
     icon.className = settings.iconClass || ('lucide ' + (settings.icon || ({
       error: 'lucide-circle-alert',
       warning: 'lucide-triangle-alert',
-      success: 'lucide-circle-check',
+      success: 'lucide-check',
       info: 'lucide-info'
     }[tone] || 'lucide-info')));
     iconShell.appendChild(icon);
@@ -24059,29 +24890,124 @@ ${selector} .arrowheadPath {
     updateStlThemes();
   });
 
-  async function nativeSaveMarkdown() {
+  async function writeLinkedMarkdownSource(tab, content) {
+    if (!isLinkedDocument(tab)) return false;
+    let diskContent = null;
     try {
-      const content = markdownEditor.value;
-      const result = await Neutralino.os.showSaveDialog("Save Markdown File", {
-        filters: [
-          { name: "Markdown files (*.md)", extensions: ["md", "markdown"] },
-          { name: "All files (*.*)", extensions: ["*"] }
-        ]
-      });
+      diskContent = await Neutralino.filesystem.readFile(tab.sourcePath);
+    } catch (_) {
+      const recreate = window.confirm('The linked file no longer exists:\n\n' + tab.sourcePath + '\n\nCreate it again at this location?');
+      if (!recreate) return true;
+    }
+
+    if (diskContent !== null && tab.sourceContentHash) {
+      const diskHash = await hashLinkedSourceContent(diskContent);
+      if (diskHash && diskHash !== tab.sourceContentHash) {
+        const overwrite = window.confirm(
+          'This file changed outside Markdown Viewer after it was opened:\n\n' +
+          tab.sourcePath +
+          '\n\nOverwrite the external changes with the current editor content?'
+        );
+        if (!overwrite) return true;
+      }
+    }
+
+    await Neutralino.filesystem.writeFile(tab.sourcePath, content);
+    const verified = await Neutralino.filesystem.readFile(tab.sourcePath);
+    if (verified !== content) throw new Error('The linked file write could not be verified.');
+    tab.sourceContentHash = await hashLinkedSourceContent(content);
+    tab.sourceMissing = false;
+    tab.sourceConflict = false;
+    tab.content = content;
+    tab.contentLoaded = true;
+    tab.lastEditedAt = Date.now();
+    saveTabsToStorage(tabs, [tab.id]);
+    renderTabBar(tabs, activeTabId);
+    renderDocumentSidebar();
+    showAppToast('Saved to ' + tab.sourcePath, {
+      tone: 'success',
+      icon: 'lucide-check',
+      title: 'Original file updated'
+    });
+    return true;
+  }
+
+  async function chooseMarkdownSavePath(tab) {
+    if (!hasDesktopFileAccess()) return null;
+    const chosen = await Neutralino.os.showSaveDialog('Save Markdown File', {
+      defaultPath: getSafeDocumentFilename(tab && tab.title, 'md', 'document.md'),
+      filters: [
+        { name: 'Markdown files (*.md)', extensions: ['md', 'markdown'] },
+        { name: 'All files (*.*)', extensions: ['*'] }
+      ]
+    });
+    if (!chosen) return null;
+    const name = getNativePathName(chosen);
+    const result = name.lastIndexOf('.') > 0 && !name.endsWith('.') ? chosen : chosen.replace(/\.+$/, '') + '.md';
+    // The native picker confirmed only the path it returned. If adding .md
+    // changes that path, explicitly protect the actual destination as well.
+    if (result !== chosen) {
+      let exists = false;
+      try {
+        await Neutralino.filesystem.getStats(result);
+        exists = true;
+      } catch (error) {
+        if (error.code !== 'NE_FS_NOPATHE') throw error;
+      }
+      if (exists && !(await showAppToastConfirmation('Replace the existing file at ' + result + '?', {
+        title: 'Replace Markdown file?', confirmLabel: 'Replace', dedupeKey: 'save-overwrite:' + result
+      }))) return null;
+    }
+    return result;
+  }
+
+  let nativeMarkdownSaveInProgress = false;
+  async function nativeSaveMarkdown(options) {
+    if (!hasDesktopFileAccess() || nativeMarkdownSaveInProgress) return;
+    nativeMarkdownSaveInProgress = true;
+    try {
+      const settings = options || {};
+      saveCurrentTabState();
+      const tab = tabs.find(function(t) { return t.id === (settings.tabId || activeTabId); });
+      if (!tab || isTemporaryDocument(tab)) return;
+      await ensureTabContent(tab);
+      const content = typeof tab.content === 'string' ? tab.content : '';
+      if (settings.useLinkedSource && tab.sourcePath) {
+        await writeLinkedMarkdownSource(tab, content);
+        return;
+      }
+      const result = await chooseMarkdownSavePath(tab);
       if (result) {
+        const createLinked = tab.workspaceId !== SECRET_WORKSPACE_ID && (settings.createLinked || settings.useLinkedSource);
+        if (createLinked && tab.sourcePath && normalizeLinkedSourcePath(result) === normalizeLinkedSourcePath(tab.sourcePath)) {
+          showAppToast('Choose a different path to create a new linked file. Use Save to update the current original.', { tone: 'warning', title: 'Choose a new file' });
+          return;
+        }
+        const existing = createLinked && findTabBySourcePath(result);
+        if (existing) {
+          await ensureTabContent(existing);
+          if (existing.sourceContentHash && await hashLinkedSourceContent(existing.content) !== existing.sourceContentHash) {
+            showAppToast('This destination already has a linked document with local changes. Choose another file to preserve that draft.', { tone: 'warning', title: 'Unsaved linked draft' });
+            return;
+          }
+        }
         await Neutralino.filesystem.writeFile(result, content);
+        if (await Neutralino.filesystem.readFile(result) !== content) throw new Error('The saved file could not be verified.');
         const fileName = result.split(/[/\\]/).pop().replace(/\.(md|markdown)$/i, "");
-        const activeTab = tabs.find(function(t) { return t.id === activeTabId; });
-        if (activeTab) {
-          activeTab.title = fileName;
-          activeTab.content = content;
-          saveTabsToStorage(tabs, [activeTab.id]);
-          renderTabBar(tabs, activeTabId);
+        if (createLinked) {
+          const linked = await openLinkedMarkdownDocument(content, fileName, result, { notify: false });
+          if (!(await _flushTabsToStorage(tabs, { changedIds: [tab.id, linked.id] }))) {
+            throw new Error('The external file was saved, but its workspace link could not be persisted.');
+          }
+          markdownEditor.focus();
         }
+        showAppToast('Saved to ' + result + (createLinked ? '. Future Ctrl+S saves update this linked file.' : ''), { tone: 'success', title: 'Markdown file saved' });
       }
     } catch (e) {
       console.error("Native save failed:", e);
-      alert("Native save failed: " + e.message);
+      showAppToast(e.message, { tone: 'error', title: 'Save failed' });
+    } finally {
+      nativeMarkdownSaveInProgress = false;
     }
   }
 
@@ -24149,6 +25075,20 @@ ${selector} .arrowheadPath {
     });
   }
 
+  if (linkFromFileButton) {
+    linkFromFileButton.addEventListener('click', function(event) {
+      event.preventDefault();
+      void nativeLinkMarkdownFiles();
+    });
+  }
+
+  if (linkFromFolderButton) {
+    linkFromFolderButton.addEventListener('click', function(event) {
+      event.preventDefault();
+      void nativeLinkMarkdownFolder();
+    });
+  }
+
   if (importFromGithubButton) {
     importFromGithubButton.addEventListener("click", function (e) {
       e.preventDefault();
@@ -24302,7 +25242,7 @@ ${selector} .arrowheadPath {
     if (!hasActiveOpenDocument()) return;
     if (isReleaseNotesActive()) return;
     if (blockShareSnapshotSourceAccess()) return;
-    if (typeof Neutralino !== 'undefined') {
+    if (hasDesktopFileAccess()) {
       nativeSaveMarkdown();
       return;
     }
@@ -29091,7 +30031,7 @@ ${selector} .arrowheadPath {
   document.addEventListener("keydown", function (e) {
     if (e.defaultPrevented) return;
     const isCmdOrCtrl = e.ctrlKey || e.metaKey;
-    const isDesktop = typeof Neutralino !== 'undefined';
+    const isDesktop = hasDesktopFileAccess();
     const key = e.key.toLowerCase();
 
     if (e.key === 'F3') {
@@ -29197,9 +30137,10 @@ ${selector} .arrowheadPath {
       }
     }
 
-    if (isCmdOrCtrl && !e.shiftKey && key === 's') {
+    if (isCmdOrCtrl && !e.shiftKey && !e.altKey && !e.isComposing && (key === 's' || e.code === 'KeyS')) {
       e.preventDefault();
-      exportMd.click();
+      if (hasDesktopFileAccess()) nativeSaveMarkdown({ useLinkedSource: true });
+      else exportMd.click();
     }
     if (isCmdOrCtrl && key === 'c') {
       const activeEl = document.activeElement;
diff --git a/desktop-app/resources/js/workspace-storage.js b/desktop-app/resources/js/workspace-storage.js
index df3eb067..85671e9b 100644
--- a/desktop-app/resources/js/workspace-storage.js
+++ b/desktop-app/resources/js/workspace-storage.js
@@ -278,6 +278,7 @@
 
     mergeCollection('workspaces');
     mergeCollection('folders');
+    mergeCollection('linkedLocations');
     merged.ui = mergeObjectChanges(base.ui || {}, local.ui || {}, remote.ui || {});
     return merged;
   }
@@ -352,6 +353,7 @@
       if (this.desktop) await this._initDesktop();
       else await this._initBrowser();
       await this._migrateLegacyNormalDocuments();
+      if (this.desktop) await this._migrateLinkedRecoveryDocuments();
       this.ready = true;
       try {
         await this.purgeExpiredTrash();
@@ -521,6 +523,7 @@
       const journalPath = await this._pathJoin(internalPath, 'journal');
       await this._ensureDirectory(vaultPath);
       await this._ensureDirectory(workspacePath);
+      await this._ensureDirectory(await this._pathJoin(vaultPath, 'Linked Workspace'));
       await this._ensureDirectory(await this._pathJoin(vaultPath, 'Secret Workspace'));
       await this._ensureDirectory(secretPath);
       await this._ensureDirectory(internalPath);
@@ -576,6 +579,25 @@
       }
     }
 
+    async _migrateLinkedRecoveryDocuments() {
+      const drafts = this.vaultIndex.documents.filter(function(item) {
+        return item.sourcePath && !String(item.vaultRelativePath || '').startsWith('Linked Workspace/');
+      }).map(function(item) {
+        return Object.assign({}, item, {
+          contentLoaded: false,
+          _storageRevision: normalizedStorageRevision(item.storageRevision)
+        });
+      });
+      // Validate all existing bodies before moving any file. Missing recovery
+      // content must stop migration rather than creating an empty replacement.
+      for (const draft of drafts) await this.loadDocumentContent(draft.id);
+      if (drafts.length) {
+        await this.saveDocuments(drafts, this.vaultOrganization, {
+          changedIds: drafts.map(function(item) { return item.id; })
+        });
+      }
+    }
+
     async _rebuildDesktopIndex(workspacePath) {
       const organization = this.vaultOrganization && typeof this.vaultOrganization === 'object'
         ? cloneJson(this.vaultOrganization, null)
@@ -605,7 +627,7 @@
         return folder;
       };
 
-      const walk = async (currentPath, relativeSegments, parentFolderId) => {
+      const walk = async (currentPath, relativeSegments, parentFolderId, storageRoot) => {
         let entries = [];
         try {
           entries = await Neutralino.filesystem.readDirectory(currentPath);
@@ -619,8 +641,8 @@
           if (!entry || !entry.entry) continue;
           const entryPath = await this._pathJoin(currentPath, entry.entry);
           if (entry.type === 'DIRECTORY') {
-            const folder = findOrCreateFolder(entry.entry, parentFolderId);
-            await walk(entryPath, relativeSegments.concat(entry.entry), folder.id);
+            const folder = storageRoot === 'Workspace' ? findOrCreateFolder(entry.entry, parentFolderId) : null;
+            await walk(entryPath, relativeSegments.concat(entry.entry), folder ? folder.id : null, storageRoot);
             continue;
           }
           if (entry.type !== 'FILE' || !/\.md$/i.test(entry.entry)) continue;
@@ -645,13 +667,17 @@
             lastOpenedAt: timestamp,
             lastEditedAt: timestamp,
             contentSize: Number(stats && stats.size) || 0,
-            vaultRelativePath: normalizePathSeparators(['Workspace'].concat(relativeSegments, entry.entry).join('/')),
+            vaultRelativePath: normalizePathSeparators([storageRoot].concat(relativeSegments, entry.entry).join('/')),
+            // A lost index cannot safely tell us the original source path.
+            // Preserve these bodies as recovery documents, not invented links.
+            kind: storageRoot === 'Linked Workspace' ? 'linked-recovery' : undefined,
             contentLoaded: false
           });
         }
       };
 
-      await walk(workspacePath, [], null);
+      await walk(workspacePath, [], null, 'Workspace');
+      await walk(await this._pathJoin(this.vaultPath, 'Linked Workspace'), [], null, 'Linked Workspace');
       if (documents.length) documents[0].isOpen = true;
       this.vaultOrganization = organization;
       return {
@@ -1095,7 +1121,8 @@
     }
 
     async _desktopDocumentRelativePath(tab, organization) {
-      const segments = ['Workspace'].concat(await this._desktopFolderSegments(tab, organization));
+      const linked = Boolean(tab.sourcePath) || tab.kind === 'linked-recovery' || tab.kind === 'linked-workspace-guide';
+      const segments = linked ? ['Linked Workspace'] : ['Workspace'].concat(await this._desktopFolderSegments(tab, organization));
       requireDocumentId(tab && tab.id);
       const suffix = await stableDocumentIdSuffix(tab.id);
       segments.push(sanitizePathSegment(tab.title, 'Untitled') + '--' + suffix + '.md');
@@ -1103,10 +1130,10 @@
     }
 
     async _backupDocumentRelativePath(tab, organization) {
-      const storedPath = normalizePathSeparators(tab && (tab.vaultRelativePath || tab._vaultRelativePath));
+      const storedPath = normalizePathSeparators(tab && (tab._vaultRelativePath || tab.vaultRelativePath));
       if (
         storedPath &&
-        storedPath.startsWith('Workspace/') &&
+        (storedPath.startsWith('Workspace/') || storedPath.startsWith('Linked Workspace/')) &&
         !storedPath.split('/').some(function(segment) { return segment === '.' || segment === '..'; })
       ) {
         return storedPath;
@@ -1290,7 +1317,8 @@
       metadata.contentSize = typeof tab.content === 'string'
         ? new TextEncoder().encode(tab.content).byteLength
         : Number(existing && existing.contentSize) || 0;
-      if (existing) Object.assign(existing, metadata);
+      // Conversion removes source fields: merging would retain them on restart.
+      if (existing) this.vaultIndex.documents[this.vaultIndex.documents.indexOf(existing)] = metadata;
       else this.vaultIndex.documents.push(metadata);
       tab._vaultRelativePath = relativePath;
       tab._pendingStorageRevision = metadata.storageRevision;
@@ -2841,6 +2869,7 @@
         }
         const ownedPaths = [
           await this._pathJoin(this.vaultPath, 'Workspace'),
+          await this._pathJoin(this.vaultPath, 'Linked Workspace'),
           await this._pathJoin(this.vaultPath, 'Secret Workspace'),
           await this._pathJoin(this.vaultPath, INTERNAL_DIR)
         ];
diff --git a/desktop-app/resources/styles.css b/desktop-app/resources/styles.css
index 478aac7d..15fecfa0 100644
--- a/desktop-app/resources/styles.css
+++ b/desktop-app/resources/styles.css
@@ -592,7 +592,6 @@ body {
   background: color-mix(in srgb, var(--accent-color) 7%, transparent);
 }
 
-.document-tree-row[data-tree-type="document"].is-selected > .document-tree-main > i:first-child,
 .document-tree-row[data-tree-type="document"].is-active > .document-tree-main > i:first-child {
   color: var(--accent-color);
 }
@@ -727,7 +726,7 @@ body {
   text-align: center;
 }
 
-.document-tree-main > .lucide-folder-open {
+.document-tree-row.is-current-location > .document-tree-main > i:first-child {
   color: var(--accent-color);
 }
 
@@ -752,6 +751,16 @@ body {
   font-size: var(--ui-font-xs);
 }
 
+.document-tree-row.is-source-missing .document-tree-meta,
+.document-tree-row.is-source-missing .document-tree-main > i {
+  color: var(--color-danger-fg);
+}
+
+.document-tree-row.is-source-conflict .document-tree-meta {
+  color: #bf8700;
+  font-weight: 600;
+}
+
 .document-tree-main > .document-favorite-indicator {
   flex: 0 0 auto;
   color: var(--favorite-color);
@@ -1326,7 +1335,8 @@ body.document-sidebar-collapsed .document-sidebar {
   color: var(--accent-color);
 }
 
-.app-toast-icon-shell > .bi {
+.app-toast-icon-shell > .bi,
+.app-toast-icon-shell > .lucide {
   font-size: var(--ui-icon-size-lg);
   line-height: 1;
 }
diff --git a/index.html b/index.html
index bd610001..d246a9f9 100644
--- a/index.html
+++ b/index.html
@@ -169,7 +169,9 @@ <h1 class="h4 mb-0">Markdown Viewer<span class="visually-hidden"> - Online Markd
                         </button>
                         <ul class="dropdown-menu app-command-menu header-command-menu header-new-menu" aria-labelledby="importDropdown">
                             <li><a class="dropdown-item app-menu-item" href="#" id="header-new-document"><i class="lucide lucide-file-plus-2" aria-hidden="true"></i><span class="app-menu-label">New document</span></a></li>
-                            <li><a class="dropdown-item app-menu-item" href="#" id="import-from-file"><i class="lucide lucide-upload" aria-hidden="true"></i><span class="app-menu-label">From files</span></a></li>
+                            <li><a class="dropdown-item app-menu-item" href="#" id="import-from-file"><i class="lucide lucide-files" aria-hidden="true"></i><span class="app-menu-label">From files</span></a></li>
+                            <li class="desktop-linked-command" hidden><a class="dropdown-item app-menu-item" href="#" id="link-from-file"><i class="lucide lucide-file-symlink" aria-hidden="true"></i><span class="app-menu-label">Link files…</span></a></li>
+                            <li class="desktop-linked-command" hidden><a class="dropdown-item app-menu-item" href="#" id="link-from-folder"><i class="lucide lucide-folder-symlink" aria-hidden="true"></i><span class="app-menu-label">Link folder…</span></a></li>
                             <li><a class="dropdown-item app-menu-item" href="#" id="import-from-github"><i class="bi bi-github" aria-hidden="true"></i><span class="app-menu-label">From GitHub</span></a></li>
                         </ul>
                     </div>
@@ -443,6 +445,12 @@ <h2 id="document-sidebar-title">Explorer</h2>
                 <button id="sidebar-new-folder" class="document-sidebar-icon-btn" type="button" aria-label="Create a folder" title="New folder">
                   <i class="lucide lucide-folder-plus" aria-hidden="true"></i>
                 </button>
+                <button id="sidebar-link-files" class="document-sidebar-icon-btn desktop-linked-command" type="button" aria-label="Link Markdown files" title="Link Markdown files" hidden>
+                  <i class="lucide lucide-file-symlink" aria-hidden="true"></i>
+                </button>
+                <button id="sidebar-link-folder" class="document-sidebar-icon-btn desktop-linked-command" type="button" aria-label="Link a Markdown folder" title="Link a Markdown folder" hidden>
+                    <i class="lucide lucide-folder-symlink" aria-hidden="true"></i>
+                </button>
                 <button id="sidebar-trash-button" class="document-sidebar-icon-btn" type="button" aria-label="Open Trash" title="Trash">
                   <i class="lucide lucide-trash-2" aria-hidden="true"></i>
                 </button>
diff --git a/script.js b/script.js
index 0484e8c7..f3f2ccf7 100644
--- a/script.js
+++ b/script.js
@@ -3,6 +3,7 @@ document.addEventListener("DOMContentLoaded", async function () {
   const PRIVATE_MODE_KEY = 'markdownViewerPrivateMode';
   const APP_VERSION = '3.10.3';
   const RELEASE_NOTES_TAB_KIND = 'release-notes';
+  const LINKED_WORKSPACE_GUIDE_KIND = 'linked-workspace-guide';
   const RELEASE_NOTES_LAST_VERSION_KEY = 'markdownViewerLastVersion';
   const RELEASE_NOTES_PENDING_VERSION_KEY = 'markdownViewerPendingReleaseNotesVersion';
   const RELEASE_NOTES_PENDING_MODE_KEY = 'markdownViewerPendingReleaseNotesMode';
@@ -44,6 +45,20 @@ document.addEventListener("DOMContentLoaded", async function () {
     );
   }
 
+  function hasDesktopFileAccess() {
+    return Boolean(typeof Neutralino !== 'undefined' && typeof NL_PORT !== 'undefined' &&
+      Neutralino.filesystem && typeof Neutralino.filesystem.readFile === 'function' &&
+      typeof Neutralino.filesystem.writeFile === 'function' && Neutralino.os);
+  }
+
+  function isLinkedDocument(tab) {
+    return Boolean(hasDesktopFileAccess() && tab && tab.sourcePath);
+  }
+
+  function isLinkedWorkspaceDocument(tab) {
+    return hasDesktopFileAccess() && Boolean(tab && (tab.sourcePath || tab.kind === LINKED_WORKSPACE_GUIDE_KIND));
+  }
+
   const workspaceStorage = typeof window.MarkdownWorkspaceStorage === 'function'
     ? new window.MarkdownWorkspaceStorage()
     : null;
@@ -361,6 +376,8 @@ document.addEventListener("DOMContentLoaded", async function () {
   const themeSwitchIcon = document.getElementById("theme-switch-icon");
   const directionToggle = document.getElementById("direction-toggle");
   const importFromFileButton = document.getElementById("import-from-file");
+  const linkFromFileButton = document.getElementById("link-from-file");
+  const linkFromFolderButton = document.getElementById("link-from-folder");
   const importFromGithubButton = document.getElementById("import-from-github");
   const fileInput = document.getElementById("file-input");
   const exportDropdown = document.getElementById("exportDropdown");
@@ -4207,7 +4224,7 @@ document.addEventListener("DOMContentLoaded", async function () {
   const UNTITLED_COUNTER_KEY = 'markdownViewerUntitledCounter';
   const DOCUMENT_ORGANIZATION_KEY = 'markdownViewerDocumentOrganization';
   const SECRET_WORKSPACE_STORAGE_KEY = 'markdownViewerSecretWorkspace';
-  const DOCUMENT_ORGANIZATION_VERSION = 3;
+  const DOCUMENT_ORGANIZATION_VERSION = 4;
   const SECRET_WORKSPACE_VERSION = 2;
   const SECRET_KDF_ITERATIONS = 250000;
   const DEFAULT_WORKSPACE_ID = 'workspace_default';
@@ -4235,6 +4252,9 @@ document.addEventListener("DOMContentLoaded", async function () {
   let documentTreeDragExpandRow = null;
   let documentTreeAutoScrollFrame = null;
   let documentTreeAutoScrollSpeed = 0;
+  const linkedSourceWatchers = new Map();
+  const linkedSourceRefreshTimers = new Map();
+  let linkedSourceMonitoringReady = false;
   let secretWorkspaceKey = null;
   let secretWorkspaceSalt = null;
   let secretWorkspaceIterations = SECRET_KDF_ITERATIONS;
@@ -4277,7 +4297,7 @@ document.addEventListener("DOMContentLoaded", async function () {
       workspaces: [
         {
           id: DEFAULT_WORKSPACE_ID,
-          name: 'Workspace',
+          name: hasDesktopFileAccess() ? 'Workspace (Vault)' : 'Workspace',
           expanded: true,
           createdAt: 0
         },
@@ -4289,8 +4309,10 @@ document.addEventListener("DOMContentLoaded", async function () {
         }
       ],
       folders: [],
+      linkedLocations: [],
       ui: {
         filter: 'all',
+        linkedWorkspaceExpanded: true,
         collapsed: false,
         width: 288,
         lastWorkspaceId: DEFAULT_WORKSPACE_ID,
@@ -4349,6 +4371,30 @@ document.addEventListener("DOMContentLoaded", async function () {
       }
     });
 
+    const seenLinkedLocationIds = new Set();
+    const linkedLocations = (Array.isArray(source.linkedLocations) ? source.linkedLocations : []).map(function(location) {
+      if (!location || typeof location !== 'object') return null;
+      const id = String(location.id || '').slice(0, 120);
+      const path = String(location.path || '').trim();
+      if (!id || !path || seenLinkedLocationIds.has(id)) return null;
+      seenLinkedLocationIds.add(id);
+      return {
+        id: id,
+        path: path,
+        name: String(location.name || '').trim().slice(0, 160) || path.split(/[/\\]/).filter(Boolean).pop() || 'Linked folder',
+        expanded: location.expanded !== false,
+        collapsedFolderPaths: Array.from(new Set((Array.isArray(location.collapsedFolderPaths) ? location.collapsedFolderPaths : [])
+          .map(function(item) { return String(item || '').replace(/\\/g, '/').replace(/^\/+/, ''); })
+          .filter(Boolean))),
+        excludedPaths: Array.from(new Set((Array.isArray(location.excludedPaths) ? location.excludedPaths : [])
+          .map(function(item) { return String(item || '').replace(/\\/g, '/').replace(/^\/+/, ''); })
+          .filter(Boolean))),
+        createdAt: Number.isFinite(Number(location.createdAt)) ? Number(location.createdAt) : Date.now(),
+        lastScanAt: Number.isFinite(Number(location.lastScanAt)) ? Number(location.lastScanAt) : 0,
+        unavailable: location.unavailable === true
+      };
+    }).filter(Boolean);
+
     const ui = source.ui && typeof source.ui === 'object' ? source.ui : {};
     const allowedFilters = new Set(['all', 'recent', 'favorites']);
     const width = Number(ui.width);
@@ -4360,8 +4406,11 @@ document.addEventListener("DOMContentLoaded", async function () {
       version: DOCUMENT_ORGANIZATION_VERSION,
       workspaces: workspaces,
       folders: folders,
+      linkedLocations: linkedLocations,
       ui: {
         filter: allowedFilters.has(ui.filter) ? ui.filter : 'all',
+        linkedWorkspaceExpanded: ui.linkedWorkspaceExpanded !== false,
+        linkedGuideInitialized: ui.linkedGuideInitialized === true,
         collapsed: ui.collapsed === true,
         width: Number.isFinite(width) ? Math.max(SIDEBAR_MIN_WIDTH, Math.min(SIDEBAR_MAX_WIDTH, width)) : 288,
         lastWorkspaceId: lastWorkspaceId,
@@ -4417,6 +4466,19 @@ document.addEventListener("DOMContentLoaded", async function () {
       folders: documentOrganization.folders.filter(function(folder) {
         return folder.workspaceId !== SECRET_WORKSPACE_ID;
       }),
+      linkedLocations: (documentOrganization.linkedLocations || []).map(function(location) {
+        return {
+          id: location.id,
+          path: location.path,
+          name: location.name,
+          expanded: location.expanded !== false,
+          collapsedFolderPaths: Array.isArray(location.collapsedFolderPaths) ? location.collapsedFolderPaths.slice() : [],
+          excludedPaths: Array.isArray(location.excludedPaths) ? location.excludedPaths.slice() : [],
+          createdAt: location.createdAt,
+          lastScanAt: location.lastScanAt || 0,
+          unavailable: location.unavailable === true
+        };
+      }),
       ui: Object.assign({}, documentOrganization.ui, {
         lastWorkspaceId: documentOrganization.ui.lastWorkspaceId === SECRET_WORKSPACE_ID && !secretWorkspaceKey
           ? DEFAULT_WORKSPACE_ID
@@ -5715,6 +5777,30 @@ document.addEventListener("DOMContentLoaded", async function () {
     document.querySelectorAll('.document-menu-dropdown').forEach(function(menu) { menu.remove(); });
   }
 
+  let linkedBackgroundUIRefreshPending = false;
+
+  function linkedSidebarState() {
+    return JSON.stringify([
+      tabs.filter(function(tab) { return tab.sourcePath; }).map(function(tab) {
+        return [tab.id, tab.title, tab.sourcePath, Boolean(tab.sourceMissing), Boolean(tab.sourceConflict),
+          tab.workspaceId, tab.folderId, tab.linkedRootId, tab.sourceRelativePath, tab.isOpen, tab.favorite];
+      }),
+      (documentOrganization.linkedLocations || []).map(function(location) {
+        return [location.id, location.name, location.path, Boolean(location.unavailable)];
+      })
+    ]);
+  }
+
+  function requestLinkedBackgroundUIRefresh() {
+    if (document.querySelector('.document-menu-dropdown.open, .tab-menu-dropdown.open, [data-tab-context-menu="true"]')) {
+      linkedBackgroundUIRefreshPending = true;
+      return;
+    }
+    linkedBackgroundUIRefreshPending = false;
+    renderTabBar(tabs, activeTabId);
+    renderDocumentSidebar();
+  }
+
   function closeDocumentSidebarMenus() {
     document.querySelectorAll('.document-menu-btn.open').forEach(function(button) {
       button.classList.remove('open');
@@ -5722,6 +5808,7 @@ document.addEventListener("DOMContentLoaded", async function () {
     });
     document.querySelectorAll('.document-menu-dropdown.open').forEach(function(menu) { menu.classList.remove('open'); });
     document.querySelectorAll('.document-menu-context').forEach(function(menu) { menu.remove(); });
+    if (linkedBackgroundUIRefreshPending) queueMicrotask(requestLinkedBackgroundUIRefresh);
   }
 
   function openDocumentMenu(button, menu, position, returnFocus, options) {
@@ -5849,11 +5936,35 @@ document.addEventListener("DOMContentLoaded", async function () {
   }
 
   function getDocumentMenuActions(tab) {
+    if (tab && tab.kind === LINKED_WORKSPACE_GUIDE_KIND) {
+      return [
+        { id: 'open', icon: 'lucide-file-text', label: 'Open', run: function() { openSidebarDocument(tab.id); } },
+        { id: 'favorite', icon: tab.favorite ? 'lucide-star-filled' : 'lucide-star', label: tab.favorite ? 'Remove from Favorites' : 'Add to Favorites', run: function() { toggleDocumentFavorite(tab.id); } },
+        { id: 'download', icon: 'lucide-download', label: 'Download Markdown', run: function() { downloadTabMarkdown(tab.id); } },
+        { id: 'delete', icon: 'lucide-trash-2', label: 'Delete', danger: true, run: function() { deleteTab(tab.id); } }
+      ];
+    }
+    if (isLinkedDocument(tab) && !isTemporaryDocument(tab)) {
+      const linkedActions = [
+        { id: 'open', icon: 'lucide-file-symlink', label: 'Open', run: function() { openSidebarDocument(tab.id); } },
+        { id: 'save', icon: 'lucide-download', label: 'Save', run: function() { void nativeSaveMarkdown({ tabId: tab.id, useLinkedSource: true }); } },
+        { id: 'save-as', icon: 'lucide-file-plus-2', label: 'Save As…', run: function() { void nativeSaveMarkdown({ tabId: tab.id, createLinked: true }); } },
+        { id: 'reload-source', icon: 'lucide-refresh-cw', label: 'Reload from disk', run: function() { void reloadLinkedDocument(tab.id, { force: true }); } },
+        { id: 'reveal-source', icon: 'lucide-folder-symlink', label: 'Open containing folder', run: function() { void revealLinkedSource(tab); } },
+        { separator: true },
+        { id: 'convert-vault', icon: 'lucide-files', label: 'Convert to Workspace copy', run: function() { void convertLinkedDocumentToVault(tab.id); } },
+        { id: 'remove-link', icon: 'lucide-x', label: 'Remove linked file', danger: true, run: function() { void removeLinkedDocument(tab.id); } }
+      ];
+      return linkedActions;
+    }
     const actions = [
       { id: 'open', icon: 'lucide-file-text', label: 'Open', run: function() { openSidebarDocument(tab.id); } }, {
       id: 'rename', icon: 'lucide-square-pen', label: 'Rename', run: function() { renameTab(tab.id); }
     }];
     if (!isTemporaryDocument(tab)) {
+      if (hasDesktopFileAccess() && tab.workspaceId !== SECRET_WORKSPACE_ID) {
+        actions.push({ id: 'save-as', icon: 'lucide-file-plus-2', label: 'Save As…', run: function() { void nativeSaveMarkdown({ tabId: tab.id, createLinked: true }); } });
+      }
       actions.push({ id: 'duplicate', icon: 'lucide-files', label: 'Duplicate', run: function() { duplicateTab(tab.id); } });
       actions.push({
         id: 'favorite',
@@ -5929,6 +6040,10 @@ document.addEventListener("DOMContentLoaded", async function () {
       const workspace = getWorkspaceById(id);
       return workspace ? getWorkspaceMenuActions(workspace) : [];
     }
+    if (type === 'linked-location') {
+      const location = (documentOrganization.linkedLocations || []).find(function(item) { return item.id === id; });
+      return location ? getLinkedLocationMenuActions(location) : [];
+    }
     return [];
   }
 
@@ -6054,6 +6169,10 @@ document.addEventListener("DOMContentLoaded", async function () {
         },
         { separator: true }
       );
+      if (getSelectedDocuments().some(function(tab) { return tab.kind === LINKED_WORKSPACE_GUIDE_KIND; })) {
+        const moveIndex = actions.findIndex(function(action) { return action.id === 'move-selected'; });
+        if (moveIndex >= 0) actions.splice(moveIndex, 1);
+      }
     }
     actions.push({
       id: 'delete-selected',
@@ -6203,8 +6322,7 @@ document.addEventListener("DOMContentLoaded", async function () {
       if (cut) replaceDocumentSurfaceSelection(context, '');
       showAppToast(cut ? 'Selection cut to clipboard.' : 'Selection copied to clipboard.', {
         tone: 'success',
-        title: cut ? 'Cut' : 'Copied',
-        icon: cut ? 'lucide-square-pen' : 'lucide-copy'
+        title: cut ? 'Cut' : 'Copied'
       });
     } catch (error) {
       showAppToast('Clipboard access failed: ' + error.message, { tone: 'error', title: 'Clipboard unavailable' });
@@ -6262,6 +6380,7 @@ document.addEventListener("DOMContentLoaded", async function () {
     const shouldAnnounce = !options || options.announce !== false;
     const tab = tabs.find(function(item) { return item.id === tabId; });
     if (!tab || isTemporaryDocument(tab)) return false;
+    if (tab.kind === LINKED_WORKSPACE_GUIDE_KIND) return false;
     if (workspaceId === SECRET_WORKSPACE_ID && !isSecretWorkspaceUnlocked()) {
       withUnlockedSecretWorkspace(function() {
         moveDocumentToLocation(tabId, workspaceId, folderId, options);
@@ -6517,7 +6636,7 @@ document.addEventListener("DOMContentLoaded", async function () {
           dragOverlay.setAttribute('aria-hidden', 'true');
         }
         const importFiles = function() {
-          handleIncomingDroppedFiles(files, { location: location });
+          handleIncomingDroppedFiles(files, { location: location, source: 'drop' });
         };
         if (location.workspaceId === SECRET_WORKSPACE_ID && !isSecretWorkspaceUnlocked()) {
           withUnlockedSecretWorkspace(importFiles);
@@ -6527,11 +6646,19 @@ document.addEventListener("DOMContentLoaded", async function () {
         return;
       }
       const tabIds = getDraggedSidebarDocumentIds(event.dataTransfer);
-      if (tabIds.length > 1) moveDocumentsToLocation(tabIds, location.workspaceId, location.folderId || null);
-      else if (tabIds.length === 1) moveDocumentToLocation(tabIds[0], location.workspaceId, location.folderId || null);
+      void dropSidebarDocuments(tabIds, location);
     });
   }
 
+  async function dropSidebarDocuments(tabIds, location) {
+    const documents = tabIds.map(function(id) { return tabs.find(function(tab) { return tab.id === id; }); }).filter(Boolean);
+    if (documents.some(isLinkedDocument) && location.workspaceId !== DEFAULT_WORKSPACE_ID) return;
+    for (const tab of documents) {
+      if (isLinkedDocument(tab)) await convertLinkedDocumentToVault(tab.id, location);
+      else await moveDocumentToLocation(tab.id, location.workspaceId, location.folderId || null);
+    }
+  }
+
   function createDocumentTreeRow(options) {
     const row = document.createElement('div');
     row.className = 'document-tree-row';
@@ -6550,6 +6677,7 @@ document.addEventListener("DOMContentLoaded", async function () {
     if (options.favorite) row.classList.add('is-favorite');
     if (options.temporary) row.classList.add('document-tree-temporary');
     if (options.locked) row.classList.add('is-secret-locked');
+    if (options.currentLocation) row.classList.add('is-current-location');
     if (typeof options.expanded === 'boolean') row.setAttribute('aria-expanded', options.expanded ? 'true' : 'false');
     row.setAttribute('aria-label', options.ariaLabel || options.label);
 
@@ -6580,7 +6708,7 @@ document.addEventListener("DOMContentLoaded", async function () {
     main.type = 'button';
     main.className = 'document-tree-main';
     main.setAttribute('tabindex', '-1');
-    main.title = options.label;
+    main.title = options.hoverTitle || options.label;
     const icon = document.createElement('i');
     icon.className = 'lucide ' + options.icon;
     icon.setAttribute('aria-hidden', 'true');
@@ -6625,7 +6753,7 @@ document.addEventListener("DOMContentLoaded", async function () {
       if (event.target.closest('input, select, textarea, a')) return;
       openDocumentTreeContextMenu(row, event);
     });
-    if (options.documentId && !options.temporary) {
+    if (options.documentId && !options.temporary && !options.disableDrag) {
       row.draggable = true;
       row.addEventListener('dragstart', function(event) {
         const rowSelectionKey = getDocumentTreeSelectionKey('document', options.documentId);
@@ -6671,9 +6799,11 @@ document.addEventListener("DOMContentLoaded", async function () {
       type: 'document',
       id: tab.id,
       documentId: tab.id,
+      disableDrag: tab.kind === LINKED_WORKSPACE_GUIDE_KIND,
       label: tab.title || 'Untitled',
-      ariaLabel: (tab.id === activeTabId ? 'Active document, ' : 'Document, ') + (tab.title || 'Untitled') + (tab.favorite ? ', favorite' : ''),
-      icon: 'lucide-file-text',
+      hoverTitle: isLinkedDocument(tab) ? tab.sourcePath : tab.title || 'Untitled',
+      ariaLabel: (tab.id === activeTabId ? 'Active document, ' : 'Document, ') + (tab.title || 'Untitled') + (isLinkedDocument(tab) ? ', linked file' : '') + (tab.favorite ? ', favorite' : ''),
+      icon: isLinkedDocument(tab) ? 'lucide-file-symlink' : 'lucide-file-text',
       depth: depth,
       favorite: tab.favorite === true,
       temporary: isTemporaryDocument(tab),
@@ -6683,6 +6813,12 @@ document.addEventListener("DOMContentLoaded", async function () {
         openSidebarDocument(tab.id);
       }
     });
+    if (isLinkedDocument(tab)) {
+      row.classList.add('is-linked-document');
+      row.title = tab.sourcePath;
+    }
+    if (isLinkedDocument(tab) && tab.sourceMissing) row.classList.add('is-source-missing');
+    if (isLinkedDocument(tab) && tab.sourceConflict) row.classList.add('is-source-conflict');
     container.appendChild(row);
     if (consumesRenderBudget) {
       documentSidebarRenderBudget.remaining = Math.max(0, documentSidebarRenderBudget.remaining - 1);
@@ -6691,6 +6827,8 @@ document.addEventListener("DOMContentLoaded", async function () {
   }
 
   function getDocumentLocationLabel(tab) {
+    if (hasDesktopFileAccess() && tab && tab.kind === LINKED_WORKSPACE_GUIDE_KIND) return 'Linked Workspace';
+    if (isLinkedDocument(tab)) return 'Linked · ' + tab.sourcePath;
     const workspace = getWorkspaceById(tab.workspaceId);
     const folder = getFolderById(tab.folderId);
     if (folder && workspace) return workspace.name + ' / ' + getFolderPath(folder.id);
@@ -6699,10 +6837,19 @@ document.addEventListener("DOMContentLoaded", async function () {
 
   function getDocumentTabHoverTitle(tab) {
     const title = tab && tab.title ? tab.title : 'Untitled';
+    if (isLinkedDocument(tab)) return title + ' — Linked file: ' + tab.sourcePath;
     const folder = tab ? getFolderById(tab.folderId) : null;
     return folder ? getFolderPath(folder.id) + ' / ' + title : title;
   }
 
+  if (hasDesktopFileAccess()) {
+    document.querySelectorAll('.desktop-linked-command').forEach(function(element) {
+      element.hidden = false;
+    });
+    const importLabel = document.querySelector('#import-from-file .app-menu-label');
+    if (importLabel) importLabel.textContent = 'Import copies';
+  }
+
   function documentMatchesSidebarSearch(tab) {
     if (!documentSidebarSearch) return true;
     const haystack = ((tab.title || '') + ' ' + getDocumentLocationLabel(tab)).toLocaleLowerCase();
@@ -6726,7 +6873,150 @@ document.addEventListener("DOMContentLoaded", async function () {
     }
     let renderedDocuments = 0;
     documents.forEach(function(tab) {
-      if (appendDocumentTreeItem(tree, tab, 0, getDocumentLocationLabel(tab))) renderedDocuments++;
+      const meta = isLinkedDocument(tab) ? getLinkedDocumentMeta(tab) : getDocumentLocationLabel(tab);
+      if (appendDocumentTreeItem(tree, tab, 0, meta)) renderedDocuments++;
+    });
+    return renderedDocuments;
+  }
+
+  function getLinkedDocumentMeta(tab) {
+    if (tab.sourceMissing) return 'Missing source';
+    if (tab.sourceConflict) return 'Conflict';
+    return '';
+  }
+
+  function getLinkedLocationMenuActions(location) {
+    return [
+      { id: 'rescan', icon: 'lucide-refresh-cw', label: 'Rescan folder', run: function() { void reconcileLinkedLocation(location.id, { notify: true, restoreExcluded: true }); } },
+      { id: 'reveal', icon: 'lucide-folder-symlink', label: 'Open folder', run: function() { void Neutralino.os.open(location.path); } },
+      { id: 'unlink', icon: 'lucide-x', label: 'Remove linked folder', danger: true, run: function() { void removeLinkedLocation(location.id); } }
+    ];
+  }
+
+  function renderLinkedLocationsTree(tree) {
+    if (!hasDesktopFileAccess()) return 0;
+    const linkedTabs = tabs.filter(function(tab) {
+      return !isTemporaryDocument(tab) && isLinkedWorkspaceDocument(tab);
+    });
+    const locations = Array.isArray(documentOrganization.linkedLocations) ? documentOrganization.linkedLocations : [];
+    let renderedDocuments = 0;
+    const activeDocument = tabs.find(function(tab) { return tab.id === activeTabId; });
+    const workspaceExpanded = documentSidebarSearch ? true : documentOrganization.ui.linkedWorkspaceExpanded !== false;
+    const toggleWorkspace = function() {
+      documentOrganization.ui.linkedWorkspaceExpanded = !workspaceExpanded;
+      saveDocumentOrganization();
+      renderDocumentSidebar();
+    };
+    tree.appendChild(createDocumentTreeRow({
+      type: 'linked-workspace',
+      id: 'linked-workspace',
+      label: 'Linked Workspace',
+      ariaLabel: 'Linked Workspace, original files remain on disk',
+      icon: 'lucide-link-2',
+      depth: 0,
+      expanded: workspaceExpanded,
+      currentLocation: isLinkedWorkspaceDocument(activeDocument),
+      meta: String(linkedTabs.length),
+      onToggle: toggleWorkspace,
+      onActivate: toggleWorkspace
+    }));
+    const workspaceGroup = document.createElement('div');
+    workspaceGroup.className = 'document-tree-group document-tree-group--workspace';
+    workspaceGroup.setAttribute('role', 'group');
+    workspaceGroup.hidden = !workspaceExpanded;
+    tree.appendChild(workspaceGroup);
+
+    const individualTabs = linkedTabs.filter(function(tab) { return !tab.linkedRootId; })
+      .filter(documentMatchesSidebarSearch)
+      .sort(function(left, right) { return (left.title || '').localeCompare(right.title || ''); });
+    individualTabs.forEach(function(tab) {
+      if (appendDocumentTreeItem(workspaceGroup, tab, 1, getLinkedDocumentMeta(tab))) renderedDocuments++;
+    });
+
+    locations.slice().sort(function(left, right) {
+      return (left.name || '').localeCompare(right.name || '');
+    }).forEach(function(location) {
+      const locationTabs = linkedTabs.filter(function(tab) { return tab.linkedRootId === location.id; });
+      const matchingTabs = locationTabs.filter(documentMatchesSidebarSearch);
+      const locationMatches = !documentSidebarSearch || (location.name + ' ' + location.path).toLocaleLowerCase().includes(documentSidebarSearch.toLocaleLowerCase());
+      if (documentSidebarSearch && !locationMatches && !matchingTabs.length) return;
+      const expanded = documentSidebarSearch ? true : location.expanded !== false;
+      const toggleLocation = function() {
+        location.expanded = !expanded;
+        saveDocumentOrganization();
+        renderDocumentSidebar();
+      };
+      const rootRow = createDocumentTreeRow({
+        type: 'linked-location',
+        id: location.id,
+        label: location.name,
+        ariaLabel: 'Linked folder, ' + location.path + (location.unavailable ? ', unavailable' : ''),
+        icon: location.unavailable ? 'lucide-triangle-alert' : 'lucide-folder-symlink',
+        depth: 1,
+        currentLocation: Boolean(activeDocument && activeDocument.linkedRootId === location.id),
+        expanded: expanded,
+        meta: location.unavailable ? 'Unavailable' : String(locationTabs.length),
+        menuActions: getLinkedLocationMenuActions(location),
+        onToggle: toggleLocation,
+        onActivate: toggleLocation
+      });
+      workspaceGroup.appendChild(rootRow);
+
+      const rootGroup = document.createElement('div');
+      rootGroup.className = 'document-tree-group document-tree-group--folder';
+      rootGroup.setAttribute('role', 'group');
+      rootGroup.hidden = !expanded;
+      const rootNode = { folders: new Map(), documents: [] };
+      matchingTabs.forEach(function(tab) {
+        const parts = String(tab.sourceRelativePath || '').replace(/\\/g, '/').split('/').filter(Boolean);
+        if (parts.length) parts.pop();
+        let node = rootNode;
+        parts.forEach(function(part) {
+          if (!node.folders.has(part)) node.folders.set(part, { folders: new Map(), documents: [] });
+          node = node.folders.get(part);
+        });
+        node.documents.push(tab);
+      });
+      const appendVirtualNode = function(node, container, depth, pathParts) {
+        Array.from(node.folders.entries()).sort(function(left, right) { return left[0].localeCompare(right[0]); }).forEach(function(entry) {
+          const folderName = entry[0];
+          const child = entry[1];
+          const folderPath = pathParts.concat(folderName).join('/');
+          const collapsedPaths = location.collapsedFolderPaths || [];
+          const folderExpanded = documentSidebarSearch ? true : !collapsedPaths.includes(folderPath);
+          const toggleFolder = function() {
+            const nextCollapsed = new Set(location.collapsedFolderPaths || []);
+            if (folderExpanded) nextCollapsed.add(folderPath);
+            else nextCollapsed.delete(folderPath);
+            location.collapsedFolderPaths = Array.from(nextCollapsed);
+            saveDocumentOrganization();
+            renderDocumentSidebar();
+          };
+          const row = createDocumentTreeRow({
+            type: 'linked-virtual-folder',
+            id: location.id + ':' + folderPath,
+            label: folderName,
+            icon: 'lucide-folder-symlink',
+            depth: depth,
+            expanded: folderExpanded,
+            meta: '',
+            onToggle: toggleFolder,
+            onActivate: toggleFolder
+          });
+          container.appendChild(row);
+          const childGroup = document.createElement('div');
+          childGroup.className = 'document-tree-group document-tree-group--folder';
+          childGroup.setAttribute('role', 'group');
+          childGroup.hidden = !folderExpanded;
+          appendVirtualNode(child, childGroup, depth + 1, pathParts.concat(folderName));
+          container.appendChild(childGroup);
+        });
+        node.documents.sort(function(left, right) { return (left.title || '').localeCompare(right.title || ''); }).forEach(function(tab) {
+          if (appendDocumentTreeItem(container, tab, depth, getLinkedDocumentMeta(tab))) renderedDocuments++;
+        });
+      };
+      appendVirtualNode(rootNode, rootGroup, 2, []);
+      workspaceGroup.appendChild(rootGroup);
     });
     return renderedDocuments;
   }
@@ -6750,9 +7040,10 @@ document.addEventListener("DOMContentLoaded", async function () {
 
     documentOrganization.workspaces.forEach(function(workspace) {
       const isSecretWorkspace = workspace.id === SECRET_WORKSPACE_ID;
+      if (isSecretWorkspace) renderedDocuments += renderLinkedLocationsTree(tree);
       const secretLocked = isSecretWorkspace && !isSecretWorkspaceUnlocked();
       const workspaceDocuments = tabs.filter(function(tab) {
-        return !isTemporaryDocument(tab) && tab.workspaceId === workspace.id;
+        return !isTemporaryDocument(tab) && !isLinkedWorkspaceDocument(tab) && tab.workspaceId === workspace.id;
       });
       const folders = documentOrganization.folders.filter(function(folder) { return folder.workspaceId === workspace.id; });
       const matchingDocuments = workspaceDocuments.filter(documentMatchesSidebarSearch);
@@ -6783,6 +7074,7 @@ document.addEventListener("DOMContentLoaded", async function () {
           ? (secretLocked ? 'lucide-shield' : 'lucide-shield-check')
           : (expanded ? 'lucide-folder-open' : 'lucide-folder'),
         depth: 0,
+        currentLocation: tabs.some(function(tab) { return tab.id === activeTabId && !isLinkedWorkspaceDocument(tab) && tab.workspaceId === workspace.id; }),
         expanded: expanded,
         meta: secretLocked ? 'Locked' : String(workspaceDocuments.length),
         locked: secretLocked,
@@ -6960,6 +7252,8 @@ document.addEventListener("DOMContentLoaded", async function () {
       : (preferredWorkspace ? preferredWorkspace.name : 'Workspace');
     const newDocumentButton = document.getElementById('sidebar-new-document');
     const newFolderButton = document.getElementById('sidebar-new-folder');
+    const linkFilesButton = document.getElementById('sidebar-link-files');
+    const linkFolderButton = document.getElementById('sidebar-link-folder');
     const collapseAllButton = document.getElementById('document-sidebar-collapse-all');
     if (newDocumentButton) {
       newDocumentButton.title = 'New Markdown file in ' + preferredLocationLabel;
@@ -7060,11 +7354,38 @@ document.addEventListener("DOMContentLoaded", async function () {
     const unlockedWorkspaceIds = new Set(documentOrganization.workspaces.filter(function(workspace) {
       return workspace.id !== SECRET_WORKSPACE_ID || isSecretWorkspaceUnlocked();
     }).map(function(workspace) { return workspace.id; }));
-    return documentOrganization.workspaces.filter(function(workspace) {
+    const items = documentOrganization.workspaces.filter(function(workspace) {
       return unlockedWorkspaceIds.has(workspace.id);
     }).concat(documentOrganization.folders.filter(function(folder) {
       return unlockedWorkspaceIds.has(folder.workspaceId);
     }));
+    if (hasDesktopFileAccess()) {
+      items.push({
+        get expanded() { return documentOrganization.ui.linkedWorkspaceExpanded !== false; },
+        set expanded(value) { documentOrganization.ui.linkedWorkspaceExpanded = value; }
+      });
+      (documentOrganization.linkedLocations || []).forEach(function(location) {
+        items.push(location);
+        const folderPaths = new Set(location.collapsedFolderPaths || []);
+        tabs.filter(function(tab) { return tab.sourcePath && tab.linkedRootId === location.id; }).forEach(function(tab) {
+          const parts = normalizeLinkedRelativePath(tab.sourceRelativePath).split('/').filter(Boolean);
+          parts.pop();
+          parts.forEach(function(_, index) { folderPaths.add(parts.slice(0, index + 1).join('/')); });
+        });
+        folderPaths.forEach(function(folderPath) {
+          items.push({
+            get expanded() { return !(location.collapsedFolderPaths || []).includes(folderPath); },
+            set expanded(value) {
+              const collapsed = new Set(location.collapsedFolderPaths || []);
+              if (value) collapsed.delete(folderPath);
+              else collapsed.add(folderPath);
+              location.collapsedFolderPaths = Array.from(collapsed);
+            }
+          });
+        });
+      });
+    }
+    return items;
   }
 
   function updateTreeExpansionButton(button, willExpand, label, enabled) {
@@ -7229,6 +7550,8 @@ document.addEventListener("DOMContentLoaded", async function () {
     const collapseAllButton = document.getElementById('document-sidebar-collapse-all');
     const newDocumentButton = document.getElementById('sidebar-new-document');
     const newFolderButton = document.getElementById('sidebar-new-folder');
+    const linkFilesButton = document.getElementById('sidebar-link-files');
+    const linkFolderButton = document.getElementById('sidebar-link-folder');
     const trashButton = document.getElementById('sidebar-trash-button');
     const search = document.getElementById('document-sidebar-search');
     const clearSearch = document.getElementById('document-sidebar-search-clear');
@@ -7240,6 +7563,8 @@ document.addEventListener("DOMContentLoaded", async function () {
     if (closeButton) closeButton.addEventListener('click', toggleDocumentSidebarCollapsed);
     if (backdrop) backdrop.addEventListener('click', closeDocumentSidebarOnMobile);
     if (collapseAllButton) collapseAllButton.addEventListener('click', toggleDocumentTreeExpansion);
+    if (linkFilesButton) linkFilesButton.addEventListener('click', function() { void nativeLinkMarkdownFiles(); });
+    if (linkFolderButton) linkFolderButton.addEventListener('click', function() { void nativeLinkMarkdownFolder(); });
     if (newDocumentButton) newDocumentButton.addEventListener('click', function() {
       const location = getPreferredDocumentLocation();
       newTab('', null, location);
@@ -10866,9 +11191,16 @@ document.addEventListener("DOMContentLoaded", async function () {
     if (!saveStatus || !saveStatusIcon || !saveStatusText) return;
     const requestedState = state === 'saving' || state === 'error' ? state : 'saved';
     const nextState = isPrivateStorageMode() && requestedState !== 'error' ? 'private' : requestedState;
+    let activeDocument = null;
+    try {
+      activeDocument = tabs.find(function(tab) { return tab.id === activeTabId; });
+    } catch (_) {
+      // Startup calls this before the workspace tab state is initialized.
+    }
+    const linkedSourcePath = isLinkedDocument(activeDocument) ? activeDocument.sourcePath : '';
     const presentation = {
       saving: { icon: 'lucide lucide-refresh-cw', text: 'Saving...' },
-      saved: { icon: 'lucide lucide-check', text: 'All changes saved' },
+      saved: { icon: 'lucide lucide-check', text: linkedSourcePath ? 'Draft saved · Ctrl+S updates original' : 'All changes saved' },
       private: { icon: 'lucide lucide-hat-glasses', text: 'Private mode is on' },
       error: { icon: 'lucide lucide-circle-alert', text: 'Changes not saved' }
     }[nextState];
@@ -10877,6 +11209,8 @@ document.addEventListener("DOMContentLoaded", async function () {
     saveStatus.dataset.state = nextState;
     if (nextState === 'private') {
       saveStatus.title = 'Private mode is on. Session changes are not saved.';
+    } else if (nextState === 'saved' && linkedSourcePath) {
+      saveStatus.title = 'Workspace recovery copy saved. Press Ctrl+S to update ' + linkedSourcePath;
     } else {
       saveStatus.removeAttribute('title');
     }
@@ -11097,6 +11431,487 @@ document.addEventListener("DOMContentLoaded", async function () {
     return tab;
   }
 
+  function normalizeLinkedSourcePath(sourcePath) {
+    const value = String(sourcePath || '').trim();
+    if (!value) return '';
+    const normalized = value.replace(/\//g, '\\').replace(/\\+$/g, '');
+    return /^[a-z]:\\/i.test(normalized) ? normalized.toLocaleLowerCase('en-US') : normalized;
+  }
+
+  function findTabBySourcePath(sourcePath) {
+    const pathKey = normalizeLinkedSourcePath(sourcePath);
+    if (!pathKey) return null;
+    return tabs.find(function(tab) {
+      return normalizeLinkedSourcePath(tab && tab.sourcePath) === pathKey;
+    }) || null;
+  }
+
+  async function hashLinkedSourceContent(content) {
+    if (!window.crypto || !window.crypto.subtle || typeof TextEncoder === 'undefined') return '';
+    const bytes = new TextEncoder().encode(String(content == null ? '' : content));
+    const digest = new Uint8Array(await window.crypto.subtle.digest('SHA-256', bytes));
+    return Array.from(digest).map(function(byte) { return byte.toString(16).padStart(2, '0'); }).join('');
+  }
+
+  async function openLinkedMarkdownDocument(content, title, sourcePath, options) {
+    if (!hasDesktopFileAccess()) return null;
+    const settings = options || {};
+    const normalizedPath = String(sourcePath || '').trim();
+    const incomingContent = String(content == null ? '' : content);
+    const incomingHash = await hashLinkedSourceContent(incomingContent);
+    let tab = findTabBySourcePath(normalizedPath);
+    let contentRefreshed = false;
+
+    // Only a matching source path identifies a linked document. A Vault copy
+    // remains independent even when its title and content match the original.
+
+    if (tab) {
+      await ensureTabContent(tab);
+      const draftHash = await hashLinkedSourceContent(tab.content);
+      const hasLocalDraft = Boolean(tab.sourceContentHash && draftHash && draftHash !== tab.sourceContentHash);
+      if (!hasLocalDraft && tab.content !== incomingContent) {
+        tab.content = incomingContent;
+        tab.contentLoaded = true;
+        tab._persistedContent = undefined;
+        contentRefreshed = true;
+      } else if (incomingHash && incomingHash !== tab.sourceContentHash) {
+        showAppToast('The file changed outside Markdown Viewer. Your workspace draft was kept; press Ctrl+S only if you want to overwrite the disk file.', {
+          tone: 'info',
+          title: 'External change detected'
+        });
+      }
+      tab.sourcePath = normalizedPath || tab.sourcePath;
+      if (!hasLocalDraft) tab.sourceContentHash = incomingHash;
+      tab.sourceMissing = false;
+      tab.sourceConflict = hasLocalDraft && Boolean(incomingHash && incomingHash !== tab.sourceContentHash);
+      tab.title = title || tab.title;
+      if (settings.open !== false) tab.isOpen = true;
+      if (settings.open !== false) tab.lastOpenedAt = Date.now();
+    } else {
+      tab = createTab(incomingContent, title || 'Untitled', 'split', { workspaceId: DEFAULT_WORKSPACE_ID, folderId: null });
+      tab.sourcePath = normalizedPath;
+      tab.sourceContentHash = incomingHash;
+      tab.sourceMissing = false;
+      tab.sourceConflict = false;
+      tab.isOpen = settings.open === false ? false : true;
+      tabs.push(tab);
+    }
+
+    tab.sourceKind = 'linked';
+    if (settings.linkedRootId) tab.linkedRootId = String(settings.linkedRootId);
+    if (settings.sourceRelativePath) tab.sourceRelativePath = String(settings.sourceRelativePath).replace(/\\/g, '/').replace(/^\/+/, '');
+
+    if (settings.open !== false) selectedDocumentId = tab.id;
+    saveTabsToStorage(tabs, [tab.id]);
+    if (settings.open === false) {
+      if (tab.id === activeTabId && contentRefreshed) {
+        markdownEditor.value = tab.content;
+        renderMarkdown();
+      }
+      if (!settings.deferUI) {
+        renderTabBar(tabs, activeTabId);
+        renderDocumentSidebar();
+      }
+    } else if (settings.activate === false) {
+      activeTabId = tab.id;
+      saveActiveTabId(tab.id);
+    } else {
+      if (tab.id === activeTabId) {
+        if (contentRefreshed) {
+          markdownEditor.value = tab.content;
+          renderMarkdown();
+        }
+        renderTabBar(tabs, activeTabId);
+        renderDocumentSidebar();
+      } else {
+        await switchTab(tab.id);
+      }
+      if (settings.notify !== false) showAppToast('Linked to ' + tab.sourcePath + '. Press Ctrl+S to save changes to the original file.', {
+        tone: 'info',
+        title: 'Linked Markdown file'
+      });
+    }
+    return tab;
+  }
+
+  function getNativePathName(filePath) {
+    return String(filePath || '').replace(/[\\/]+$/, '').split(/[\\/]/).pop() || '';
+  }
+
+  function getNativeParentPath(filePath) {
+    const value = String(filePath || '').replace(/[\\/]+$/, '');
+    const separator = Math.max(value.lastIndexOf('\\'), value.lastIndexOf('/'));
+    return separator > 2 ? value.slice(0, separator) : value.slice(0, separator + 1);
+  }
+
+  function getLinkedLocation(locationId) {
+    return (documentOrganization.linkedLocations || []).find(function(location) { return location.id === locationId; }) || null;
+  }
+
+  function normalizeLinkedRelativePath(value) {
+    return String(value || '').replace(/\\/g, '/').replace(/^\/+/, '');
+  }
+
+  async function collectMarkdownFilesFromFolder(rootPath) {
+    const files = [];
+    const ignoredDirectories = new Set(['.git', 'node_modules']);
+    async function visit(folderPath, relativePrefix) {
+      if (files.length >= 5000) throw new Error('This folder contains more than 5,000 Markdown files. Link a smaller folder instead.');
+      const entries = await Neutralino.filesystem.readDirectory(folderPath);
+      for (const entry of entries) {
+        if (!entry || !entry.entry || entry.entry === '.' || entry.entry === '..') continue;
+        const childPath = await Neutralino.filesystem.getJoinedPath(folderPath, entry.entry);
+        const relativePath = normalizeLinkedRelativePath(relativePrefix ? relativePrefix + '/' + entry.entry : entry.entry);
+        if (entry.type === 'DIRECTORY') {
+          if (!ignoredDirectories.has(String(entry.entry).toLowerCase())) await visit(childPath, relativePath);
+        } else if (entry.type === 'FILE' && /\.(md|markdown)$/i.test(entry.entry)) {
+          files.push({ path: childPath, relativePath: relativePath });
+        }
+      }
+    }
+    await visit(rootPath, '');
+    return files;
+  }
+
+  async function reloadLinkedDocument(tabId, options) {
+    const tab = tabs.find(function(item) { return item.id === tabId; });
+    if (!isLinkedDocument(tab)) return false;
+    const settings = options || {};
+    const previousSidebarState = linkedSidebarState();
+    function refreshUI() {
+      if (settings.background) {
+        if (previousSidebarState !== linkedSidebarState()) requestLinkedBackgroundUIRefresh();
+      } else renderDocumentSidebar();
+    }
+    let diskContent;
+    try {
+      diskContent = await Neutralino.filesystem.readFile(tab.sourcePath);
+    } catch (_) {
+      tab.sourceMissing = true;
+      tab.sourceConflict = false;
+      saveTabsToStorage(tabs, [tab.id]);
+      refreshUI();
+      return false;
+    }
+    await ensureTabContent(tab);
+    const diskHash = await hashLinkedSourceContent(diskContent);
+    const draftHash = await hashLinkedSourceContent(tab.content);
+    const hasLocalDraft = Boolean(tab.sourceContentHash && draftHash && draftHash !== tab.sourceContentHash);
+    const hasExternalChange = Boolean(tab.sourceContentHash && diskHash && diskHash !== tab.sourceContentHash);
+    if (hasLocalDraft && hasExternalChange && !settings.force) {
+      tab.sourceConflict = true;
+      tab.sourceMissing = false;
+      saveTabsToStorage(tabs, [tab.id]);
+      refreshUI();
+      showAppToast('The original changed on disk while a local draft exists. The draft was kept.', { tone: 'info', title: 'Linked file conflict' });
+      return false;
+    }
+    if (hasLocalDraft && settings.force) {
+      const replaceDraft = window.confirm('Discard the current workspace draft and reload this linked file from disk?\n\n' + tab.sourcePath);
+      if (!replaceDraft) return false;
+    }
+    if (!hasExternalChange && !tab.sourceMissing && !settings.force) return true;
+    tab.content = String(diskContent == null ? '' : diskContent);
+    tab.contentLoaded = true;
+    tab._persistedContent = undefined;
+    tab.sourceContentHash = diskHash;
+    tab.sourceMissing = false;
+    tab.sourceConflict = false;
+    tab.lastEditedAt = Date.now();
+    saveTabsToStorage(tabs, [tab.id]);
+    if (tab.id === activeTabId) {
+      markdownEditor.value = tab.content;
+      renderMarkdown();
+    }
+    if (!settings.background) renderTabBar(tabs, activeTabId);
+    refreshUI();
+    return true;
+  }
+
+  async function reconcileLinkedLocation(locationId, options) {
+    const location = getLinkedLocation(locationId);
+    if (!location) return 0;
+    const settings = options || {};
+    const previousSidebarState = linkedSidebarState();
+    function refreshUI() {
+      if (settings.background) {
+        if (previousSidebarState !== linkedSidebarState()) requestLinkedBackgroundUIRefresh();
+      } else {
+        renderTabBar(tabs, activeTabId);
+        renderDocumentSidebar();
+      }
+    }
+    let files;
+    try {
+      files = await collectMarkdownFilesFromFolder(location.path);
+      location.unavailable = false;
+    } catch (error) {
+      location.unavailable = true;
+      saveDocumentOrganization();
+      refreshUI();
+      if (settings.notify) showAppToast('The linked folder is unavailable: ' + location.path, { tone: 'error', title: 'Folder scan failed' });
+      return 0;
+    }
+    // Explicit rescans/re-linking restore removed links; background refreshes
+    // continue respecting exclusions. Only reset after a successful folder scan.
+    if (settings.restoreExcluded) location.excludedPaths = [];
+    const excluded = new Set((location.excludedPaths || []).map(normalizeLinkedRelativePath));
+    const discoveredPaths = new Set();
+    let added = 0;
+    for (const file of files) {
+      if (excluded.has(file.relativePath)) continue;
+      discoveredPaths.add(normalizeLinkedSourcePath(file.path));
+      let existing = findTabBySourcePath(file.path);
+      try {
+        const content = await Neutralino.filesystem.readFile(file.path);
+        await openLinkedMarkdownDocument(content, getNativePathName(file.path).replace(/\.(md|markdown)$/i, ''), file.path, {
+          activate: false,
+          open: false,
+          deferUI: true,
+          linkedRootId: location.id,
+          sourceRelativePath: file.relativePath
+        });
+        if (!existing) added++;
+      } catch (error) {
+        console.warn('Could not read linked Markdown file:', file.path, error);
+      }
+    }
+    tabs.filter(function(tab) { return tab.linkedRootId === location.id; }).forEach(function(tab) {
+      if (!discoveredPaths.has(normalizeLinkedSourcePath(tab.sourcePath))) tab.sourceMissing = true;
+    });
+    location.lastScanAt = Date.now();
+    saveDocumentOrganization();
+    saveTabsToStorage(tabs);
+    refreshUI();
+    if (settings.notify) showAppToast('Linked folder scanned. ' + added + ' new Markdown file' + (added === 1 ? '' : 's') + ' found.', { tone: 'success', title: location.name });
+    return added;
+  }
+
+  async function addLinkedFolderPath(folderPath, options) {
+    if (!hasDesktopFileAccess()) return null;
+    const normalized = normalizeLinkedSourcePath(folderPath);
+    let location = (documentOrganization.linkedLocations || []).find(function(item) {
+      return normalizeLinkedSourcePath(item.path) === normalized;
+    });
+    if (!location) {
+      location = {
+        id: createDocumentEntityId('linked'),
+        path: String(folderPath),
+        name: getNativePathName(folderPath) || 'Linked folder',
+        expanded: true,
+        excludedPaths: [],
+        createdAt: Date.now(),
+        lastScanAt: 0,
+        unavailable: false
+      };
+      documentOrganization.linkedLocations.push(location);
+      saveDocumentOrganization();
+    }
+    await reconcileLinkedLocation(location.id, { notify: !(options && options.silent), restoreExcluded: true });
+    await refreshLinkedSourceMonitoring();
+    return location;
+  }
+
+  async function addLinkedFilePath(filePath, options) {
+    if (!/\.(md|markdown)$/i.test(filePath)) return null;
+    const content = await Neutralino.filesystem.readFile(filePath);
+    const tab = await openLinkedMarkdownDocument(content, getNativePathName(filePath).replace(/\.(md|markdown)$/i, ''), filePath, {
+      activate: options && options.activate === true,
+      open: options && options.open === true
+    });
+    await refreshLinkedSourceMonitoring();
+    return tab;
+  }
+
+  async function nativeLinkMarkdownFiles() {
+    if (!hasDesktopFileAccess()) return 0;
+    try {
+      const paths = await Neutralino.os.showOpenDialog('Link Markdown files', {
+        filters: [{ name: 'Markdown files (*.md, *.markdown)', extensions: ['md', 'markdown'] }],
+        multiSelections: true
+      });
+      if (!paths || !paths.length) return 0;
+      let count = 0;
+      for (const filePath of paths) {
+        if (await addLinkedFilePath(filePath, { open: false })) count++;
+      }
+      showAppToast(count + ' file' + (count === 1 ? '' : 's') + ' linked. Originals remain on disk.', { tone: 'success', title: 'Linked files' });
+      return count;
+    } catch (error) {
+      console.warn('Could not link Markdown files:', error);
+      showAppToast(error.message || 'The selected files could not be linked.', { tone: 'error', title: 'Link failed' });
+      return 0;
+    }
+  }
+
+  async function nativeLinkMarkdownFolder() {
+    if (!hasDesktopFileAccess()) return;
+    try {
+      const folderPath = await Neutralino.os.showFolderDialog('Link Markdown folder');
+      if (folderPath) await addLinkedFolderPath(folderPath);
+    } catch (error) {
+      console.warn('Could not link Markdown folder:', error);
+      showAppToast(error.message || 'The selected folder could not be linked.', { tone: 'error', title: 'Link failed' });
+    }
+  }
+
+  async function revealLinkedSource(tab) {
+    if (!isLinkedDocument(tab)) return;
+    await Neutralino.os.open(getNativeParentPath(tab.sourcePath));
+  }
+
+  async function convertLinkedDocumentToVault(tabId, destination) {
+    const tab = tabs.find(function(item) { return item.id === tabId; });
+    if (!isLinkedDocument(tab)) return;
+    await ensureTabContent(tab);
+    const previous = Object.assign({}, tab);
+    const sourcePath = tab.sourcePath;
+    const location = tab.linkedRootId ? getLinkedLocation(tab.linkedRootId) : null;
+    const previousExcluded = location ? (location.excludedPaths || []).slice() : null;
+    if (location && tab.sourceRelativePath) {
+      location.excludedPaths = Array.from(new Set((location.excludedPaths || []).concat(normalizeLinkedRelativePath(tab.sourceRelativePath))));
+      saveDocumentOrganization();
+    }
+    delete tab.sourcePath;
+    delete tab.sourceContentHash;
+    delete tab.sourceKind;
+    delete tab.linkedRootId;
+    delete tab.sourceRelativePath;
+    delete tab.sourceMissing;
+    delete tab.sourceConflict;
+    setDocumentLocation(tab, DEFAULT_WORKSPACE_ID, destination && destination.folderId || null);
+    tab.isOpen = true;
+    try {
+      if (!(await _flushTabsToStorage(tabs, { changedIds: [tab.id] }))) throw new Error('Workspace copy could not be saved.');
+    } catch (error) {
+      Object.keys(tab).forEach(function(key) { delete tab[key]; });
+      Object.assign(tab, previous);
+      if (location) location.excludedPaths = previousExcluded;
+      saveDocumentOrganization();
+      renderDocumentSidebar();
+      showAppToast(error.message, { tone: 'error', title: 'Conversion failed' });
+      return false;
+    }
+    renderTabBar(tabs, activeTabId);
+    renderDocumentSidebar();
+    await refreshLinkedSourceMonitoring();
+    showAppToast('A separate Vault copy was created. The original file was left unchanged at ' + sourcePath, {
+      tone: 'success',
+      icon: 'lucide-check',
+      title: 'Converted to Workspace copy'
+    });
+    return true;
+  }
+
+  async function removeLinkedDocument(tabId) {
+    const tab = tabs.find(function(item) { return item.id === tabId; });
+    if (!tab || !tab.sourcePath) return;
+    const location = tab.linkedRootId ? getLinkedLocation(tab.linkedRootId) : null;
+    if (location && tab.sourceRelativePath) {
+      location.excludedPaths = Array.from(new Set((location.excludedPaths || []).concat(normalizeLinkedRelativePath(tab.sourceRelativePath))));
+      saveDocumentOrganization();
+    }
+    await deleteTab(tab.id);
+    await refreshLinkedSourceMonitoring();
+    showAppToast('Link removed. The original file remains on disk.', { tone: 'success', title: 'Linked file closed' });
+  }
+
+  async function removeLinkedLocation(locationId) {
+    const location = getLinkedLocation(locationId);
+    if (!location) return;
+    const linkedTabs = tabs.filter(function(tab) { return tab.linkedRootId === locationId; });
+    const confirmed = await showAppToastConfirmation(
+      'Remove this linked folder and ' + linkedTabs.length + ' file link' + (linkedTabs.length === 1 ? '' : 's') + '? Original files remain on disk.',
+      { title: 'Remove linked folder', confirmLabel: 'Remove link', dedupeKey: 'remove-linked-folder:' + location.id }
+    );
+    if (!confirmed) return;
+    documentOrganization.linkedLocations = documentOrganization.linkedLocations.filter(function(item) { return item.id !== locationId; });
+    saveDocumentOrganization();
+    for (const tab of linkedTabs.slice()) await deleteTab(tab.id);
+    await refreshLinkedSourceMonitoring();
+    renderDocumentSidebar();
+    showAppToast('Linked folder removed. Original files remain on disk.', { tone: 'success', title: 'Folder unlinked' });
+  }
+
+  async function stopLinkedSourceMonitoring() {
+    const watchers = Array.from(linkedSourceWatchers.values());
+    linkedSourceWatchers.clear();
+    for (const watcher of watchers) {
+      try { await Neutralino.filesystem.removeWatcher(watcher.id); } catch (_) {}
+    }
+  }
+
+  async function refreshLinkedSourceMonitoring() {
+    if (!linkedSourceMonitoringReady || !hasDesktopFileAccess() || !Neutralino.filesystem.createWatcher) return;
+    await stopLinkedSourceMonitoring();
+    const targets = [];
+    (documentOrganization.linkedLocations || []).forEach(function(location) {
+      targets.push({ key: 'folder:' + location.id, path: location.path, locationId: location.id });
+      const watchedDirectories = new Set([normalizeLinkedSourcePath(location.path)]);
+      tabs.filter(function(tab) { return tab.linkedRootId === location.id && tab.sourcePath; }).forEach(function(tab) {
+        const parentPath = getNativeParentPath(tab.sourcePath);
+        const normalizedParent = normalizeLinkedSourcePath(parentPath);
+        if (watchedDirectories.has(normalizedParent)) return;
+        watchedDirectories.add(normalizedParent);
+        targets.push({ key: 'folder:' + location.id + ':' + normalizedParent, path: parentPath, locationId: location.id });
+      });
+    });
+    const seenParents = new Set();
+    tabs.filter(function(tab) { return tab.sourcePath && !tab.linkedRootId; }).forEach(function(tab) {
+      const parentPath = getNativeParentPath(tab.sourcePath);
+      const key = normalizeLinkedSourcePath(parentPath);
+      if (!seenParents.has(key)) {
+        seenParents.add(key);
+        targets.push({ key: 'files:' + key, path: parentPath, individual: true });
+      }
+    });
+    for (const target of targets) {
+      try {
+        const watcherId = await Neutralino.filesystem.createWatcher(target.path);
+        linkedSourceWatchers.set(target.key, Object.assign({ id: watcherId }, target));
+      } catch (error) {
+        console.warn('Could not watch linked location:', target.path, error);
+      }
+    }
+  }
+
+  function scheduleLinkedWatcherRefresh(watcher) {
+    if (!watcher) return;
+    const key = watcher.locationId ? 'location:' + watcher.locationId : watcher.key;
+    clearTimeout(linkedSourceRefreshTimers.get(key));
+    linkedSourceRefreshTimers.set(key, setTimeout(async function() {
+      linkedSourceRefreshTimers.delete(key);
+      if (watcher.locationId) {
+        await reconcileLinkedLocation(watcher.locationId, { background: true });
+        await refreshLinkedSourceMonitoring();
+      }
+      else {
+        for (const tab of tabs.filter(function(item) { return item.sourcePath && !item.linkedRootId && normalizeLinkedSourcePath(getNativeParentPath(item.sourcePath)) === normalizeLinkedSourcePath(watcher.path); })) {
+          await reloadLinkedDocument(tab.id, { background: true });
+        }
+      }
+    }, 350));
+  }
+
+  async function initializeLinkedSourceMonitoring() {
+    if (linkedSourceMonitoringReady || !hasDesktopFileAccess()) return;
+    linkedSourceMonitoringReady = true;
+    if (Neutralino.events && typeof Neutralino.events.on === 'function') {
+      await Neutralino.events.on('watchFile', function(event) {
+        const watcher = Array.from(linkedSourceWatchers.values()).find(function(item) { return item.id === event.detail.id; });
+        scheduleLinkedWatcherRefresh(watcher);
+      });
+      await Neutralino.events.on('windowFocus', function() {
+        Array.from(linkedSourceWatchers.values()).forEach(scheduleLinkedWatcherRefresh);
+      });
+    }
+    await refreshLinkedSourceMonitoring();
+  }
+
+  window.NL_START_LINKED_MONITORING = function() {
+    return initializeLinkedSourceMonitoring();
+  };
+
   function isTabOpen(tab) {
     return Boolean(tab && tab.isOpen !== false);
   }
@@ -11628,7 +12443,7 @@ document.addEventListener("DOMContentLoaded", async function () {
         fileIcon.setAttribute('aria-hidden', 'true');
       } else {
         fileIcon = document.createElement('i');
-        fileIcon.className = 'lucide ' + (splitPartner ? 'lucide-columns-2' : 'lucide-file-text') + ' tab-file-icon';
+        fileIcon.className = 'lucide ' + (splitPartner ? 'lucide-columns-2' : (isLinkedDocument(tab) ? 'lucide-file-symlink' : 'lucide-file-text')) + ' tab-file-icon';
         fileIcon.setAttribute('aria-hidden', 'true');
       }
 
@@ -12545,14 +13360,9 @@ document.addEventListener("DOMContentLoaded", async function () {
     const content = typeof tab.content === 'string' ? tab.content : '';
     const filename = getSafeDocumentFilename(tab.title, "md", "document.md");
 
-    if (typeof Neutralino !== 'undefined') {
+    if (hasDesktopFileAccess()) {
       try {
-        const result = await Neutralino.os.showSaveDialog("Save Markdown File", {
-          filters: [
-            { name: "Markdown files (*.md)", extensions: ["md", "markdown"] },
-            { name: "All files (*.*)", extensions: ["*"] }
-          ]
-        });
+        const result = await chooseMarkdownSavePath(tab);
         if (result) {
           await Neutralino.filesystem.writeFile(result, content);
         }
@@ -12735,21 +13545,47 @@ document.addEventListener("DOMContentLoaded", async function () {
     const hadExistingWorkspace = tabs.length > 0;
     activeTabId = loadActiveTabId();
 
-    // Check if Neutralino passed an initial file via command line (early load)
-    if (window.NL_INITIAL_FILE_CONTENT) {
-      const initialFile = window.NL_INITIAL_FILE_CONTENT;
-      const tab = createTab(initialFile.content, initialFile.name);
+    // Seed the default Vault document before opening an initial linked file.
+    // File-association launches must not skip the Welcome on a fresh workspace.
+    if (!hadExistingWorkspace) {
+      const tab = createTab(sampleMarkdown, 'Welcome to Markdown', 'split', {
+        workspaceId: DEFAULT_WORKSPACE_ID,
+        folderId: null
+      });
       tabs.push(tab);
       activeTabId = tab.id;
       saveTabsToStorage(tabs);
       saveActiveTabId(activeTabId);
+    }
+
+    // Seed a real, editable internal guide once, including existing installations.
+    // It has no external source path and must never be watched or written back.
+    if (hasDesktopFileAccess() && !documentOrganization.ui.linkedGuideInitialized) {
+      if (!tabs.some(function(tab) { return tab.kind === LINKED_WORKSPACE_GUIDE_KIND; })) {
+        const response = await fetch('assets/linked-workspace-guide.md');
+        if (!response.ok) throw new Error('Unable to load the Linked Workspace guide.');
+        const guide = createTab(await response.text(), 'Welcome to Linked Workspace', 'preview', {
+          workspaceId: DEFAULT_WORKSPACE_ID, folderId: null
+        });
+        guide.kind = LINKED_WORKSPACE_GUIDE_KIND;
+        guide.isOpen = false;
+        tabs.push(guide);
+        if (!(await _flushTabsToStorage(tabs, { changedIds: [guide.id] }))) throw new Error('Unable to save the Linked Workspace guide.');
+      }
+      documentOrganization.ui.linkedGuideInitialized = true;
+      saveDocumentOrganization();
+    }
+
+    // Check if Neutralino passed an initial file via command line (early load)
+    if (window.NL_INITIAL_FILE_CONTENT) {
+      const initialFile = window.NL_INITIAL_FILE_CONTENT;
+      await openLinkedMarkdownDocument(
+        initialFile.content,
+        initialFile.name,
+        initialFile.sourcePath,
+        { activate: false }
+      );
       delete window.NL_INITIAL_FILE_CONTENT;
-    } else if (tabs.length === 0) {
-      const tab = createTab(sampleMarkdown, 'Welcome to Markdown');
-      tabs.push(tab);
-      activeTabId = tab.id;
-      saveTabsToStorage(tabs);
-      saveActiveTabId(activeTabId);
     } else if (!tabs.find(function(t) { return t.id === activeTabId && isTabOpen(t) && !t.storageCorruption; })) {
       const firstOpenTab = getOpenTabs().find(function(tab) { return !tab.storageCorruption; });
       activeTabId = firstOpenTab ? firstOpenTab.id : null;
@@ -12854,14 +13690,9 @@ document.addEventListener("DOMContentLoaded", async function () {
   }
 
   // Late-load callback hook for Neutralino command-line files
-  window.NL_IMPORT_EXTERNAL_FILE = function(content, name) {
+  window.NL_IMPORT_EXTERNAL_FILE = async function(content, name, sourcePath) {
     if (typeof tabs === 'undefined') return;
-    const existing = tabs.find(function(t) { return t.title === name && t.content === content; });
-    if (existing) {
-      switchTab(existing.id);
-      return;
-    }
-    newTab(content, name);
+    await openLinkedMarkdownDocument(content, name, sourcePath, { activate: true });
   };
 
   function showPreviewSkeleton() {
@@ -14881,7 +15712,7 @@ ${selector} .arrowheadPath {
     icon.className = settings.iconClass || ('lucide ' + (settings.icon || ({
       error: 'lucide-circle-alert',
       warning: 'lucide-triangle-alert',
-      success: 'lucide-circle-check',
+      success: 'lucide-check',
       info: 'lucide-info'
     }[tone] || 'lucide-info')));
     iconShell.appendChild(icon);
@@ -24059,29 +24890,124 @@ ${selector} .arrowheadPath {
     updateStlThemes();
   });
 
-  async function nativeSaveMarkdown() {
+  async function writeLinkedMarkdownSource(tab, content) {
+    if (!isLinkedDocument(tab)) return false;
+    let diskContent = null;
     try {
-      const content = markdownEditor.value;
-      const result = await Neutralino.os.showSaveDialog("Save Markdown File", {
-        filters: [
-          { name: "Markdown files (*.md)", extensions: ["md", "markdown"] },
-          { name: "All files (*.*)", extensions: ["*"] }
-        ]
-      });
+      diskContent = await Neutralino.filesystem.readFile(tab.sourcePath);
+    } catch (_) {
+      const recreate = window.confirm('The linked file no longer exists:\n\n' + tab.sourcePath + '\n\nCreate it again at this location?');
+      if (!recreate) return true;
+    }
+
+    if (diskContent !== null && tab.sourceContentHash) {
+      const diskHash = await hashLinkedSourceContent(diskContent);
+      if (diskHash && diskHash !== tab.sourceContentHash) {
+        const overwrite = window.confirm(
+          'This file changed outside Markdown Viewer after it was opened:\n\n' +
+          tab.sourcePath +
+          '\n\nOverwrite the external changes with the current editor content?'
+        );
+        if (!overwrite) return true;
+      }
+    }
+
+    await Neutralino.filesystem.writeFile(tab.sourcePath, content);
+    const verified = await Neutralino.filesystem.readFile(tab.sourcePath);
+    if (verified !== content) throw new Error('The linked file write could not be verified.');
+    tab.sourceContentHash = await hashLinkedSourceContent(content);
+    tab.sourceMissing = false;
+    tab.sourceConflict = false;
+    tab.content = content;
+    tab.contentLoaded = true;
+    tab.lastEditedAt = Date.now();
+    saveTabsToStorage(tabs, [tab.id]);
+    renderTabBar(tabs, activeTabId);
+    renderDocumentSidebar();
+    showAppToast('Saved to ' + tab.sourcePath, {
+      tone: 'success',
+      icon: 'lucide-check',
+      title: 'Original file updated'
+    });
+    return true;
+  }
+
+  async function chooseMarkdownSavePath(tab) {
+    if (!hasDesktopFileAccess()) return null;
+    const chosen = await Neutralino.os.showSaveDialog('Save Markdown File', {
+      defaultPath: getSafeDocumentFilename(tab && tab.title, 'md', 'document.md'),
+      filters: [
+        { name: 'Markdown files (*.md)', extensions: ['md', 'markdown'] },
+        { name: 'All files (*.*)', extensions: ['*'] }
+      ]
+    });
+    if (!chosen) return null;
+    const name = getNativePathName(chosen);
+    const result = name.lastIndexOf('.') > 0 && !name.endsWith('.') ? chosen : chosen.replace(/\.+$/, '') + '.md';
+    // The native picker confirmed only the path it returned. If adding .md
+    // changes that path, explicitly protect the actual destination as well.
+    if (result !== chosen) {
+      let exists = false;
+      try {
+        await Neutralino.filesystem.getStats(result);
+        exists = true;
+      } catch (error) {
+        if (error.code !== 'NE_FS_NOPATHE') throw error;
+      }
+      if (exists && !(await showAppToastConfirmation('Replace the existing file at ' + result + '?', {
+        title: 'Replace Markdown file?', confirmLabel: 'Replace', dedupeKey: 'save-overwrite:' + result
+      }))) return null;
+    }
+    return result;
+  }
+
+  let nativeMarkdownSaveInProgress = false;
+  async function nativeSaveMarkdown(options) {
+    if (!hasDesktopFileAccess() || nativeMarkdownSaveInProgress) return;
+    nativeMarkdownSaveInProgress = true;
+    try {
+      const settings = options || {};
+      saveCurrentTabState();
+      const tab = tabs.find(function(t) { return t.id === (settings.tabId || activeTabId); });
+      if (!tab || isTemporaryDocument(tab)) return;
+      await ensureTabContent(tab);
+      const content = typeof tab.content === 'string' ? tab.content : '';
+      if (settings.useLinkedSource && tab.sourcePath) {
+        await writeLinkedMarkdownSource(tab, content);
+        return;
+      }
+      const result = await chooseMarkdownSavePath(tab);
       if (result) {
+        const createLinked = tab.workspaceId !== SECRET_WORKSPACE_ID && (settings.createLinked || settings.useLinkedSource);
+        if (createLinked && tab.sourcePath && normalizeLinkedSourcePath(result) === normalizeLinkedSourcePath(tab.sourcePath)) {
+          showAppToast('Choose a different path to create a new linked file. Use Save to update the current original.', { tone: 'warning', title: 'Choose a new file' });
+          return;
+        }
+        const existing = createLinked && findTabBySourcePath(result);
+        if (existing) {
+          await ensureTabContent(existing);
+          if (existing.sourceContentHash && await hashLinkedSourceContent(existing.content) !== existing.sourceContentHash) {
+            showAppToast('This destination already has a linked document with local changes. Choose another file to preserve that draft.', { tone: 'warning', title: 'Unsaved linked draft' });
+            return;
+          }
+        }
         await Neutralino.filesystem.writeFile(result, content);
+        if (await Neutralino.filesystem.readFile(result) !== content) throw new Error('The saved file could not be verified.');
         const fileName = result.split(/[/\\]/).pop().replace(/\.(md|markdown)$/i, "");
-        const activeTab = tabs.find(function(t) { return t.id === activeTabId; });
-        if (activeTab) {
-          activeTab.title = fileName;
-          activeTab.content = content;
-          saveTabsToStorage(tabs, [activeTab.id]);
-          renderTabBar(tabs, activeTabId);
+        if (createLinked) {
+          const linked = await openLinkedMarkdownDocument(content, fileName, result, { notify: false });
+          if (!(await _flushTabsToStorage(tabs, { changedIds: [tab.id, linked.id] }))) {
+            throw new Error('The external file was saved, but its workspace link could not be persisted.');
+          }
+          markdownEditor.focus();
         }
+        showAppToast('Saved to ' + result + (createLinked ? '. Future Ctrl+S saves update this linked file.' : ''), { tone: 'success', title: 'Markdown file saved' });
       }
     } catch (e) {
       console.error("Native save failed:", e);
-      alert("Native save failed: " + e.message);
+      showAppToast(e.message, { tone: 'error', title: 'Save failed' });
+    } finally {
+      nativeMarkdownSaveInProgress = false;
     }
   }
 
@@ -24149,6 +25075,20 @@ ${selector} .arrowheadPath {
     });
   }
 
+  if (linkFromFileButton) {
+    linkFromFileButton.addEventListener('click', function(event) {
+      event.preventDefault();
+      void nativeLinkMarkdownFiles();
+    });
+  }
+
+  if (linkFromFolderButton) {
+    linkFromFolderButton.addEventListener('click', function(event) {
+      event.preventDefault();
+      void nativeLinkMarkdownFolder();
+    });
+  }
+
   if (importFromGithubButton) {
     importFromGithubButton.addEventListener("click", function (e) {
       e.preventDefault();
@@ -24302,7 +25242,7 @@ ${selector} .arrowheadPath {
     if (!hasActiveOpenDocument()) return;
     if (isReleaseNotesActive()) return;
     if (blockShareSnapshotSourceAccess()) return;
-    if (typeof Neutralino !== 'undefined') {
+    if (hasDesktopFileAccess()) {
       nativeSaveMarkdown();
       return;
     }
@@ -29091,7 +30031,7 @@ ${selector} .arrowheadPath {
   document.addEventListener("keydown", function (e) {
     if (e.defaultPrevented) return;
     const isCmdOrCtrl = e.ctrlKey || e.metaKey;
-    const isDesktop = typeof Neutralino !== 'undefined';
+    const isDesktop = hasDesktopFileAccess();
     const key = e.key.toLowerCase();
 
     if (e.key === 'F3') {
@@ -29197,9 +30137,10 @@ ${selector} .arrowheadPath {
       }
     }
 
-    if (isCmdOrCtrl && !e.shiftKey && key === 's') {
+    if (isCmdOrCtrl && !e.shiftKey && !e.altKey && !e.isComposing && (key === 's' || e.code === 'KeyS')) {
       e.preventDefault();
-      exportMd.click();
+      if (hasDesktopFileAccess()) nativeSaveMarkdown({ useLinkedSource: true });
+      else exportMd.click();
     }
     if (isCmdOrCtrl && key === 'c') {
       const activeEl = document.activeElement;
diff --git a/styles.css b/styles.css
index 478aac7d..15fecfa0 100644
--- a/styles.css
+++ b/styles.css
@@ -592,7 +592,6 @@ body {
   background: color-mix(in srgb, var(--accent-color) 7%, transparent);
 }
 
-.document-tree-row[data-tree-type="document"].is-selected > .document-tree-main > i:first-child,
 .document-tree-row[data-tree-type="document"].is-active > .document-tree-main > i:first-child {
   color: var(--accent-color);
 }
@@ -727,7 +726,7 @@ body {
   text-align: center;
 }
 
-.document-tree-main > .lucide-folder-open {
+.document-tree-row.is-current-location > .document-tree-main > i:first-child {
   color: var(--accent-color);
 }
 
@@ -752,6 +751,16 @@ body {
   font-size: var(--ui-font-xs);
 }
 
+.document-tree-row.is-source-missing .document-tree-meta,
+.document-tree-row.is-source-missing .document-tree-main > i {
+  color: var(--color-danger-fg);
+}
+
+.document-tree-row.is-source-conflict .document-tree-meta {
+  color: #bf8700;
+  font-weight: 600;
+}
+
 .document-tree-main > .document-favorite-indicator {
   flex: 0 0 auto;
   color: var(--favorite-color);
@@ -1326,7 +1335,8 @@ body.document-sidebar-collapsed .document-sidebar {
   color: var(--accent-color);
 }
 
-.app-toast-icon-shell > .bi {
+.app-toast-icon-shell > .bi,
+.app-toast-icon-shell > .lucide {
   font-size: var(--ui-icon-size-lg);
   line-height: 1;
 }
diff --git a/tests/e2e/desktop-linked-file.spec.js b/tests/e2e/desktop-linked-file.spec.js
new file mode 100644
index 00000000..bdf18a18
--- /dev/null
+++ b/tests/e2e/desktop-linked-file.spec.js
@@ -0,0 +1,307 @@
+const { test, expect } = require('@playwright/test');
+const { openApp, editorValue } = require('../helpers/app');
+
+// These scenarios simulate desktop linking while retaining browser test storage.
+test.beforeEach(async ({ page }) => {
+  await page.addInitScript(() => {
+    window.NL_PORT = 1;
+    window.NL_OS = 'Windows';
+    window.Neutralino = { filesystem: { readFile: async () => '', writeFile: async () => true }, os: {} };
+  });
+});
+
+test('linked sidebar rows show source paths only on hover across All, Recent and Favs', async ({ page }) => {
+  await page.addInitScript(() => {
+    const records = ['healthy', 'missing', 'conflict'].map((title, index) => ({
+      id: 'linked_' + title, title, content: '# ' + title,
+      sourcePath: 'C:/Original/' + title + '.md',
+      sourceMissing: title === 'missing', sourceConflict: title === 'conflict',
+      favorite: true, isOpen: true, workspaceId: 'workspace_default',
+      createdAt: index + 1, lastOpenedAt: index + 1, lastEditedAt: index + 1
+    }));
+    localStorage.setItem('markdownViewerTabs', JSON.stringify(records));
+  });
+  await openApp(page);
+  await page.evaluate(async () => {
+    await window.NL_IMPORT_EXTERNAL_FILE('# healthy', 'healthy', 'C:/Original/healthy.md');
+  });
+  const tree = page.locator('#document-tree');
+  if (!(await tree.isVisible())) await page.locator('#document-sidebar-open').click();
+  for (const filter of ['all', 'recent', 'favorites']) {
+    await page.locator(`[data-document-filter="${filter}"]`).click();
+    const row = title => tree.locator(`[data-document-id="linked_${title}"]`);
+    await expect(row('healthy')).toBeVisible();
+    await expect(row('healthy').locator('.document-tree-meta')).toHaveCount(0);
+    await expect(row('healthy').locator('.lucide-file-symlink')).toHaveCount(1);
+    await expect(row('healthy')).toHaveAttribute('title', 'C:/Original/healthy.md');
+    await expect(row('healthy').locator('.document-tree-main')).toHaveAttribute('title', 'C:/Original/healthy.md');
+    await expect(row('healthy')).not.toContainText('C:/Original');
+    await expect(row('missing').locator('.document-tree-meta')).toHaveText('Missing source');
+    await expect(row('conflict').locator('.document-tree-meta')).toHaveText('Conflict');
+  }
+  await page.locator('#document-sidebar-search').fill('C:/Original/healthy.md');
+  await expect(tree.locator('[data-tree-type="document"]')).toHaveCount(1);
+});
+
+test('first file-association launch seeds Welcome in the Vault without replacing the linked document', async ({ page }) => {
+  await page.addInitScript(() => {
+    window.NL_INITIAL_FILE_CONTENT = { content: '# Initial original', name: 'initial', sourcePath: 'C:/Docs/initial.md' };
+  });
+  await openApp(page);
+  const welcome = page.locator('#document-tree [data-tree-type="document"]').filter({ hasText: 'Welcome to Markdown' });
+  await expect(welcome).toHaveCount(1);
+  await expect(welcome.locator('.lucide-file-text')).toHaveCount(1);
+  await expect(welcome).not.toHaveClass(/is-linked-document/);
+  await expect(welcome).toHaveAttribute('data-tree-depth', '1');
+  await expect.poll(() => editorValue(page)).toBe('# Initial original');
+  await expect(page.locator('.tab-item.active .tab-title')).toHaveText('initial');
+  await welcome.locator('.document-tree-main').click();
+  await expect.poll(() => editorValue(page)).toContain('# Welcome to Markdown Viewer');
+  await page.waitForTimeout(700);
+  await page.reload();
+  await page.waitForFunction(() => document.documentElement.dataset.appReady === 'true');
+  await expect(welcome).toHaveCount(1);
+  await expect.poll(() => editorValue(page)).toBe('# Initial original');
+  await welcome.dispatchEvent('contextmenu', { clientX: 120, clientY: 120 });
+  await page.locator('.document-menu-context.open').getByRole('menuitem', { name: 'Delete', exact: true }).click();
+  await expect(welcome).toHaveCount(0);
+  await page.waitForTimeout(700);
+  await page.reload();
+  await page.waitForFunction(() => document.documentElement.dataset.appReady === 'true');
+  await expect(welcome).toHaveCount(0);
+  await expect.poll(() => editorValue(page)).toBe('# Initial original');
+});
+
+test('deduplicates Windows source paths and writes the original only on Ctrl+S', async ({ page }) => {
+  await openApp(page);
+  await page.evaluate(async () => {
+    await window.NL_IMPORT_EXTERNAL_FILE('# original', 'notes', 'C:\\Docs\\notes.md');
+    await window.NL_IMPORT_EXTERNAL_FILE('# changed on disk', 'notes', 'c:/docs/notes.md');
+  });
+
+  await expect(page.locator('.tab-item .tab-title').filter({ hasText: 'notes' })).toHaveCount(1);
+  await expect.poll(() => editorValue(page)).toBe('# changed on disk');
+
+  await page.evaluate(() => {
+    window.__linkedDiskContent = '# changed on disk';
+    window.__linkedWrites = [];
+    window.Neutralino = {
+      filesystem: {
+        readFile: async () => window.__linkedDiskContent,
+        writeFile: async (path, content) => {
+          window.__linkedWrites.push({ path, content });
+          window.__linkedDiskContent = content;
+        }
+      },
+      os: { showSaveDialog: async () => null }
+    };
+  });
+
+  const editor = page.locator('#markdown-editor');
+  await editor.fill('# local edit');
+  await editor.dispatchEvent('input');
+  await page.waitForTimeout(700);
+  await expect.poll(() => page.evaluate(() => window.__linkedWrites.length)).toBe(0);
+
+  await editor.press('Control+s');
+  await expect.poll(() => page.evaluate(() => window.__linkedWrites)).toEqual([
+    { path: 'c:/docs/notes.md', content: '# local edit' }
+  ]);
+});
+
+test('links a folder, discovers external additions, and converts a file to a copy', async ({ page }) => {
+  await openApp(page);
+  await page.evaluate(() => {
+    window.__folderEntries = ['one.md'];
+    window.__fileContents = {
+      'C:\\Notes\\one.md': '# one',
+      'C:\\Notes\\two.md': '# two'
+    };
+    window.__watchHandlers = {};
+    window.__linkedWrites = [];
+    window.Neutralino = {
+      filesystem: {
+        readDirectory: async path => path === 'C:\\Notes'
+          ? window.__folderEntries.map(entry => ({ entry, type: 'FILE' })) : [],
+        getJoinedPath: async (...parts) => parts.join('\\'),
+        readFile: async path => window.__fileContents[path],
+        writeFile: async () => true,
+        createWatcher: async () => 1,
+        removeWatcher: async () => 1
+      },
+      events: { on: async (name, handler) => { window.__watchHandlers[name] = handler; } },
+      os: {
+        showFolderDialog: async () => 'C:\\Notes',
+        open: async () => ({ success: true })
+      },
+      storage: { setData: async () => ({ success: true }) }
+    };
+    document.getElementById('sidebar-link-folder').click();
+  });
+
+  await page.locator('#document-sidebar-open').click();
+  await expect(page.locator('#document-tree')).toContainText('Linked Workspace');
+  await page.evaluate(async () => {
+    await window.NL_START_LINKED_MONITORING();
+    window.__folderEntries.push('two.md');
+    window.__watchHandlers.watchFile({ detail: { id: 1 } });
+  });
+  await expect(page.locator('.document-tree-row[data-tree-type="document"]').filter({ hasText: 'two' })).toHaveCount(1);
+
+  const linkedRow = page.locator('.document-tree-row[data-tree-type="document"]').filter({ hasText: 'one' });
+  await linkedRow.dispatchEvent('contextmenu', { clientX: 120, clientY: 120 });
+  const missingMenuIcons = await page.locator('.document-menu-context [role="menuitem"] i').evaluateAll(nodes => nodes
+    .filter(node => getComputedStyle(node).maskImage === 'none' && getComputedStyle(node).webkitMaskImage === 'none')
+    .map(node => node.className));
+  expect(missingMenuIcons).toEqual([]);
+  await page.getByRole('menuitem', { name: 'Convert to Workspace copy' }).click();
+
+  await expect(page.locator('#document-tree')).toContainText('Workspace (Vault)');
+  await expect(linkedRow).not.toHaveClass(/is-linked-document/);
+  await expect(linkedRow.locator('.lucide-file-text')).toHaveCount(1);
+  await expect(page.locator('.document-tree-row[data-tree-type="linked-location"]').filter({ hasText: 'Notes' })).toContainText('1');
+  await expect.poll(() => page.evaluate(() => window.__fileContents['C:\\Notes\\one.md'])).toBe('# one');
+  await expect.poll(() => page.evaluate(() => window.__linkedWrites)).toEqual([]);
+});
+
+test('groups linked files under Workspaces and persists independent nested folder expansion', async ({ page }) => {
+  await openApp(page);
+  await page.evaluate(async () => {
+    const directories = {
+      'C:/Notes': [{ entry: 'first', type: 'DIRECTORY' }, { entry: 'second', type: 'DIRECTORY' }],
+      'C:/Notes/first': [{ entry: 'deep', type: 'DIRECTORY' }, { entry: 'one.md', type: 'FILE' }],
+      'C:/Notes/first/deep': [{ entry: 'nested.md', type: 'FILE' }],
+      'C:/Notes/second': [{ entry: 'two.md', type: 'FILE' }]
+    };
+    window.Neutralino = {
+      filesystem: {
+        getStats: async path => ({ isDirectory: Boolean(directories[path.replace(/\\/g, '/')]), isFile: !directories[path.replace(/\\/g, '/')] }),
+        readDirectory: async path => directories[path.replace(/\\/g, '/')] || [],
+        getJoinedPath: async (...parts) => parts.join('/'),
+        readFile: async path => '# ' + path,
+        writeFile: async () => true,
+        createWatcher: async () => 1,
+        removeWatcher: async () => 1
+      },
+      events: { on: async () => ({ success: true }) },
+      storage: { setData: async () => ({ success: true }) },
+      os: {}
+    };
+    Neutralino.os = { showFolderDialog: async () => 'C:/Notes' };
+    document.getElementById('sidebar-link-folder').click();
+    await window.NL_IMPORT_EXTERNAL_FILE('# loose', 'loose', 'C:/loose.md');
+  });
+  const tree = page.locator('#document-tree');
+  if (!(await tree.isVisible())) await page.locator('#document-sidebar-open').click();
+  const roots = tree.locator('.document-tree-row[data-tree-depth="0"]');
+  await expect(roots.locator('.document-tree-label')).toHaveText(['Workspace (Vault)', 'Linked Workspace', 'Secret Workspace']);
+  await expect(tree).not.toContainText('Linked Locations');
+  await expect(tree.locator('[data-tree-type="linked-workspace"] > .document-tree-main > i')).toHaveClass('lucide lucide-link-2');
+  await expect(tree.locator('[data-tree-type="linked-location"] > .document-tree-main > i')).toHaveClass('lucide lucide-folder-symlink');
+  const symlinkMasks = await tree.locator('[data-tree-type="linked-virtual-folder"] > .document-tree-main > i').evaluateAll(icons => icons.map(icon => ({ className: icon.className, mask: getComputedStyle(icon).maskImage })));
+  expect(symlinkMasks.length).toBeGreaterThan(0);
+  expect(symlinkMasks.every(icon => icon.className === 'lucide lucide-folder-symlink' && icon.mask !== 'none')).toBe(true);
+  const folder = name => tree.locator('[data-tree-type="linked-virtual-folder"]').filter({ has: page.locator('.document-tree-label', { hasText: new RegExp('^' + name + '$') }) });
+  const documentRow = name => tree.locator('[data-tree-type="document"]').filter({ has: page.locator('.document-tree-label', { hasText: new RegExp('^' + name + '$') }) });
+  await folder('deep').locator('.document-tree-toggle').click();
+  await expect(folder('deep')).toHaveAttribute('aria-expanded', 'false');
+  await expect(documentRow('nested')).toBeHidden();
+  await expect(documentRow('one')).toBeVisible();
+  await folder('first').locator('.document-tree-toggle').click();
+  await expect(documentRow('one')).toBeHidden();
+  await expect(documentRow('two')).toBeVisible();
+  await folder('first').locator('.document-tree-main').click();
+  await expect(documentRow('one')).toBeVisible();
+  await expect(documentRow('nested')).toBeHidden();
+
+  await documentRow('one').locator('.document-tree-main').click();
+  const colors = await tree.evaluate(element => {
+    const iconColor = row => getComputedStyle(row.querySelector('.document-tree-main > i')).color;
+    const rows = Array.from(element.querySelectorAll('[data-tree-type="document"]'));
+    return {
+      active: iconColor(rows.find(row => row.classList.contains('is-active'))),
+      inactive: rows.filter(row => !row.classList.contains('is-active')).map(iconColor),
+      folders: Array.from(element.querySelectorAll('[data-tree-type="linked-virtual-folder"]')).map(iconColor),
+      root: iconColor(element.querySelector('[data-tree-type="linked-location"]')),
+      gray: getComputedStyle(element.querySelector('.document-tree-meta')).color
+    };
+  });
+  expect(colors.active).not.toBe(colors.gray);
+  expect(colors.root).toBe(colors.active);
+  expect(colors.inactive.every(color => color === colors.gray)).toBe(true);
+  expect(colors.folders.every(color => color === colors.gray)).toBe(true);
+
+  const linkedRoot = tree.locator('[data-tree-type="linked-workspace"]');
+  await linkedRoot.locator('.document-tree-toggle').click();
+  await expect(documentRow('loose')).toBeHidden();
+  await page.waitForTimeout(700);
+  await page.reload();
+  await page.waitForFunction(() => document.documentElement.dataset.appReady === 'true');
+  await page.evaluate(async () => {
+    await window.NL_IMPORT_EXTERNAL_FILE('# loose', 'loose', 'C:/loose.md');
+  });
+  await expect(linkedRoot).toHaveAttribute('aria-expanded', 'false');
+  await linkedRoot.locator('.document-tree-main').click();
+  await expect(folder('deep')).toHaveAttribute('aria-expanded', 'false');
+  await expect(documentRow('nested')).toBeHidden();
+  await folder('deep').focus();
+  await folder('deep').press('ArrowRight');
+  await expect(documentRow('nested')).toBeVisible();
+  await page.locator('#document-sidebar-collapse-all').click();
+  await expect(linkedRoot).toHaveAttribute('aria-expanded', 'false');
+  await expect(folder('deep')).toHaveAttribute('aria-expanded', 'false');
+  await page.locator('#document-sidebar-collapse-all').click();
+  await expect(linkedRoot).toHaveAttribute('aria-expanded', 'true');
+  await expect(documentRow('nested')).toBeVisible();
+});
+
+test('removing an individual link leaves the source on disk', async ({ page }) => {
+  await openApp(page);
+  await page.evaluate(() => {
+    window.__original = '# original';
+    window.__linkedWrites = [];
+    window.Neutralino = {
+      filesystem: {
+        readFile: async () => window.__original,
+        writeFile: async () => true,
+        createWatcher: async () => 1,
+        removeWatcher: async () => 1
+      },
+      os: {
+        showOpenDialog: async () => ['C:\\Notes\\original.md'],
+        open: async () => ({ success: true })
+      },
+      storage: { setData: async () => ({ success: true }) },
+      events: { on: async () => ({ success: true }) }
+    };
+    document.getElementById('sidebar-link-files').click();
+  });
+  await page.locator('#document-sidebar-open').click();
+  const linkedRow = page.locator('.document-tree-row[data-tree-type="document"]').filter({ hasText: 'original' });
+  await expect(linkedRow).toHaveClass(/is-linked-document/);
+  await page.evaluate(() => {
+    window.confirm = () => { throw new Error('browser confirm must not be used'); };
+  });
+  await linkedRow.dispatchEvent('contextmenu', { clientX: 120, clientY: 120 });
+  await page.getByRole('menuitem', { name: 'Remove linked file' }).click();
+
+  await expect(linkedRow).toHaveCount(0);
+  await expect.poll(() => page.evaluate(() => window.__original)).toBe('# original');
+  await expect.poll(() => page.evaluate(() => window.__linkedWrites)).toEqual([]);
+  await expect(page.locator('.app-toast').filter({ hasText: 'original file remains on disk' })).toBeVisible();
+});
+
+test('desktop link commands have separate available icons', async ({ page }) => {
+  await openApp(page);
+  await page.locator('#document-sidebar-open').click();
+  await expect(page.locator('#document-tree')).toContainText('Workspace');
+  await expect(page.locator('#document-tree')).toContainText('Workspace (Vault)');
+  await expect(page.locator('#sidebar-new-folder i')).toHaveClass(/lucide-folder-plus/);
+  await expect(page.locator('#sidebar-link-folder i')).toHaveClass(/lucide-folder-symlink/);
+  await expect(page.locator('#sidebar-link-files i')).toHaveClass(/lucide-file-symlink/);
+  const icons = await page.locator('#sidebar-new-folder i, #sidebar-link-folder i, #sidebar-link-files i').evaluateAll(nodes => nodes.map(node => ({
+    mask: getComputedStyle(node).maskImage,
+    webkitMask: getComputedStyle(node).webkitMaskImage
+  })));
+  expect(icons.every(icon => icon.mask !== 'none' || icon.webkitMask !== 'none')).toBeTruthy();
+});
diff --git a/tests/e2e/desktop-linked-recovery-storage.spec.js b/tests/e2e/desktop-linked-recovery-storage.spec.js
new file mode 100644
index 00000000..cfae24ad
--- /dev/null
+++ b/tests/e2e/desktop-linked-recovery-storage.spec.js
@@ -0,0 +1,190 @@
+const { test, expect } = require('@playwright/test');
+const { openApp } = require('../helpers/app');
+const { installDesktopFilesystem } = require('../helpers/desktop-filesystem');
+
+for (const action of ['rescan', 're-add']) {
+  test(`${action} restores excluded folder links without relinking a converted Vault copy`, async ({ page }) => {
+    await page.addInitScript('(' + installDesktopFilesystem.toString() + ')(window);');
+    await openApp(page);
+    await page.evaluate(async () => {
+      await Neutralino.filesystem.createDirectory('C:/Original');
+      window.__desktopFiles.set('C:/Original/notes.md', '# original');
+      window.__linkedHandlers = {};
+      Neutralino.events.on = async (name, handler) => { window.__linkedHandlers[name] = handler; };
+      const readDirectory = Neutralino.filesystem.readDirectory;
+      window.__folderReads = 0;
+      Neutralino.filesystem.readDirectory = async path => {
+        if (path === 'C:/Original') window.__folderReads++;
+        return readDirectory(path);
+      };
+      Neutralino.os.showFolderDialog = async () => 'C:/Original';
+      document.getElementById('sidebar-link-folder').click();
+      await window.NL_START_LINKED_MONITORING();
+    });
+    const rows = page.locator('#document-tree [data-tree-type="document"]').filter({ hasText: 'notes' });
+    const location = page.locator('#document-tree [data-tree-type="linked-location"]');
+    const copyId = await rows.getAttribute('data-document-id');
+    await rows.dispatchEvent('contextmenu', { clientX: 120, clientY: 120 });
+    await page.getByRole('menuitem', { name: 'Convert to Workspace copy' }).click();
+    await expect(rows).not.toHaveClass(/is-linked-document/);
+    const reads = await page.evaluate(() => window.__folderReads);
+    await page.evaluate(() => window.__linkedHandlers.windowFocus());
+    await expect.poll(() => page.evaluate(() => window.__folderReads)).toBeGreaterThan(reads);
+    await page.waitForTimeout(500);
+    await expect(rows).toHaveCount(1);
+
+    const restore = async () => {
+      if (action === 'rescan') {
+        await location.dispatchEvent('contextmenu', { clientX: 120, clientY: 120 });
+        await page.getByRole('menuitem', { name: 'Rescan folder' }).click();
+      } else {
+        await page.locator('#sidebar-link-folder').click();
+      }
+      await expect(rows).toHaveCount(2);
+      await expect(location).toHaveCount(1);
+      await expect(page.locator(`#document-tree [data-document-id="${copyId}"]`)).not.toHaveClass(/is-linked-document/);
+    };
+    await restore();
+    await restore();
+    const linked = page.locator('#document-tree [data-tree-type="document"].is-linked-document').filter({ hasText: 'notes' });
+    await expect(linked).toHaveCount(1);
+    await linked.dispatchEvent('contextmenu', { clientX: 120, clientY: 120 });
+    await page.getByRole('menuitem', { name: 'Remove linked file' }).click();
+    await expect(rows).toHaveCount(1);
+    await restore();
+    await expect(linked).toHaveCount(1);
+    await expect.poll(() => page.evaluate(() => {
+      const index = JSON.parse(window.__desktopFiles.get('C:/Documents/Markdown Viewer Vault/.markdown-viewer/index.json'));
+      return index.documents.filter(item => item.title === 'notes').length;
+    })).toBe(2);
+    const records = await page.evaluate(async id => {
+      const restarted = new window.MarkdownWorkspaceStorage();
+      await restarted.init();
+      const metadata = await restarted.listDocumentMetadata();
+      const copy = metadata.find(item => item.id === id);
+      return { copyLinked: Boolean(copy.sourcePath), copyPath: copy._vaultRelativePath,
+        links: metadata.filter(item => item.sourcePath === 'C:/Original/notes.md').length,
+        original: window.__desktopFiles.get('C:/Original/notes.md') };
+    }, copyId);
+    expect(records.copyLinked).toBe(false);
+    expect(records.copyPath).toMatch(/^Workspace\//);
+    expect(records.links).toBe(1);
+    expect(records.original).toBe('# original');
+  });
+}
+
+test('linked context menus use the normal danger style and omit Copy source path', async ({ page }) => {
+  await page.addInitScript('(' + installDesktopFilesystem.toString() + ')(window);');
+  await openApp(page);
+  await page.evaluate(async () => {
+    await Neutralino.filesystem.createDirectory('C:/Original');
+    window.__desktopFiles.set('C:/Original/notes.md', '# original');
+    Neutralino.os.showFolderDialog = async () => 'C:/Original';
+    document.getElementById('sidebar-link-folder').click();
+    await window.NL_IMPORT_EXTERNAL_FILE('# loose', 'loose', 'C:/loose.md');
+  });
+  const menu = page.locator('.document-menu-context.open');
+  const tree = page.locator('#document-tree');
+  await tree.locator('[data-tree-type="document"]').filter({ hasText: 'Welcome to Markdown' })
+    .dispatchEvent('contextmenu', { clientX: 120, clientY: 120 });
+  const deleteColor = await menu.getByRole('menuitem', { name: 'Delete', exact: true }).evaluate(item => getComputedStyle(item).color);
+  await page.keyboard.press('Escape');
+  await tree.locator('[data-tree-type="document"]').filter({ hasText: 'loose' })
+    .dispatchEvent('contextmenu', { clientX: 120, clientY: 120 });
+  await expect(menu.getByRole('menuitem')).toHaveText(['Open', 'Save', 'Save As…', 'Reload from disk', 'Open containing folder', 'Convert to Workspace copy', 'Remove linked file']);
+  const removeFile = menu.getByRole('menuitem', { name: 'Remove linked file' });
+  await expect(removeFile).toHaveClass(/tab-menu-item-danger/);
+  expect(await removeFile.evaluate(item => getComputedStyle(item).color)).toBe(deleteColor);
+  await page.keyboard.press('Escape');
+  await tree.locator('[data-tree-type="linked-location"]').dispatchEvent('contextmenu', { clientX: 120, clientY: 120 });
+  const removeFolder = menu.getByRole('menuitem', { name: 'Remove linked folder' });
+  await expect(removeFolder).toHaveClass(/tab-menu-item-danger/);
+  expect(await removeFolder.evaluate(item => getComputedStyle(item).color)).toBe(deleteColor);
+});
+
+test('desktop linked autosave uses recovery storage and UI conversion persists a normal Vault copy', async ({ page }) => {
+  await page.addInitScript('(' + installDesktopFilesystem.toString() + ')(window);');
+  await openApp(page);
+  await page.evaluate(async () => {
+    window.__desktopFiles.set('C:/Original/notes.md', '# original');
+    await window.NL_IMPORT_EXTERNAL_FILE('# original', 'notes', 'C:/Original/notes.md');
+  });
+  const editor = page.locator('#markdown-editor');
+  await editor.fill('# local unsaved draft');
+  await editor.dispatchEvent('input');
+  const readIndex = () => page.evaluate(() => JSON.parse(window.__desktopFiles.get('C:/Documents/Markdown Viewer Vault/.markdown-viewer/index.json')));
+  await expect.poll(async () => (await readIndex()).documents.find(item => item.title === 'notes')?.vaultRelativePath).toMatch(/^Linked Workspace\//);
+  await expect.poll(() => page.evaluate(() => {
+    const index = JSON.parse(window.__desktopFiles.get('C:/Documents/Markdown Viewer Vault/.markdown-viewer/index.json'));
+    return window.__desktopFiles.get('C:/Documents/Markdown Viewer Vault/' + index.documents.find(item => item.title === 'notes').vaultRelativePath);
+  })).toBe('# local unsaved draft');
+  const before = (await readIndex()).documents;
+  expect(before.find(item => item.title === 'Welcome to Markdown').vaultRelativePath).toMatch(/^Workspace\//);
+  const oldPath = before.find(item => item.title === 'notes').vaultRelativePath;
+  const row = page.locator('#document-tree [data-tree-type="document"]').filter({ hasText: 'notes' });
+  await row.dispatchEvent('contextmenu', { clientX: 120, clientY: 120 });
+  await page.getByRole('menuitem', { name: 'Convert to Workspace copy' }).click();
+  const toast = page.locator('.app-toast').filter({ hasText: 'Converted to Workspace copy' });
+  await expect(toast.locator('.lucide-check')).toBeVisible();
+  expect(await toast.locator('.lucide-check').evaluate(icon => getComputedStyle(icon).maskImage)).not.toBe('none');
+  await expect.poll(async () => (await readIndex()).documents.find(item => item.title === 'notes')?.vaultRelativePath).toMatch(/^Workspace\//);
+  const result = await page.evaluate(async oldRelativePath => {
+    const restarted = new window.MarkdownWorkspaceStorage();
+    await restarted.init();
+    const record = (await restarted.listDocumentMetadata()).find(item => item.title === 'notes');
+    return {
+      linked: Boolean(record.sourcePath),
+      content: await restarted.loadDocumentContent(record.id),
+      original: window.__desktopFiles.get('C:/Original/notes.md'),
+      oldRecoveryExists: window.__desktopFiles.has('C:/Documents/Markdown Viewer Vault/' + oldRelativePath)
+    };
+  }, oldPath);
+  expect(result).toEqual({ linked: false, content: '# local unsaved draft', original: '# original', oldRecoveryExists: false });
+});
+
+for (const edited of [false, true]) {
+  test(`reopening the original keeps an ${edited ? 'edited' : 'identical'} converted Vault copy independent`, async ({ page }) => {
+    await page.addInitScript('(' + installDesktopFilesystem.toString() + ')(window);');
+    await openApp(page);
+    await page.evaluate(async () => {
+      window.__desktopFiles.set('C:/Original/notes.md', '# original');
+      await window.NL_IMPORT_EXTERNAL_FILE('# original', 'notes', 'C:/Original/notes.md');
+    });
+    const rows = page.locator('#document-tree [data-tree-type="document"]').filter({ hasText: 'notes' });
+    const copyId = await rows.getAttribute('data-document-id');
+    await rows.dispatchEvent('contextmenu', { clientX: 120, clientY: 120 });
+    await page.getByRole('menuitem', { name: 'Convert to Workspace copy' }).click();
+    await expect(rows).not.toHaveClass(/is-linked-document/);
+    if (edited) {
+      await page.locator('#markdown-editor').fill('# independent copy edit');
+      await page.locator('#markdown-editor').dispatchEvent('input');
+    }
+    await page.evaluate(async () => {
+      await window.NL_IMPORT_EXTERNAL_FILE('# original', 'notes', 'C:/Original/notes.md');
+      await window.NL_IMPORT_EXTERNAL_FILE('# original', 'notes', 'c:\\original\\notes.md');
+    });
+    await expect(rows).toHaveCount(2);
+    await expect(rows.filter({ has: page.locator('.lucide-file-symlink') })).toHaveCount(1);
+    await expect(page.locator(`#document-tree [data-document-id="${copyId}"]`)).not.toHaveClass(/is-linked-document/);
+    await expect.poll(() => page.evaluate(() => {
+      const index = JSON.parse(window.__desktopFiles.get('C:/Documents/Markdown Viewer Vault/.markdown-viewer/index.json'));
+      return index.documents.filter(item => item.title === 'notes').length;
+    })).toBe(2);
+    const result = await page.evaluate(async id => {
+      const restarted = new window.MarkdownWorkspaceStorage();
+      await restarted.init();
+      const records = (await restarted.listDocumentMetadata()).filter(item => item.title === 'notes');
+      const copy = records.find(item => item.id === id);
+      const linked = records.find(item => item.sourcePath);
+      return { count: records.length, copyLinked: Boolean(copy.sourcePath), copyPath: copy._vaultRelativePath,
+        linkedPath: linked._vaultRelativePath, copyContent: await restarted.loadDocumentContent(copy.id),
+        original: window.__desktopFiles.get('C:/Original/notes.md') };
+    }, copyId);
+    expect(result.count).toBe(2);
+    expect(result.copyLinked).toBe(false);
+    expect(result.copyPath).toMatch(/^Workspace\//);
+    expect(result.linkedPath).toMatch(/^Linked Workspace\//);
+    expect(result.copyContent).toBe(edited ? '# independent copy edit' : '# original');
+    expect(result.original).toBe('# original');
+  });
+}
diff --git a/tests/e2e/desktop-save.spec.js b/tests/e2e/desktop-save.spec.js
new file mode 100644
index 00000000..a4868cae
--- /dev/null
+++ b/tests/e2e/desktop-save.spec.js
@@ -0,0 +1,149 @@
+const { test, expect } = require('@playwright/test');
+const { openApp } = require('../helpers/app');
+const { installDesktopFilesystem } = require('../helpers/desktop-filesystem');
+
+async function setup(page) {
+  await page.addInitScript('(' + installDesktopFilesystem.toString() + ')(window);');
+  await openApp(page);
+  await page.evaluate(() => {
+    window.__saveChoices = [];
+    window.__saveDialogs = [];
+    Neutralino.os.showSaveDialog = async (title, options) => {
+      window.__saveDialogs.push({ title, options });
+      return window.__saveChoices.shift() || '';
+    };
+  });
+}
+async function importNotes(page) {
+  await page.evaluate(async () => {
+    window.__desktopFiles.set('C:/Original/notes.md', '# original');
+    await window.NL_IMPORT_EXTERNAL_FILE('# original', 'notes', 'C:/Original/notes.md');
+    await window.MarkdownViewerFlushWorkspace();
+  });
+}
+async function menu(page, name, action) {
+  await page.locator('#document-tree [data-tree-type="document"]').filter({ hasText: name }).dispatchEvent('contextmenu', {clientX:120,clientY:120});
+  await page.locator('.document-menu-context.open').getByRole('menuitem', {name:action,exact:true}).click();
+}
+async function records(page) {
+  return page.evaluate(async () => {
+    const storage = new window.MarkdownWorkspaceStorage();
+    await storage.init();
+    return storage.listDocumentMetadata();
+  });
+}
+
+test('Greek Ctrl+S creates and focuses a linked copy while preserving the Vault document and proposed filename', async ({ page }) => {
+  await setup(page);
+  const originalId = await page.locator('#tab-list .tab-item.active').getAttribute('data-tab-id');
+  await page.locator('#markdown-editor').fill('# Vault draft');
+  await page.evaluate(() => window.__saveChoices.push('C:/Saved/example'));
+  await page.locator('#markdown-editor').dispatchEvent('keydown', { key:'σ',code:'KeyS',ctrlKey:true });
+  await expect(page.locator('#tab-list .tab-item.active .tab-title')).toHaveText('example');
+  await expect(page.locator('#markdown-editor')).toBeFocused();
+  expect(await page.evaluate(() => window.__saveDialogs[0].options.defaultPath)).toBe('Welcome to Markdown.md');
+  const metadata = await records(page);
+  expect(metadata.find(item => item.id === originalId).sourcePath).toBeFalsy();
+  expect(metadata.find(item => item.sourcePath === 'C:/Saved/example.md')).toBeTruthy();
+  expect(await page.evaluate(() => window.__desktopFiles.get('C:/Saved/example.md'))).toBe('# Vault draft');
+  await page.locator('#markdown-editor').fill('# updated original');
+  await page.locator('#markdown-editor').dispatchEvent('keydown', {key:'σ',code:'KeyS',ctrlKey:true});
+  await expect.poll(() => page.evaluate(() => window.__desktopFiles.get('C:/Saved/example.md'))).toBe('# updated original');
+  expect(await page.evaluate(() => window.__saveDialogs.length)).toBe(1);
+});
+
+test('linked Save As creates a second linked document, keeping the old draft and disk original', async ({ page }) => {
+  await setup(page);
+  await importNotes(page);
+  await page.locator('#markdown-editor').fill('# edited draft');
+  await page.evaluate(() => window.__saveChoices.push('C:/Saved/copy.MD'));
+  await menu(page, 'notes', 'Save As…');
+  await expect(page.locator('#tab-list .tab-item.active .tab-title')).toHaveText('copy');
+  await expect(page.locator('#markdown-editor')).toBeFocused();
+  expect(await page.evaluate(() => window.__saveDialogs[0].options.defaultPath)).toBe('notes.md');
+  const metadata = await records(page);
+  expect(metadata.filter(item => item.sourcePath)).toHaveLength(2);
+  expect(metadata.some(item => item.sourcePath === 'C:/Saved/copy.MD')).toBe(true);
+  expect(await page.evaluate(() => window.__desktopFiles.get('C:/Original/notes.md'))).toBe('# original');
+  await menu(page, 'notes', 'Save');
+  await expect.poll(() => page.evaluate(() => window.__desktopFiles.get('C:/Original/notes.md'))).toBe('# edited draft');
+  expect(await page.evaluate(() => window.__saveDialogs.length)).toBe(1);
+  await expect(page.locator('#tab-list .tab-item.active .tab-title')).toHaveText('copy');
+});
+
+test('Vault context Save As targets an inactive document and preserves it', async ({ page }) => {
+  await setup(page);
+  await page.locator('#markdown-editor').fill('# Vault content');
+  await importNotes(page);
+  await page.evaluate(() => window.__saveChoices.push('C:/Saved/welcome.markdown'));
+  await menu(page, 'Welcome to Markdown', 'Save As…');
+  await expect(page.locator('#tab-list .tab-item.active .tab-title')).toHaveText('welcome');
+  expect(await page.evaluate(() => window.__desktopFiles.get('C:/Saved/welcome.markdown'))).toBe('# Vault content');
+  expect((await records(page)).some(item => item.title === 'Welcome to Markdown' && !item.sourcePath)).toBe(true);
+});
+
+test('appended .md overwrite prompts protect the real destination and cancellation changes nothing', async ({ page }) => {
+  await setup(page);
+  await page.locator('#markdown-editor').fill('# new');
+  await page.evaluate(() => {
+    window.__desktopFiles.set('C:/Saved/existing.md', '# old');
+    window.__saveChoices.push('C:/Saved/existing');
+  });
+  await menu(page, 'Welcome to Markdown', 'Save As…');
+  const toast = page.locator('.app-toast').filter({hasText:'Replace Markdown file?'});
+  await expect(toast).toBeVisible();
+  await toast.getByRole('button', {name:'Cancel',exact:true}).click();
+  expect(await page.evaluate(() => window.__desktopFiles.get('C:/Saved/existing.md'))).toBe('# old');
+  expect((await records(page)).filter(item => item.sourcePath)).toHaveLength(0);
+  await page.evaluate(() => window.__saveChoices.push('C:/Saved/existing'));
+  await menu(page, 'Welcome to Markdown', 'Save As…');
+  await toast.getByRole('button', {name:'Replace',exact:true}).click();
+  await expect(page.locator('#tab-list .tab-item.active .tab-title')).toHaveText('existing');
+  expect(await page.evaluate(() => window.__desktopFiles.get('C:/Saved/existing.md'))).toBe('# new');
+});
+
+test('cancelled or failed Save As does not create a link or change focus', async ({ page }) => {
+  await setup(page);
+  await importNotes(page);
+  const id = await page.locator('#tab-list .tab-item.active').getAttribute('data-tab-id');
+  await menu(page, 'notes', 'Save As…');
+  await expect.poll(() => page.evaluate(() => window.__saveDialogs.length)).toBe(1);
+  await page.evaluate(() => {
+    window.__saveChoices.push('C:/Saved/failure.md');
+    const write = Neutralino.filesystem.writeFile;
+    Neutralino.filesystem.writeFile = async (path, content) => {
+      if (path === 'C:/Saved/failure.md') throw new Error('Permission denied');
+      return write(path, content);
+    };
+  });
+  await menu(page, 'notes', 'Save As…');
+  await expect(page.locator('.app-toast').filter({hasText:'Save failed'})).toBeVisible();
+  await expect(page.locator('#tab-list .tab-item.active')).toHaveAttribute('data-tab-id',id);
+  expect((await records(page)).filter(item => item.sourcePath)).toHaveLength(1);
+});
+
+test('Ctrl+Shift+S retains scroll-sync behavior and does not open Save As', async ({ page }) => {
+  await setup(page);
+  await page.locator('#markdown-editor').press('Control+Shift+s');
+  expect(await page.evaluate(() => window.__saveDialogs.length)).toBe(0);
+});
+
+test('Save As refuses the current linked source path rather than overwriting it', async ({ page }) => {
+  await setup(page);
+  await importNotes(page);
+  await page.locator('#markdown-editor').fill('# draft');
+  await page.evaluate(() => window.__saveChoices.push('C:/Original/notes.md'));
+  await menu(page, 'notes', 'Save As…');
+  await expect(page.locator('.app-toast').filter({hasText:'Choose a new file'})).toBeVisible();
+  expect(await page.evaluate(() => window.__desktopFiles.get('C:/Original/notes.md'))).toBe('# original');
+  expect((await records(page)).filter(item => item.sourcePath)).toHaveLength(1);
+});
+
+test('Download Markdown uses the same filename and extension rules without creating a link', async ({ page }) => {
+  await setup(page);
+  await page.evaluate(() => window.__saveChoices.push('C:/Saved/download'));
+  await menu(page, 'Welcome to Markdown', 'Download Markdown');
+  await expect.poll(() => page.evaluate(() => window.__desktopFiles.has('C:/Saved/download.md'))).toBe(true);
+  expect(await page.evaluate(() => window.__saveDialogs[0].options.defaultPath)).toBe('Welcome to Markdown.md');
+  expect((await records(page)).filter(item => item.sourcePath)).toHaveLength(0);
+});
diff --git a/tests/e2e/desktop-toast-icons.spec.js b/tests/e2e/desktop-toast-icons.spec.js
new file mode 100644
index 00000000..010ec22f
--- /dev/null
+++ b/tests/e2e/desktop-toast-icons.spec.js
@@ -0,0 +1,58 @@
+const { test, expect } = require('@playwright/test');
+const { openApp } = require('../helpers/app');
+const { installDesktopFilesystem } = require('../helpers/desktop-filesystem');
+
+for (const theme of ['light', 'dark']) {
+  test(`linked workflow toast icons are consistent and render in ${theme} theme`, async ({ page }) => {
+    await page.addInitScript('(' + installDesktopFilesystem.toString() + ')(window); window.NL_TOKEN = "test-token";');
+    await openApp(page);
+    await page.evaluate(theme => {
+      document.documentElement.setAttribute('data-theme', theme);
+      window.__desktopFiles.set('C:/Original/notes.md', '# original');
+      Neutralino.os.showFolderDialog = async () => 'C:/Original';
+      Neutralino.os.showOpenDialog = async () => ['C:/Original/notes.md'];
+    }, theme);
+    await page.evaluate(() => Neutralino.filesystem.createDirectory('C:/Original'));
+    const assertToast = async (text, tone, iconClass) => {
+      const toast = page.locator('.app-toast').filter({ hasText: text }).last();
+      await expect(toast).toBeVisible();
+      await expect(toast).toHaveAttribute('data-tone', tone);
+      const icon = toast.locator('.app-toast-icon-shell > i');
+      await expect(icon).toHaveClass('lucide ' + iconClass);
+      const rendered = await icon.evaluate(element => {
+        const style = getComputedStyle(element);
+        return { mask: style.maskImage, width: style.width, height: style.height };
+      });
+      expect(rendered.mask).not.toBe('none');
+      expect(rendered.width).toBe(rendered.height);
+      expect(parseFloat(rendered.width)).toBeGreaterThan(0);
+      return toast;
+    };
+    await page.locator('#sidebar-link-folder').click();
+    await assertToast('Linked folder scanned.', 'success', 'lucide-check');
+    const location = page.locator('#document-tree [data-tree-type="linked-location"]');
+    await location.dispatchEvent('contextmenu', { clientX: 120, clientY: 120 });
+    await page.getByRole('menuitem', { name: 'Rescan folder' }).click();
+    await assertToast('Linked folder scanned.', 'success', 'lucide-check');
+    await page.locator('#sidebar-link-files').click();
+    await assertToast('Linked files', 'success', 'lucide-check');
+    await page.evaluate(async () => {
+      await window.NL_IMPORT_EXTERNAL_FILE('# loose', 'loose', 'C:/loose.md');
+    });
+    await assertToast('Linked Markdown file', 'info', 'lucide-info');
+    const loose = page.locator('#document-tree [data-tree-type="document"]').filter({ hasText: 'loose' });
+    await loose.dispatchEvent('contextmenu', { clientX: 120, clientY: 120 });
+    await page.getByRole('menuitem', { name: 'Remove linked file' }).click();
+    await assertToast('Linked file closed', 'success', 'lucide-check');
+    await location.dispatchEvent('contextmenu', { clientX: 120, clientY: 120 });
+    await page.getByRole('menuitem', { name: 'Remove linked folder' }).click();
+    const confirmation = await assertToast('Remove linked folder', 'warning', 'lucide-triangle-alert');
+    await confirmation.getByRole('button', { name: 'Remove link', exact: true }).click();
+    await assertToast('Folder unlinked', 'success', 'lucide-check');
+    await page.evaluate(() => {
+      Neutralino.os.showFolderDialog = async () => { throw new Error('Picker unavailable'); };
+    });
+    await page.locator('#sidebar-link-folder').click();
+    await assertToast('Link failed', 'error', 'lucide-circle-alert');
+  });
+}
diff --git a/tests/e2e/document-sidebar.spec.js b/tests/e2e/document-sidebar.spec.js
index 086ce6d0..da90f0df 100644
--- a/tests/e2e/document-sidebar.spec.js
+++ b/tests/e2e/document-sidebar.spec.js
@@ -95,7 +95,8 @@ test('documents open on a single click and collapse all is available', async ({
   const closedFolderIcon = workspaceRow.locator('.document-tree-main > i.lucide-folder');
   await expect(closedFolderIcon).toHaveCount(1);
   const closedFolderColor = await closedFolderIcon.evaluate(icon => getComputedStyle(icon).color);
-  expect(closedFolderColor).not.toBe(openFolderColor);
+  // The current workspace stays accented; expansion alone does not select a folder.
+  expect(closedFolderColor).toBe(openFolderColor);
   await expect(page.locator('#document-sidebar-collapse-all')).toHaveAttribute('aria-label', 'Expand all folders');
   await expect(page.locator('#document-sidebar-collapse-all i')).toHaveClass(/lucide-unfold-vertical/);
   await page.locator('#document-sidebar-collapse-all').click();
diff --git a/tests/e2e/linked-focus-menu.spec.js b/tests/e2e/linked-focus-menu.spec.js
new file mode 100644
index 00000000..7b79a860
--- /dev/null
+++ b/tests/e2e/linked-focus-menu.spec.js
@@ -0,0 +1,65 @@
+const { test, expect } = require('@playwright/test');
+const { openApp } = require('../helpers/app');
+const { installDesktopFilesystem } = require('../helpers/desktop-filesystem');
+
+test.beforeEach(async ({ page }) => {
+  await page.addInitScript('(' + installDesktopFilesystem.toString() + ')(window);');
+  await page.addInitScript(() => {
+    window.__nativeHandlers = {};
+    window.Neutralino.events.on = async (name, handler) => { window.__nativeHandlers[name] = handler; };
+  });
+  await openApp(page);
+});
+
+for (const change of ['none', 'added', 'content']) {
+  test(`focus rescan preserves the sidebar menu (${change})`, async ({ page }) => {
+    await page.evaluate(async () => {
+      await Neutralino.filesystem.createDirectory('C:/Notes');
+      window.__desktopFiles.set('C:/Notes/one.md', '# original');
+      Neutralino.os.showFolderDialog = async () => 'C:/Notes';
+      document.getElementById('sidebar-link-folder').click();
+      await window.NL_START_LINKED_MONITORING();
+    });
+    const row = page.locator('#document-tree [data-tree-type="document"]').filter({hasText:'one'});
+    await row.locator('.document-tree-main').click();
+    await row.dispatchEvent('contextmenu', {clientX:120,clientY:120});
+    const menu = page.locator('.document-menu-context.open');
+    await expect(menu).toBeVisible();
+    await page.evaluate(change => {
+      window.__originalMenu = document.querySelector('.document-menu-context.open');
+      window.__originalRow = document.querySelector('#document-tree [data-document-id="' + document.querySelector('#tab-list .tab-item.active').dataset.tabId + '"]');
+      if (change === 'added') window.__desktopFiles.set('C:/Notes/two.md', '# new');
+      if (change === 'content') window.__desktopFiles.set('C:/Notes/one.md', '# external edit');
+      window.__nativeHandlers.windowFocus();
+    }, change);
+    // The focus handler debounces its asynchronous scan by 350 ms.
+    await page.waitForTimeout(800);
+    await expect(menu).toBeVisible();
+    expect(await page.evaluate(() => window.__originalMenu.isConnected)).toBe(true);
+    expect(await page.evaluate(() => window.__originalRow.isConnected)).toBe(true);
+    if (change === 'content') await expect(page.locator('#markdown-editor')).toHaveValue('# external edit');
+    if (change === 'added') await expect(page.locator('#document-tree [data-tree-type="document"]').filter({hasText:'two'})).toHaveCount(0);
+    await page.keyboard.press('Escape');
+    await expect(menu).toHaveCount(0);
+    if (change === 'added') await expect(page.locator('#document-tree [data-tree-type="document"]').filter({hasText:'two'})).toBeVisible();
+  });
+}
+
+test('individual missing-source refresh waits until the context menu closes', async ({ page }) => {
+  await page.evaluate(async () => {
+    window.__desktopFiles.set('C:/one.md', '# original');
+    await window.NL_IMPORT_EXTERNAL_FILE('# original', 'one', 'C:/one.md');
+    await window.NL_START_LINKED_MONITORING();
+  });
+  const row = page.locator('#document-tree [data-tree-type="document"]').filter({hasText:'one'});
+  await row.dispatchEvent('contextmenu', {clientX:120,clientY:120});
+  await page.evaluate(() => {
+    window.__desktopFiles.delete('C:/one.md');
+    window.__nativeHandlers.windowFocus();
+  });
+  await page.waitForTimeout(800);
+  await expect(page.locator('.document-menu-context.open')).toBeVisible();
+  await expect(row).not.toHaveClass(/is-source-missing/);
+  await page.keyboard.press('Escape');
+  await expect(row).toHaveClass(/is-source-missing/);
+});
diff --git a/tests/e2e/linked-workspace-guide.spec.js b/tests/e2e/linked-workspace-guide.spec.js
new file mode 100644
index 00000000..aafb1d9d
--- /dev/null
+++ b/tests/e2e/linked-workspace-guide.spec.js
@@ -0,0 +1,62 @@
+const { test, expect } = require('@playwright/test');
+const { openApp } = require('../helpers/app');
+const { installDesktopFilesystem } = require('../helpers/desktop-filesystem');
+
+test('desktop guide is stored separately, editable, and does not take startup focus', async ({ page }) => {
+  await page.addInitScript('(' + installDesktopFilesystem.toString() + ')(window);');
+  await openApp(page);
+  const guide = page.locator('#document-tree [data-tree-type="document"]').filter({hasText:'Welcome to Linked Workspace'});
+  await expect(guide).toHaveCount(1);
+  await expect(guide).not.toHaveClass(/is-linked-document/);
+  await expect(page.locator('#tab-list .tab-item.active .tab-title')).toHaveText('Welcome to Markdown');
+  expect(await page.evaluate(() => Array.from(window.__desktopFiles.keys()).some(path => path.includes('/Linked Workspace/Welcome to Linked Workspace--')))).toBe(true);
+  await guide.locator('.document-tree-main').click();
+  await expect(page.locator('#markdown-editor')).toHaveValue(/# Welcome to Linked Workspace/);
+  await expect(page.locator('#markdown-preview')).toContainText('Welcome to Linked Workspace');
+  await guide.dispatchEvent('contextmenu', {clientX:120,clientY:120});
+  const menu = page.locator('.document-menu-context.open');
+  for (const name of ['Save', 'Reload from disk', 'Open containing folder', 'Remove linked file']) {
+    await expect(menu.getByRole('menuitem',{name,exact:true})).toHaveCount(0);
+  }
+  await expect(menu.getByRole('menuitem',{name:'Delete',exact:true})).toBeVisible();
+  await page.keyboard.press('Escape');
+  await page.locator('.header-view-toolbar [data-view-mode="editor"]').click();
+  await page.locator('#markdown-editor').fill('# Edited internal guide');
+  await expect.poll(() => page.evaluate(() => Array.from(window.__desktopFiles.entries())
+    .find(([path]) => path.includes('/Linked Workspace/Welcome to Linked Workspace--'))?.[1]
+  )).toBe('# Edited internal guide');
+});
+
+test('guide is seeded once in existing desktop workspaces and deletion is respected', async ({ page }) => {
+  // Native capabilities with browser-backed persistence survive page reloads.
+  await page.addInitScript(() => {
+    window.NL_PORT = 1;
+    window.Neutralino = {filesystem:{readFile:async()=>'',writeFile:async()=>true},os:{}};
+    if (!localStorage.getItem('markdownViewerTabs')) {
+      localStorage.setItem('markdownViewerTabs', JSON.stringify([{
+        id:'existing-document', title:'Existing document', content:'# existing',
+        workspaceId:'workspace_default', isOpen:true, createdAt:1, lastOpenedAt:1
+      }]));
+      localStorage.setItem('markdownViewerActiveTab', 'existing-document');
+    }
+  });
+  await openApp(page);
+  const guide = page.locator('#document-tree [data-tree-type="document"]').filter({hasText:'Welcome to Linked Workspace'});
+  await expect(guide).toHaveCount(1);
+  await page.reload();
+  await page.waitForFunction(() => document.documentElement.dataset.appReady === 'true');
+  await expect(guide).toHaveCount(1);
+  await guide.dispatchEvent('contextmenu',{clientX:120,clientY:120});
+  await page.locator('.document-menu-context.open').getByRole('menuitem',{name:'Delete',exact:true}).click();
+  await expect(guide).toHaveCount(0);
+  await page.waitForTimeout(700);
+  await page.reload();
+  await page.waitForFunction(() => document.documentElement.dataset.appReady === 'true');
+  await expect(guide).toHaveCount(0);
+});
+
+test('web does not seed a desktop Linked Workspace guide', async ({ page }) => {
+  await openApp(page);
+  await expect(page.locator('#document-tree [data-tree-type="linked-workspace"]')).toHaveCount(0);
+  await expect(page.locator('#document-tree')).not.toContainText('Welcome to Linked Workspace');
+});
diff --git a/tests/e2e/sidebar-linked-drop.spec.js b/tests/e2e/sidebar-linked-drop.spec.js
new file mode 100644
index 00000000..571545aa
--- /dev/null
+++ b/tests/e2e/sidebar-linked-drop.spec.js
@@ -0,0 +1,69 @@
+const { test, expect } = require('@playwright/test');
+const { openApp } = require('../helpers/app');
+const { installDesktopFilesystem } = require('../helpers/desktop-filesystem');
+
+// Exercise the existing HTML drop entry point without the custom pointer layer.
+async function dropDocument(page, row, target) {
+  const id = await row.getAttribute('data-document-id');
+  const transfer = await page.evaluateHandle(id => {
+    const data = new DataTransfer();
+    data.setData('application/x-markdown-viewer-document', id);
+    return data;
+  }, id);
+  await target.dispatchEvent('drop', { dataTransfer: transfer });
+  await transfer.dispose();
+}
+
+for (const destination of ['root', 'folder']) {
+  test(`HTML sidebar drop converts linked files into the Vault ${destination}`, async ({ page }) => {
+    await page.addInitScript('(' + installDesktopFilesystem.toString() + ')(window);');
+    await openApp(page);
+    await page.locator('#sidebar-new-folder').click();
+    await page.locator('#document-name-modal-input').fill('Destination');
+    await page.locator('#document-name-modal-confirm').click();
+    await page.evaluate(async () => {
+      window.__desktopFiles.set('C:/Original/notes.md', '# original');
+      await window.NL_IMPORT_EXTERNAL_FILE('# original', 'notes', 'C:/Original/notes.md');
+    });
+    const row = page.locator('#document-tree [data-tree-type="document"]').filter({ hasText: 'notes' });
+    const secret = page.locator('#document-tree [data-tree-type="workspace"]').filter({ hasText: 'Secret Workspace' });
+    await dropDocument(page, row, secret);
+    await expect(row).toHaveClass(/is-linked-document/);
+    const target = destination === 'folder'
+      ? page.locator('#document-tree [data-tree-type="folder"]').filter({ hasText: 'Destination' })
+      : page.locator('#document-tree [data-tree-type="workspace"]').filter({ hasText: 'Workspace (Vault)' });
+    await dropDocument(page, row, target);
+    await expect(row).not.toHaveClass(/is-linked-document/);
+    await expect(row).toHaveAttribute('data-tree-depth', destination === 'folder' ? '2' : '1');
+    const result = await page.evaluate(async () => {
+      const storage = new window.MarkdownWorkspaceStorage();
+      await storage.init();
+      const record = (await storage.listDocumentMetadata()).find(item => item.title === 'notes');
+      return { linked: Boolean(record.sourcePath), path: record.vaultRelativePath, original: window.__desktopFiles.get('C:/Original/notes.md') };
+    });
+    expect(result.linked).toBe(false);
+    expect(result.original).toBe('# original');
+    expect(result.path).toMatch(destination === 'folder' ? /^Workspace\/Destination\// : /^Workspace\/notes-/);
+  });
+}
+
+test('HTML conversion failure preserves the linked document', async ({ page }) => {
+  await page.addInitScript('(' + installDesktopFilesystem.toString() + ')(window);');
+  await openApp(page);
+  await page.evaluate(async () => {
+    window.__desktopFiles.set('C:/Original/notes.md', '# original');
+    await window.NL_IMPORT_EXTERNAL_FILE('# original', 'notes', 'C:/Original/notes.md');
+    await window.MarkdownViewerFlushWorkspace();
+    const save = window.MarkdownWorkspaceStorage.prototype.saveDocuments;
+    window.MarkdownWorkspaceStorage.prototype.saveDocuments = function(documents, ...args) {
+      if (documents.some(item => item.title === 'notes' && !item.sourcePath)) return Promise.reject(new Error('Simulated disk failure'));
+      return save.call(this, documents, ...args);
+    };
+  });
+  const row = page.locator('#document-tree [data-tree-type="document"]').filter({ hasText: 'notes' });
+  const target = page.locator('#document-tree [data-tree-type="workspace"]').filter({ hasText: 'Workspace (Vault)' });
+  await dropDocument(page, row, target);
+  await expect(page.locator('.app-toast').filter({ hasText: 'Conversion failed' })).toBeVisible();
+  await expect(row).toHaveClass(/is-linked-document/);
+  expect(await page.evaluate(() => window.__desktopFiles.get('C:/Original/notes.md'))).toBe('# original');
+});
diff --git a/tests/e2e/status-toolbar-followup.spec.js b/tests/e2e/status-toolbar-followup.spec.js
index af7d09ce..0dfdb659 100644
--- a/tests/e2e/status-toolbar-followup.spec.js
+++ b/tests/e2e/status-toolbar-followup.spec.js
@@ -88,7 +88,7 @@ test('header consolidates icon document actions in the requested order', async (
   await header.locator('#importDropdown').click();
   const newMenu = page.locator('[aria-labelledby="importDropdown"]');
   await expect(newMenu).toBeVisible();
-  await expect(newMenu.locator('.app-menu-label')).toHaveText(['New document', 'From files', 'From GitHub']);
+  await expect(newMenu.locator('.app-menu-label:visible')).toHaveText(['New document', 'From files', 'From GitHub']);
   // Verify the layout width, not the transient visual scale during menu-open motion.
   const newWidth = await newMenu.evaluate(menu => menu.offsetWidth);
   expect(newWidth).toBeGreaterThanOrEqual(167.5);
diff --git a/tests/e2e/tab-split-sidebar-update.spec.js b/tests/e2e/tab-split-sidebar-update.spec.js
index 38187fb1..ba5b6365 100644
--- a/tests/e2e/tab-split-sidebar-update.spec.js
+++ b/tests/e2e/tab-split-sidebar-update.spec.js
@@ -330,7 +330,7 @@ test('header groups document actions before application preferences', async ({ p
   await header.locator('#importDropdown').click();
   const newMenu = header.locator('[aria-labelledby="importDropdown"]');
   await expect(newMenu).toBeVisible();
-  await expect(newMenu.locator('.app-menu-label')).toHaveText(['New document', 'From files', 'From GitHub']);
+  await expect(newMenu.locator('.app-menu-label:visible')).toHaveText(['New document', 'From files', 'From GitHub']);
   await expect(newMenu.locator('.settings-menu-header, .app-menu-description')).toHaveCount(0);
   await newMenu.locator('#header-new-document').click();
   await expect(page.locator('#tab-list .tab-item')).toHaveCount(initialTabCount + 1);
diff --git a/tests/e2e/web-desktop-isolation.spec.js b/tests/e2e/web-desktop-isolation.spec.js
new file mode 100644
index 00000000..9183e016
--- /dev/null
+++ b/tests/e2e/web-desktop-isolation.spec.js
@@ -0,0 +1,66 @@
+const { test, expect } = require('@playwright/test');
+const { openApp } = require('../helpers/app');
+const { installDesktopFilesystem } = require('../helpers/desktop-filesystem');
+
+for (const partialRuntime of [false, true]) {
+  test(`web keeps linked recovery documents usable without native controls (${partialRuntime ? 'partial library' : 'no runtime'})`, async ({ page }) => {
+    await page.addInitScript(partial => {
+      if (partial) { window.Neutralino = {}; window.NL_PORT = 1; }
+      localStorage.setItem('markdownViewerTabs', JSON.stringify([{
+        id: 'recovered-linked', title: 'Recovered', content: '# recovery draft',
+        sourcePath: 'C:/Original/recovered.md', sourceMissing: true, sourceConflict: true,
+        favorite: true, isOpen: true, workspaceId: 'workspace_default',
+        createdAt: 1, lastOpenedAt: 1, lastEditedAt: 1
+      }]));
+    }, partialRuntime);
+    await openApp(page);
+    const tree = page.locator('#document-tree');
+    await expect(tree).not.toContainText('Workspace (Vault)');
+    const row = tree.locator('[data-document-id="recovered-linked"]');
+    await expect(tree.locator('[data-tree-type="linked-workspace"]')).toHaveCount(0);
+    for (const filter of ['all', 'recent', 'favorites']) {
+      await page.locator(`[data-document-filter="${filter}"]`).click();
+      await expect(row).toBeVisible();
+      await expect(row).not.toHaveClass(/is-linked-document|is-source-missing|is-source-conflict/);
+      await expect(row.locator('.lucide-file-text')).toHaveCount(1);
+      await expect(row.locator('.document-tree-main')).toHaveAttribute('title','Recovered');
+      await expect(row).toHaveAttribute('draggable','true');
+      await row.dispatchEvent('contextmenu', {clientX:120,clientY:120});
+      const menu = page.locator('.document-menu-context.open');
+      for (const action of ['Save','Save As…','Reload from disk','Open containing folder','Convert to Workspace copy','Remove linked file']) {
+        await expect(menu.getByRole('menuitem',{name:action,exact:true})).toHaveCount(0);
+      }
+      await expect(menu.getByRole('menuitem',{name:'Download Markdown',exact:true})).toBeVisible();
+      await page.keyboard.press('Escape');
+    }
+    await expect(page.locator('#sidebar-link-files')).toBeHidden();
+    await expect(page.locator('#sidebar-link-folder')).toBeHidden();
+    await row.locator('.document-tree-main').click();
+    await expect(page.locator('#markdown-editor')).toHaveValue('# recovery draft');
+    await expect(page.locator('#save-status')).not.toContainText('updates original');
+    const download = page.waitForEvent('download');
+    await page.locator('#markdown-editor').dispatchEvent('keydown',{key:'σ',code:'KeyS',ctrlKey:true});
+    expect((await download).suggestedFilename()).toBe('Recovered.md');
+    await page.evaluate(async () => {
+      await window.NL_IMPORT_EXTERNAL_FILE('# ignored','Ignored','C:/Ignored.md');
+    });
+    await expect(tree.locator('[data-tree-type="document"]')).toHaveCount(1);
+    await expect(page.locator('.app-toast').filter({hasText:'Save failed'})).toHaveCount(0);
+  });
+}
+
+test('standard desktop HTML dragging converts a linked document without the custom pointer layer', async ({ page }) => {
+  await page.addInitScript('(' + installDesktopFilesystem.toString() + ')(window);');
+  await openApp(page);
+  await page.evaluate(async () => {
+    window.__desktopFiles.set('C:/Original/notes.md', '# original');
+    await window.NL_IMPORT_EXTERNAL_FILE('# original','notes','C:/Original/notes.md');
+  });
+  const row = page.locator('#document-tree [data-tree-type="document"]').filter({hasText:'notes'});
+  const root = page.locator('#document-tree [data-tree-type="workspace"]').filter({hasText:'Workspace (Vault)'});
+  await expect(row).toHaveAttribute('draggable','true');
+  await row.locator('.document-tree-main').dragTo(root);
+  await expect(row).not.toHaveClass(/is-linked-document/);
+  await expect(row).toHaveAttribute('data-tree-depth','1');
+  expect(await page.evaluate(() => window.__desktopFiles.get('C:/Original/notes.md'))).toBe('# original');
+});
diff --git a/tests/helpers/desktop-filesystem.js b/tests/helpers/desktop-filesystem.js
new file mode 100644
index 00000000..80728661
--- /dev/null
+++ b/tests/helpers/desktop-filesystem.js
@@ -0,0 +1,70 @@
+// In-memory Neutralino filesystem for testing the real desktop storage backend.
+function installDesktopFilesystem(target) {
+  const files = new Map();
+  const directories = new Set(['C:', 'C:/Documents']);
+  const normalize = value => String(value).replace(/\\/g, '/').replace(/\/+/g, '/').replace(/\/$/, '');
+  const join = (...parts) => normalize(parts.filter(Boolean).join('/'));
+  const storageData = new Map();
+  target.__desktopFiles = files;
+  target.NL_PORT = 1;
+  target.Neutralino = {
+    os: { getPath: async () => 'C:/Documents', open: async () => true },
+    events: { on: async () => true },
+    storage: {
+      getData: async key => {
+        if (!storageData.has(key)) throw new Error('missing');
+        return storageData.get(key);
+      },
+      setData: async (key, value) => storageData.set(key, value),
+      removeData: async key => storageData.delete(key)
+    },
+    filesystem: {
+      getJoinedPath: async (...parts) => join(...parts),
+      getStats: async path => {
+        path = normalize(path);
+        if (directories.has(path)) return { isDirectory: true, size: 0, modifiedAt: Date.now() };
+        if (files.has(path)) return { isDirectory: false, size: files.get(path).length, modifiedAt: Date.now() };
+        throw Object.assign(new Error('missing'), { code: 'NE_FS_NOPATHE' });
+      },
+      createDirectory: async path => directories.add(normalize(path)),
+      readFile: async path => {
+        path = normalize(path);
+        if (!files.has(path)) throw new Error('missing');
+        return files.get(path);
+      },
+      writeFile: async (path, value) => files.set(normalize(path), String(value)),
+      copy: async (source, destination) => files.set(normalize(destination), files.get(normalize(source))),
+      move: async (source, destination) => {
+        source = normalize(source);
+        destination = normalize(destination);
+        if (!files.has(source)) throw new Error('missing');
+        files.set(destination, files.get(source));
+        files.delete(source);
+      },
+      remove: async path => {
+        path = normalize(path);
+        files.delete(path);
+        directories.delete(path);
+      },
+      readDirectory: async path => {
+        const prefix = normalize(path) + '/';
+        const entries = new Map();
+        directories.forEach(candidate => {
+          if (!candidate.startsWith(prefix)) return;
+          const rest = candidate.slice(prefix.length);
+          if (rest && !rest.includes('/')) entries.set(rest, { entry: rest, type: 'DIRECTORY' });
+        });
+        files.forEach((_, candidate) => {
+          if (!candidate.startsWith(prefix)) return;
+          const rest = candidate.slice(prefix.length);
+          if (rest && !rest.includes('/')) entries.set(rest, { entry: rest, type: 'FILE' });
+        });
+        return Array.from(entries.values());
+      },
+      createWatcher: async () => 1,
+      removeWatcher: async () => true
+    }
+  };
+}
+
+module.exports = { installDesktopFilesystem };
diff --git a/tests/unit/linked-workspace-storage.test.mjs b/tests/unit/linked-workspace-storage.test.mjs
new file mode 100644
index 00000000..10cd8042
--- /dev/null
+++ b/tests/unit/linked-workspace-storage.test.mjs
@@ -0,0 +1,133 @@
+import test from 'node:test';
+import assert from 'node:assert/strict';
+import fs from 'node:fs';
+import vm from 'node:vm';
+import { webcrypto } from 'node:crypto';
+import mock from '../helpers/desktop-filesystem.js';
+
+const source = fs.readFileSync(new URL('../../workspace-storage.js', import.meta.url), 'utf8');
+const vault = 'C:/Documents/Markdown Viewer Vault/';
+const indexPath = vault + '.markdown-viewer/index.json';
+
+async function setupLegacyLinkedDraft() {
+  const target = { crypto: webcrypto, TextEncoder, console, localStorage: { getItem: () => null, removeItem() {} } };
+  target.self = target;
+  target.window = target;
+  mock.installDesktopFilesystem(target);
+  vm.runInNewContext(source, target);
+  const storage = new target.MarkdownWorkspaceStorage();
+  await storage.init();
+  const draft = { id: 'linked_draft', title: 'Notes', content: '# unsaved draft', contentLoaded: true, workspaceId: 'workspace_default', _storageRevision: 0 };
+  await storage.saveDocuments([draft], { folders: [] }, { forceContent: true });
+  const metadata = storage.vaultIndex.documents[0];
+  metadata.sourcePath = 'C:/Original/notes.md';
+  metadata.sourceContentHash = 'original-hash';
+  target.__desktopFiles.set(metadata.sourcePath, '# original on disk');
+  target.__desktopFiles.set(indexPath, JSON.stringify(storage.vaultIndex));
+  return { target, oldPath: vault + metadata.vaultRelativePath };
+}
+
+test('upgrade moves existing linked recovery drafts without changing originals', async () => {
+  const { target, oldPath } = await setupLegacyLinkedDraft();
+  const upgraded = new target.MarkdownWorkspaceStorage();
+  await upgraded.init();
+  const record = upgraded.vaultIndex.documents[0];
+  assert.match(record.vaultRelativePath, /^Linked Workspace\//);
+  assert.equal(await upgraded.loadDocumentContent(record.id), '# unsaved draft');
+  assert.equal(record.sourcePath, 'C:/Original/notes.md');
+  assert.equal(target.__desktopFiles.get(record.sourcePath), '# original on disk');
+  assert.equal(target.__desktopFiles.has(oldPath), false);
+  const restarted = new target.MarkdownWorkspaceStorage();
+  await restarted.init();
+  assert.equal(await restarted.loadDocumentContent(record.id), '# unsaved draft');
+});
+
+test('interrupted linked-draft migration recovers its move and index journals', async () => {
+  const { target } = await setupLegacyLinkedDraft();
+  const write = target.Neutralino.filesystem.writeFile;
+  let failOnce = true;
+  target.Neutralino.filesystem.writeFile = async (path, content) => {
+    if (failOnce && path.includes('/journal/') && path.endsWith('.index.json')) {
+      failOnce = false;
+      throw new Error('Simulated interruption before index commit');
+    }
+    return write(path, content);
+  };
+  await assert.rejects(new target.MarkdownWorkspaceStorage().init(), /Simulated interruption/);
+  const restarted = new target.MarkdownWorkspaceStorage();
+  await restarted.init();
+  assert.match(restarted.vaultIndex.documents[0].vaultRelativePath, /^Linked Workspace\//);
+  assert.equal(await restarted.loadDocumentContent('linked_draft'), '# unsaved draft');
+  assert.equal(target.__desktopFiles.get('C:/Original/notes.md'), '# original on disk');
+});
+
+test('migration stops if an indexed draft body is missing and retains the old index', async () => {
+  const { target, oldPath } = await setupLegacyLinkedDraft();
+  const oldIndex = target.__desktopFiles.get(indexPath);
+  target.__desktopFiles.delete(oldPath);
+  await assert.rejects(new target.MarkdownWorkspaceStorage().init(), error => error.name === 'WorkspaceCorruptionError');
+  assert.equal(target.__desktopFiles.get(indexPath), oldIndex);
+});
+
+test('conversion moves the draft to Workspace and backup preserves both storage roots', async () => {
+  const { target } = await setupLegacyLinkedDraft();
+  const storage = new target.MarkdownWorkspaceStorage();
+  await storage.init();
+  const draft = (await storage.listDocumentMetadata())[0];
+  const linkedPath = vault + draft._vaultRelativePath;
+  assert.match(await storage._backupDocumentRelativePath(draft, {}), /^Linked Workspace\//);
+  draft.content = await storage.loadDocumentContent(draft.id);
+  draft.contentLoaded = true;
+  delete draft.sourcePath;
+  delete draft.sourceContentHash;
+  await storage.saveDocuments([draft], { folders: [] }, { changedIds: [draft.id] });
+  assert.match(draft._vaultRelativePath, /^Workspace\//);
+  assert.equal(target.__desktopFiles.has(linkedPath), false);
+  assert.equal(target.__desktopFiles.get(vault + draft._vaultRelativePath), '# unsaved draft');
+  assert.equal(target.__desktopFiles.get('C:/Original/notes.md'), '# original on disk');
+  assert.match(await storage._backupDocumentRelativePath(draft, {}), /^Workspace\//);
+  const restarted = new target.MarkdownWorkspaceStorage();
+  await restarted.init();
+  assert.equal(restarted.vaultIndex.documents[0].sourcePath, undefined);
+  assert.match(restarted.vaultIndex.documents[0].vaultRelativePath, /^Workspace\//);
+});
+
+test('index rebuilding preserves recovery files from Linked Workspace', async () => {
+  const { target } = await setupLegacyLinkedDraft();
+  const storage = new target.MarkdownWorkspaceStorage();
+  await storage.init();
+  target.__desktopFiles.delete(indexPath);
+  const rebuilt = new target.MarkdownWorkspaceStorage();
+  await rebuilt.init();
+  const record = rebuilt.vaultIndex.documents[0];
+  assert.equal(record.kind, 'linked-recovery');
+  assert.equal(await rebuilt.loadDocumentContent(record.id), '# unsaved draft');
+  assert.match(await rebuilt._desktopDocumentRelativePath(record, {}), /^Linked Workspace\//);
+});
+
+test('new linked drafts and normal documents use separate physical roots', async () => {
+  const { target } = await setupLegacyLinkedDraft();
+  const storage = new target.MarkdownWorkspaceStorage();
+  await storage.init();
+  const organization = { folders: [{ id: 'folder', name: 'Projects', workspaceId: 'workspace_default', parentFolderId: null }] };
+  const linked = { id: 'new_linked', title: 'Same title', content: '# recovery', contentLoaded: true, sourcePath: 'C:/Original/new.md', folderId: 'folder', workspaceId: 'workspace_default' };
+  const normal = { id: 'new_normal', title: 'Same title', content: '# normal', contentLoaded: true, folderId: 'folder', workspaceId: 'workspace_default' };
+  target.__desktopFiles.set(linked.sourcePath, '# source unchanged');
+  await storage.saveDocuments([linked, normal], organization, { forceContent: true });
+  assert.match(linked._vaultRelativePath, /^Linked Workspace\//);
+  assert.match(normal._vaultRelativePath, /^Workspace\/Projects\//);
+  assert.equal(target.__desktopFiles.get(vault + linked._vaultRelativePath), '# recovery');
+  assert.equal(target.__desktopFiles.get(vault + normal._vaultRelativePath), '# normal');
+  assert.equal(target.__desktopFiles.get(linked.sourcePath), '# source unchanged');
+});
+
+test('migration validates all bodies before moving any legacy draft', async () => {
+  const { target, oldPath } = await setupLegacyLinkedDraft();
+  const index = JSON.parse(target.__desktopFiles.get(indexPath));
+  index.documents.push({ ...index.documents[0], id: 'missing_draft', vaultRelativePath: 'Workspace/missing.md' });
+  target.__desktopFiles.set(indexPath, JSON.stringify(index));
+  const oldIndex = target.__desktopFiles.get(indexPath);
+  await assert.rejects(new target.MarkdownWorkspaceStorage().init(), error => error.name === 'WorkspaceCorruptionError');
+  assert.equal(target.__desktopFiles.get(oldPath), '# unsaved draft');
+  assert.equal(target.__desktopFiles.get(indexPath), oldIndex);
+});
diff --git a/workspace-storage.js b/workspace-storage.js
index df3eb067..85671e9b 100644
--- a/workspace-storage.js
+++ b/workspace-storage.js
@@ -278,6 +278,7 @@
 
     mergeCollection('workspaces');
     mergeCollection('folders');
+    mergeCollection('linkedLocations');
     merged.ui = mergeObjectChanges(base.ui || {}, local.ui || {}, remote.ui || {});
     return merged;
   }
@@ -352,6 +353,7 @@
       if (this.desktop) await this._initDesktop();
       else await this._initBrowser();
       await this._migrateLegacyNormalDocuments();
+      if (this.desktop) await this._migrateLinkedRecoveryDocuments();
       this.ready = true;
       try {
         await this.purgeExpiredTrash();
@@ -521,6 +523,7 @@
       const journalPath = await this._pathJoin(internalPath, 'journal');
       await this._ensureDirectory(vaultPath);
       await this._ensureDirectory(workspacePath);
+      await this._ensureDirectory(await this._pathJoin(vaultPath, 'Linked Workspace'));
       await this._ensureDirectory(await this._pathJoin(vaultPath, 'Secret Workspace'));
       await this._ensureDirectory(secretPath);
       await this._ensureDirectory(internalPath);
@@ -576,6 +579,25 @@
       }
     }
 
+    async _migrateLinkedRecoveryDocuments() {
+      const drafts = this.vaultIndex.documents.filter(function(item) {
+        return item.sourcePath && !String(item.vaultRelativePath || '').startsWith('Linked Workspace/');
+      }).map(function(item) {
+        return Object.assign({}, item, {
+          contentLoaded: false,
+          _storageRevision: normalizedStorageRevision(item.storageRevision)
+        });
+      });
+      // Validate all existing bodies before moving any file. Missing recovery
+      // content must stop migration rather than creating an empty replacement.
+      for (const draft of drafts) await this.loadDocumentContent(draft.id);
+      if (drafts.length) {
+        await this.saveDocuments(drafts, this.vaultOrganization, {
+          changedIds: drafts.map(function(item) { return item.id; })
+        });
+      }
+    }
+
     async _rebuildDesktopIndex(workspacePath) {
       const organization = this.vaultOrganization && typeof this.vaultOrganization === 'object'
         ? cloneJson(this.vaultOrganization, null)
@@ -605,7 +627,7 @@
         return folder;
       };
 
-      const walk = async (currentPath, relativeSegments, parentFolderId) => {
+      const walk = async (currentPath, relativeSegments, parentFolderId, storageRoot) => {
         let entries = [];
         try {
           entries = await Neutralino.filesystem.readDirectory(currentPath);
@@ -619,8 +641,8 @@
           if (!entry || !entry.entry) continue;
           const entryPath = await this._pathJoin(currentPath, entry.entry);
           if (entry.type === 'DIRECTORY') {
-            const folder = findOrCreateFolder(entry.entry, parentFolderId);
-            await walk(entryPath, relativeSegments.concat(entry.entry), folder.id);
+            const folder = storageRoot === 'Workspace' ? findOrCreateFolder(entry.entry, parentFolderId) : null;
+            await walk(entryPath, relativeSegments.concat(entry.entry), folder ? folder.id : null, storageRoot);
             continue;
           }
           if (entry.type !== 'FILE' || !/\.md$/i.test(entry.entry)) continue;
@@ -645,13 +667,17 @@
             lastOpenedAt: timestamp,
             lastEditedAt: timestamp,
             contentSize: Number(stats && stats.size) || 0,
-            vaultRelativePath: normalizePathSeparators(['Workspace'].concat(relativeSegments, entry.entry).join('/')),
+            vaultRelativePath: normalizePathSeparators([storageRoot].concat(relativeSegments, entry.entry).join('/')),
+            // A lost index cannot safely tell us the original source path.
+            // Preserve these bodies as recovery documents, not invented links.
+            kind: storageRoot === 'Linked Workspace' ? 'linked-recovery' : undefined,
             contentLoaded: false
           });
         }
       };
 
-      await walk(workspacePath, [], null);
+      await walk(workspacePath, [], null, 'Workspace');
+      await walk(await this._pathJoin(this.vaultPath, 'Linked Workspace'), [], null, 'Linked Workspace');
       if (documents.length) documents[0].isOpen = true;
       this.vaultOrganization = organization;
       return {
@@ -1095,7 +1121,8 @@
     }
 
     async _desktopDocumentRelativePath(tab, organization) {
-      const segments = ['Workspace'].concat(await this._desktopFolderSegments(tab, organization));
+      const linked = Boolean(tab.sourcePath) || tab.kind === 'linked-recovery' || tab.kind === 'linked-workspace-guide';
+      const segments = linked ? ['Linked Workspace'] : ['Workspace'].concat(await this._desktopFolderSegments(tab, organization));
       requireDocumentId(tab && tab.id);
       const suffix = await stableDocumentIdSuffix(tab.id);
       segments.push(sanitizePathSegment(tab.title, 'Untitled') + '--' + suffix + '.md');
@@ -1103,10 +1130,10 @@
     }
 
     async _backupDocumentRelativePath(tab, organization) {
-      const storedPath = normalizePathSeparators(tab && (tab.vaultRelativePath || tab._vaultRelativePath));
+      const storedPath = normalizePathSeparators(tab && (tab._vaultRelativePath || tab.vaultRelativePath));
       if (
         storedPath &&
-        storedPath.startsWith('Workspace/') &&
+        (storedPath.startsWith('Workspace/') || storedPath.startsWith('Linked Workspace/')) &&
         !storedPath.split('/').some(function(segment) { return segment === '.' || segment === '..'; })
       ) {
         return storedPath;
@@ -1290,7 +1317,8 @@
       metadata.contentSize = typeof tab.content === 'string'
         ? new TextEncoder().encode(tab.content).byteLength
         : Number(existing && existing.contentSize) || 0;
-      if (existing) Object.assign(existing, metadata);
+      // Conversion removes source fields: merging would retain them on restart.
+      if (existing) this.vaultIndex.documents[this.vaultIndex.documents.indexOf(existing)] = metadata;
       else this.vaultIndex.documents.push(metadata);
       tab._vaultRelativePath = relativePath;
       tab._pendingStorageRevision = metadata.storageRevision;
@@ -2841,6 +2869,7 @@
         }
         const ownedPaths = [
           await this._pathJoin(this.vaultPath, 'Workspace'),
+          await this._pathJoin(this.vaultPath, 'Linked Workspace'),
           await this._pathJoin(this.vaultPath, 'Secret Workspace'),
           await this._pathJoin(this.vaultPath, INTERNAL_DIR)
         ];