From 833ab52986566bf449537fb392426bcc0e0b7744 Mon Sep 17 00:00:00 2001
From: Henri Jamet <42291955+hjamet@users.noreply.github.com>
Date: Sun, 29 Dec 2024 12:51:52 +0100
Subject: [PATCH 1/5] Add manual sync command to Khoj plugin

- Introduced a new command 'Sync new changes' to allow users to manually synchronize new modifications.
- The command updates the content index without regenerating it, ensuring only new changes are synced.
- User-triggered notifications are displayed upon successful sync.
---
 src/interface/obsidian/src/main.ts | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/src/interface/obsidian/src/main.ts b/src/interface/obsidian/src/main.ts
index bf7cad548..f5f80cfc4 100644
--- a/src/interface/obsidian/src/main.ts
+++ b/src/interface/obsidian/src/main.ts
@@ -34,6 +34,21 @@ export default class Khoj extends Plugin {
             callback: () => { this.activateView(KhojView.CHAT); }
         });
 
+        // Add sync command to manually sync new changes
+        this.addCommand({
+            id: 'sync',
+            name: 'Sync new changes',
+            callback: async () => {
+                this.settings.lastSync = await updateContentIndex(
+                    this.app.vault,
+                    this.settings,
+                    this.settings.lastSync,
+                    false, // regenerate = false pour ne synchroniser que les nouvelles modifications
+                    true  // userTriggered = true pour afficher une notification
+                );
+            }
+        });
+
         this.registerView(KhojView.CHAT, (leaf) => new KhojChatView(leaf, this.settings));
 
         // Create an icon in the left ribbon.

From c5c9e0072c6a541fed9015c3d6d72b7216653a9e Mon Sep 17 00:00:00 2001
From: Henri Jamet <42291955+hjamet@users.noreply.github.com>
Date: Sun, 29 Dec 2024 13:07:21 +0100
Subject: [PATCH 2/5] Enhance Khoj plugin settings and UI for folder
 synchronization

- Added a new setting to manage sync folders, allowing users to specify which folders to sync or to sync the entire vault.
- Implemented a modal for folder suggestions to facilitate folder selection.
- Updated the folder list display to show currently selected folders with options to remove them.
- Improved CSS styles for chat interface and folder list for better user experience.
- Refactored code for consistency and readability across multiple files.
---
 src/interface/obsidian/src/settings.ts | 110 ++++++++++++++++-
 src/interface/obsidian/src/utils.ts    | 100 ++++++++-------
 src/interface/obsidian/styles.css      | 162 ++++++++++++++++++++++---
 3 files changed, 308 insertions(+), 64 deletions(-)

diff --git a/src/interface/obsidian/src/settings.ts b/src/interface/obsidian/src/settings.ts
index 6f70d609c..62467b88a 100644
--- a/src/interface/obsidian/src/settings.ts
+++ b/src/interface/obsidian/src/settings.ts
@@ -1,4 +1,4 @@
-import { App, Notice, PluginSettingTab, Setting, TFile } from 'obsidian';
+import { App, Notice, PluginSettingTab, Setting, TFile, SuggestModal } from 'obsidian';
 import Khoj from 'src/main';
 import { canConnectToBackend, getBackendStatusMessage, updateContentIndex } from './utils';
 
@@ -15,6 +15,7 @@ interface SyncFileTypes {
     images: boolean;
     pdf: boolean;
 }
+
 export interface KhojSetting {
     resultsCount: number;
     khojUrl: string;
@@ -24,6 +25,7 @@ export interface KhojSetting {
     lastSync: Map<TFile, number>;
     syncFileType: SyncFileTypes;
     userInfo: UserInfo | null;
+    syncFolders: string[];
 }
 
 export const DEFAULT_SETTINGS: KhojSetting = {
@@ -39,6 +41,7 @@ export const DEFAULT_SETTINGS: KhojSetting = {
         pdf: true,
     },
     userInfo: null,
+    syncFolders: [],
 }
 
 export class KhojSettingTab extends PluginSettingTab {
@@ -60,7 +63,8 @@ export class KhojSettingTab extends PluginSettingTab {
                 this.plugin.settings.userInfo?.email,
                 this.plugin.settings.khojUrl,
                 this.plugin.settings.khojApiKey
-            )}
+            )
+        }
         );
         let backendStatusMessage: string = '';
 
@@ -109,7 +113,7 @@ export class KhojSettingTab extends PluginSettingTab {
                 }));
 
         // Add new "Sync" heading
-        containerEl.createEl('h3', {text: 'Sync'});
+        containerEl.createEl('h3', { text: 'Sync' });
 
         // Add setting to sync markdown notes
         new Setting(containerEl)
@@ -153,6 +157,29 @@ export class KhojSettingTab extends PluginSettingTab {
                     this.plugin.settings.autoConfigure = value;
                     await this.plugin.saveSettings();
                 }));
+
+        // Add setting to manage sync folders
+        const syncFoldersContainer = containerEl.createDiv('sync-folders-container');
+        const foldersSetting = new Setting(syncFoldersContainer)
+            .setName('Sync Folders')
+            .setDesc('Specify folders to sync (leave empty to sync entire vault)')
+            .addButton(button => button
+                .setButtonText('Add Folder')
+                .onClick(() => {
+                    const modal = new FolderSuggestModal(this.app, (folder: string) => {
+                        if (!this.plugin.settings.syncFolders.includes(folder)) {
+                            this.plugin.settings.syncFolders.push(folder);
+                            this.plugin.saveSettings();
+                            this.updateFolderList(folderListEl);
+                        }
+                    });
+                    modal.open();
+                }));
+
+        // Create a list to display selected folders
+        const folderListEl = syncFoldersContainer.createDiv('folder-list');
+        this.updateFolderList(folderListEl);
+
         let indexVaultSetting = new Setting(containerEl);
         indexVaultSetting
             .setName('Force Sync')
@@ -200,4 +227,81 @@ export class KhojSettingTab extends PluginSettingTab {
                 })
             );
     }
+
+    // Helper method to update the folder list display
+    private updateFolderList(containerEl: HTMLElement) {
+        containerEl.empty();
+        if (this.plugin.settings.syncFolders.length === 0) {
+            containerEl.createEl('div', {
+                text: 'Syncing entire vault',
+                cls: 'folder-list-empty'
+            });
+            return;
+        }
+
+        const list = containerEl.createEl('ul', { cls: 'folder-list' });
+        this.plugin.settings.syncFolders.forEach(folder => {
+            const item = list.createEl('li', { cls: 'folder-list-item' });
+            item.createSpan({ text: folder });
+
+            const removeButton = item.createEl('button', {
+                cls: 'folder-list-remove',
+                text: '×'
+            });
+            removeButton.addEventListener('click', async () => {
+                this.plugin.settings.syncFolders = this.plugin.settings.syncFolders.filter(f => f !== folder);
+                await this.plugin.saveSettings();
+                this.updateFolderList(containerEl);
+            });
+        });
+    }
+}
+
+// Modal with folder suggestions
+class FolderSuggestModal extends SuggestModal<string> {
+    constructor(app: App, private onChoose: (folder: string) => void) {
+        super(app);
+    }
+
+    getSuggestions(query: string): string[] {
+        const folders = this.getAllFolders();
+        if (!query) return folders;
+
+        return folders.filter(folder =>
+            folder.toLowerCase().includes(query.toLowerCase())
+        );
+    }
+
+    renderSuggestion(folder: string, el: HTMLElement) {
+        el.createSpan({
+            text: folder || '/',
+            cls: 'folder-suggest-item'
+        });
+    }
+
+    onChooseSuggestion(folder: string, _: MouseEvent | KeyboardEvent) {
+        this.onChoose(folder);
+    }
+
+    private getAllFolders(): string[] {
+        const folders = new Set<string>();
+        folders.add(''); // Root folder
+
+        // Récupérer tous les fichiers et extraire les chemins des dossiers
+        this.app.vault.getAllLoadedFiles().forEach(file => {
+            const folderPath = file.parent?.path;
+            if (folderPath) {
+                folders.add(folderPath);
+
+                // Ajouter aussi tous les dossiers parents
+                let parent = folderPath;
+                while (parent.includes('/')) {
+                    parent = parent.substring(0, parent.lastIndexOf('/'));
+                    folders.add(parent);
+                }
+            }
+        });
+
+        return Array.from(folders).sort();
+    }
 }
diff --git a/src/interface/obsidian/src/utils.ts b/src/interface/obsidian/src/utils.ts
index 3cc83fb88..b0dbf61f6 100644
--- a/src/interface/obsidian/src/utils.ts
+++ b/src/interface/obsidian/src/utils.ts
@@ -9,7 +9,7 @@ export function getVaultAbsolutePath(vault: Vault): string {
     return '';
 }
 
-function fileExtensionToMimeType (extension: string): string {
+function fileExtensionToMimeType(extension: string): string {
     switch (extension) {
         case 'pdf':
             return 'application/pdf';
@@ -28,7 +28,7 @@ function fileExtensionToMimeType (extension: string): string {
     }
 }
 
-function filenameToMimeType (filename: TFile): string {
+function filenameToMimeType(filename: TFile): string {
     switch (filename.extension) {
         case 'pdf':
             return 'application/pdf';
@@ -63,15 +63,24 @@ export async function updateContentIndex(vault: Vault, setting: KhojSetting, las
     // Get all markdown, pdf files in the vault
     console.log(`Khoj: Updating Khoj content index...`)
     const files = vault.getFiles()
-                        // Filter supported file types for syncing
-                        .filter(file => supportedFileTypes.includes(file.extension))
-                        // Filter user configured file types for syncing
-                        .filter(file => {
-                            if (fileTypeToExtension.markdown.includes(file.extension)) return setting.syncFileType.markdown;
-                            if (fileTypeToExtension.pdf.includes(file.extension)) return setting.syncFileType.pdf;
-                            if (fileTypeToExtension.image.includes(file.extension)) return setting.syncFileType.images;
-                            return false;
-                        });
+        // Filter supported file types for syncing
+        .filter(file => supportedFileTypes.includes(file.extension))
+        // Filter user configured file types for syncing
+        .filter(file => {
+            if (fileTypeToExtension.markdown.includes(file.extension)) return setting.syncFileType.markdown;
+            if (fileTypeToExtension.pdf.includes(file.extension)) return setting.syncFileType.pdf;
+            if (fileTypeToExtension.image.includes(file.extension)) return setting.syncFileType.images;
+            return false;
+        })
+        // Filter files based on specified folders
+        .filter(file => {
+            // Si aucun dossier n'est spécifié, synchroniser tous les fichiers
+            if (setting.syncFolders.length === 0) return true;
+            // Sinon, vérifier si le fichier est dans un des dossiers spécifiés
+            return setting.syncFolders.some(folder =>
+                file.path.startsWith(folder + '/') || file.path === folder
+            );
+        });
 
     let countOfFilesToIndex = 0;
     let countOfFilesToDelete = 0;
@@ -81,7 +90,7 @@ export async function updateContentIndex(vault: Vault, setting: KhojSetting, las
     const fileData = [];
     for (const file of files) {
         // Only push files that have been modified since last sync if not regenerating
-        if (!regenerate && file.stat.mtime < (lastSync.get(file) ?? 0)){
+        if (!regenerate && file.stat.mtime < (lastSync.get(file) ?? 0)) {
             continue;
         }
 
@@ -89,7 +98,7 @@ export async function updateContentIndex(vault: Vault, setting: KhojSetting, las
         const encoding = supportedBinaryFileTypes.includes(file.extension) ? "binary" : "utf8";
         const mimeType = fileExtensionToMimeType(file.extension) + (encoding === "utf8" ? "; charset=UTF-8" : "");
         const fileContent = encoding == 'binary' ? await vault.readBinary(file) : await vault.read(file);
-        fileData.push({blob: new Blob([fileContent], { type: mimeType }), path: file.path});
+        fileData.push({ blob: new Blob([fileContent], { type: mimeType }), path: file.path });
     }
 
     // Add any previously synced files to be deleted to multipart form data
@@ -98,13 +107,13 @@ export async function updateContentIndex(vault: Vault, setting: KhojSetting, las
         if (!files.includes(lastSyncedFile)) {
             countOfFilesToDelete++;
             let fileObj = new Blob([""], { type: filenameToMimeType(lastSyncedFile) });
-            fileData.push({blob: fileObj, path: lastSyncedFile.path});
+            fileData.push({ blob: fileObj, path: lastSyncedFile.path });
             filesToDelete.push(lastSyncedFile);
         }
     }
 
     // Iterate through all indexable files in vault, 1000 at a time
-    let responses: string[]  = [];
+    let responses: string[] = [];
     let error_message = null;
     for (let i = 0; i < fileData.length; i += 1000) {
         const filesGroup = fileData.slice(i, i + 1000);
@@ -166,17 +175,17 @@ export async function updateContentIndex(vault: Vault, setting: KhojSetting, las
     }
 
     // Update last sync time for each successfully indexed file
-   files
-    .filter(file => responses.find(response => response.includes(file.path)))
-    .reduce((newSync, file) => {
-        newSync.set(file, new Date().getTime());
-        return newSync;
-    }, lastSync);
+    files
+        .filter(file => responses.find(response => response.includes(file.path)))
+        .reduce((newSync, file) => {
+            newSync.set(file, new Date().getTime());
+            return newSync;
+        }, lastSync);
 
     // Remove files that were deleted from last sync
     filesToDelete
-    .filter(file => responses.find(response => response.includes(file.path)))
-    .forEach(file => lastSync.delete(file));
+        .filter(file => responses.find(response => response.includes(file.path)))
+        .forEach(file => lastSync.delete(file));
 
     if (error_message) {
         new Notice(error_message);
@@ -188,31 +197,30 @@ export async function updateContentIndex(vault: Vault, setting: KhojSetting, las
     return lastSync;
 }
 
-export async function openKhojPluginSettings(): Promise<void>
- {
-     const setting = this.app.setting;
-     await setting.open();
-     setting.openTabById('khoj');
+export async function openKhojPluginSettings(): Promise<void> {
+    const setting = this.app.setting;
+    await setting.open();
+    setting.openTabById('khoj');
 }
 
 export async function createNote(name: string, newLeaf = false): Promise<void> {
     try {
-      let pathPrefix: string
-      switch (this.app.vault.getConfig('newFileLocation')) {
-        case 'current':
-          pathPrefix = (this.app.workspace.getActiveFile()?.parent.path ?? '') + '/'
-          break
-        case 'folder':
-          pathPrefix = this.app.vault.getConfig('newFileFolderPath') + '/'
-          break
-        default: // 'root'
-          pathPrefix = ''
-          break
-      }
-      await this.app.workspace.openLinkText(`${pathPrefix}${name}.md`, '', newLeaf)
+        let pathPrefix: string
+        switch (this.app.vault.getConfig('newFileLocation')) {
+            case 'current':
+                pathPrefix = (this.app.workspace.getActiveFile()?.parent.path ?? '') + '/'
+                break
+            case 'folder':
+                pathPrefix = this.app.vault.getConfig('newFileFolderPath') + '/'
+                break
+            default: // 'root'
+                pathPrefix = ''
+                break
+        }
+        await this.app.workspace.openLinkText(`${pathPrefix}${name}.md`, '', newLeaf)
     } catch (e) {
-      console.error('Khoj: Could not create note.\n' + (e as any).message);
-      throw e
+        console.error('Khoj: Could not create note.\n' + (e as any).message);
+        throw e
     }
 }
 
@@ -236,7 +244,7 @@ export async function canConnectToBackend(
     let userInfo: UserInfo | null = null;
 
     if (!!khojUrl) {
-        let headers  = !!khojApiKey ? { "Authorization": `Bearer ${khojApiKey}` } : undefined;
+        let headers = !!khojApiKey ? { "Authorization": `Bearer ${khojApiKey}` } : undefined;
         try {
             let response = await request({ url: `${khojUrl}/api/v1/user`, method: "GET", headers: headers })
             connectedToBackend = true;
@@ -387,7 +395,7 @@ function copyParentText(event: MouseEvent, message: string, originalButton: stri
 }
 
 export function createCopyParentText(message: string, originalButton: string = 'copy-plus') {
-    return function(event: MouseEvent) {
+    return function (event: MouseEvent) {
         return copyParentText(event, message, originalButton);
     }
 }
@@ -406,7 +414,7 @@ export function pasteTextAtCursor(text: string | undefined) {
     // If there is a selection, replace it with the text
     if (editor?.getSelection()) {
         editor.replaceSelection(text);
-    // If there is no selection, insert the text at the cursor position
+        // If there is no selection, insert the text at the cursor position
     } else if (cursor) {
         editor.replaceRange(text, cursor);
     }
diff --git a/src/interface/obsidian/styles.css b/src/interface/obsidian/styles.css
index 0d2ea1d4d..35573b0c4 100644
--- a/src/interface/obsidian/styles.css
+++ b/src/interface/obsidian/styles.css
@@ -13,11 +13,12 @@ If your plugin does not need CSS, delete this file.
     --khoj-storm-grey: #475569;
     --chat-icon: url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' width='24px' height='24px' viewBox='0 0 24 24' fill='currentColor' stroke-linecap='round' stroke-linejoin='round' class='svg-icon' version='1.1'%3E%3Cpath d='m 14.024348,9.8497703 0.04627,1.9750167' stroke='%231c274c' stroke-width='2' stroke-linecap='round' /%3E%3Cpath d='m 9.6453624,9.7953624 0.046275,1.9750166' stroke='%231c274c' stroke-width='2' stroke-linecap='round' /%3E%3Cpath d='m 11.90538,2.3619994 c -5.4939109,0 -9.6890976,4.0608185 -9.6890976,9.8578926 0,1.477202 0.2658016,2.542848 0.6989332,3.331408 0.433559,0.789293 1.0740097,1.372483 1.9230615,1.798517 1.7362861,0.87132 4.1946007,1.018626 7.0671029,1.018626 0.317997,0 0.593711,0.167879 0.784844,0.458501 0.166463,0.253124 0.238617,0.552748 0.275566,0.787233 0.07263,0.460801 0.05871,1.030165 0.04785,1.474824 v 4.8e-5 l -2.26e-4,0.0091 c -0.0085,0.348246 -0.01538,0.634247 -0.0085,0.861186 0.105589,-0.07971 0.227925,-0.185287 0.36735,-0.31735 0.348613,-0.330307 0.743513,-0.767362 1.176607,-1.246635 l 0.07837,-0.08673 c 0.452675,-0.500762 0.941688,-1.037938 1.41216,-1.473209 0.453774,-0.419787 0.969948,-0.822472 1.476003,-0.953853 1.323661,-0.343655 2.330132,-0.904027 3.005749,-1.76381 0.658957,-0.838568 1.073167,-2.051868 1.073167,-3.898667 0,-5.7970748 -4.195186,-9.8578946 -9.689097,-9.8578946 z M 0.92440678,12.219892 c 0,-7.0067939 5.05909412,-11.47090892 10.98097322,-11.47090892 5.921878,0 10.980972,4.46411502 10.980972,11.47090892 0,2.172259 -0.497596,3.825405 -1.442862,5.028357 -0.928601,1.181693 -2.218843,1.837914 -3.664937,2.213334 -0.211641,0.05502 -0.53529,0.268579 -0.969874,0.670658 -0.417861,0.386604 -0.865628,0.876836 -1.324566,1.384504 l -0.09131,0.101202 c -0.419252,0.464136 -0.849637,0.94059 -1.239338,1.309807 -0.210187,0.199169 -0.425281,0.383422 -0.635348,0.523424 -0.200911,0.133819 -0.449635,0.263369 -0.716376,0.281474 -0.327812,0.02226 -0.61539,-0.149209 -0.804998,-0.457293 -0.157614,-0.255993 -0.217622,-0.557143 -0.246564,-0.778198 -0.0542,-0.414027 -0.04101,-0.933065 -0.03027,-1.355183 l 0.0024,-0.0922 c 0.01099,-0.463865 0.01489,-0.820507 -0.01611,-1.06842 C 8.9434608,19.975238 6.3139711,19.828758 4.356743,18.84659 3.3355029,18.334136 2.4624526,17.578678 1.8500164,16.463713 1.2372016,15.348029 0.92459928,13.943803 0.92459928,12.219967 Z' clip-rule='evenodd' stroke-width='2' fill='currentColor' fill-rule='evenodd' fill-opacity='1' /%3E%3C/svg%3E%0A");
     --search-icon: url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' width='24px' height='24px' viewBox='0 0 24 24' fill='currentColor' stroke-linecap='round' stroke-linejoin='round' class='svg-icon' version='1.1'%3E%3Cpath d='m 18.562765,17.147843 c 1.380497,-1.679442 2.307667,-4.013099 2.307667,-6.330999 C 20.870432,5.3951476 16.353958,1 10.782674,1 5.2113555,1 0.69491525,5.3951476 0.69491525,10.816844 c 0,5.421663 4.51644025,9.816844 10.08775875,9.816844 2.381867,0 4.570922,-0.803307 6.296712,-2.14673 0.508475,-0.508475 4.514633,4.192839 4.514633,4.192839 1.036377,1.008544 2.113087,-0.02559 1.07671,-1.034139 z m -7.780091,1.925408 c -4.3394583,0 -8.6708434,-4.033489 -8.6708434,-8.256407 0,-4.2229187 4.3313851,-8.2564401 8.6708434,-8.2564401 4.339458,0 8.670809,4.2369112 8.670809,8.4598301 0,4.222918 -4.331351,8.053017 -8.670809,8.053017 z' fill='currentColor' fill-rule='evenodd' clip-rule='evenodd' fill-opacity='1' stroke-width='1.10519' stroke-dasharray='none' /%3E%3Cpath d='m 13.337351,9.3402647 0.05184,2.1532893' stroke='%231c274c' stroke-width='2' stroke-linecap='round' /%3E%3Cpath d='M 8.431347,9.2809457 8.483191,11.434235' stroke='%231c274c' stroke-width='2' stroke-linecap='round' /%3E%3C/svg%3E%0A");
- }
+}
 
 .khoj-chat p {
     margin: 0;
 }
+
 .khoj-chat pre {
     text-wrap: unset;
 }
@@ -33,7 +34,8 @@ If your plugin does not need CSS, delete this file.
     font-weight: 300;
     line-height: 1.5em;
 }
-.khoj-chat > * {
+
+.khoj-chat>* {
     padding: 10px;
     margin: 10px;
 }
@@ -47,8 +49,10 @@ If your plugin does not need CSS, delete this file.
     font-size: var(--font-ui-medium);
     margin: 0px;
     line-height: 20px;
-    overflow-y: scroll; /* Make chat body scroll to see history */
+    overflow-y: scroll;
+    /* Make chat body scroll to see history */
 }
+
 /* add chat metatdata to bottom of bubble */
 .khoj-chat-message.khoj::after {
     content: attr(data-meta);
@@ -57,16 +61,19 @@ If your plugin does not need CSS, delete this file.
     color: var(--text-muted);
     margin: -12px 7px 0 0px;
 }
+
 /* move message by khoj to left */
 .khoj-chat-message.khoj {
     margin-left: auto;
     text-align: left;
 }
+
 /* move message by you to right */
 .khoj-chat-message.you {
     margin-right: auto;
     text-align: right;
 }
+
 /* basic style chat message text */
 .khoj-chat-message-text {
     margin: 10px;
@@ -80,6 +87,7 @@ If your plugin does not need CSS, delete this file.
     background-color: var(--active-bg);
     word-break: break-word;
 }
+
 /* color chat bubble by khoj blue */
 .khoj-chat-message-text.khoj {
     border-left: 2px solid var(--khoj-sun);
@@ -87,12 +95,14 @@ If your plugin does not need CSS, delete this file.
     margin-left: auto;
     white-space: pre-line;
 }
+
 /* Override white-space for ul, ol, li under khoj-chat-message-text.khoj */
 .khoj-chat-message-text.khoj ul,
 .khoj-chat-message-text.khoj ol,
 .khoj-chat-message-text.khoj li {
     white-space: normal;
 }
+
 /* add left protrusion to khoj chat bubble */
 .khoj-chat-message-text.khoj:after {
     content: '';
@@ -103,12 +113,14 @@ If your plugin does not need CSS, delete this file.
     border-bottom: 0;
     transform: rotate(-60deg);
 }
+
 /* color chat bubble by you dark grey */
 .khoj-chat-message-text.you {
     color: var(--text-normal);
     margin-right: auto;
     background-color: var(--background-modifier-cover);
 }
+
 /* add right protrusion to you chat bubble */
 .khoj-chat-message-text.you:after {
     content: '';
@@ -125,6 +137,7 @@ If your plugin does not need CSS, delete this file.
 .khoj-chat-message-text ol {
     margin: 0px 0 0;
 }
+
 .khoj-chat-message-text ol li {
     white-space: normal;
 }
@@ -146,9 +159,11 @@ code.chat-response {
 div.collapsed {
     display: none;
 }
+
 div.expanded {
     display: block;
 }
+
 div.reference {
     display: grid;
     grid-template-rows: auto;
@@ -157,6 +172,7 @@ div.reference {
     grid-row-gap: 10px;
     margin: 10px;
 }
+
 div.expanded.reference-section {
     display: grid;
     grid-template-rows: auto;
@@ -165,6 +181,7 @@ div.expanded.reference-section {
     grid-row-gap: 10px;
     margin: 10px 0;
 }
+
 button.reference-button {
     border: 1px solid var(--khoj-storm-grey);
     background-color: transparent;
@@ -183,15 +200,18 @@ button.reference-button {
     display: inline-block;
     text-wrap: inherit;
 }
+
 button.reference-button.expanded {
     height: auto;
     max-height: none;
     white-space: pre-wrap;
 }
-button.reference-button.expanded > :nth-child(2) {
+
+button.reference-button.expanded> :nth-child(2) {
     display: block;
 }
-button.reference-button.collapsed > :nth-child(2) {
+
+button.reference-button.collapsed> :nth-child(2) {
     display: none;
 }
 
@@ -201,11 +221,13 @@ button.reference-button::before {
     display: inline-block;
     transition: transform 0.1s ease-in-out;
 }
+
 button.reference-button.expanded::before,
 button.reference-button:active:before,
 button.reference-button[aria-expanded="true"]::before {
     transform: rotate(90deg);
 }
+
 button.reference-expand-button {
     background-color: transparent;
     border: 1px solid var(--khoj-storm-grey);
@@ -219,15 +241,18 @@ button.reference-expand-button {
     transition: background 0.2s ease-in-out;
     text-align: left;
 }
+
 button.reference-expand-button:hover {
     background: var(--background-modifier-active-hover);
     color: var(--text-normal);
 }
+
 a.inline-chat-link {
     color: #475569;
     text-decoration: none;
     border-bottom: 1px dotted #475569;
 }
+
 .reference-link {
     color: var(--khoj-storm-grey);
     border-bottom: 1px dotted var(--khoj-storm-grey);
@@ -247,11 +272,13 @@ div.new-conversation {
     z-index: 10;
     background-color: var(--background-primary)
 }
+
 div.conversation-header-title {
     text-align: left;
     font-size: larger;
     line-height: 1.5em;
 }
+
 div.conversation-session {
     color: var(--color-base-90);
     border: 1px solid var(--khoj-storm-grey);
@@ -298,9 +325,11 @@ div.conversation-menu {
     grid-gap: 4px;
     grid-auto-flow: column;
 }
+
 div.conversation-session:hover {
     transform: scale(1.03);
 }
+
 div.selected-conversation {
     background: var(--background-modifier-active-hover) !important;
 }
@@ -312,6 +341,7 @@ div.selected-conversation {
     grid-column-gap: 10px;
     grid-row-gap: 10px;
 }
+
 .khoj-input-row {
     display: grid;
     grid-template-columns: 32px auto 32px 32px;
@@ -324,9 +354,11 @@ div.selected-conversation {
     bottom: 0;
     z-index: 10;
 }
+
 #khoj-chat-input.option:hover {
     box-shadow: 0 0 11px var(--background-modifier-box-shadow);
 }
+
 #khoj-chat-input {
     font-size: var(--font-ui-medium);
     padding: 4px 0 0 12px;
@@ -334,6 +366,7 @@ div.selected-conversation {
     height: 32px;
     resize: none;
 }
+
 .khoj-input-row-button {
     border-radius: 50%;
     padding: 4px;
@@ -346,43 +379,55 @@ div.selected-conversation {
     padding: 0;
     position: relative;
 }
+
 #khoj-chat-send .lucide-arrow-up-circle {
     background: var(--background-modifier-active-hover);
     border-radius: 50%;
 }
+
 #khoj-chat-send .lucide-stop-circle {
     transform: rotateY(-180deg) rotateZ(-90deg);
 }
+
 #khoj-chat-send .lucide-stop-circle circle {
-    stroke-dasharray: 62px;  /* The circumference of the circle with 7px radius */
+    stroke-dasharray: 62px;
+    /* The circumference of the circle with 7px radius */
     stroke-dashoffset: 0px;
     stroke-linecap: round;
     stroke-width: 2px;
     stroke: var(--main-text-color);
     fill: none;
 }
+
 @keyframes countdown {
     from {
         stroke-dashoffset: 0px;
     }
+
     to {
-        stroke-dashoffset: -62px;  /* The circumference of the circle with 7px radius */
+        stroke-dashoffset: -62px;
+        /* The circumference of the circle with 7px radius */
     }
 }
 
-@media (pointer: coarse), (hover: none) {
+@media (pointer: coarse),
+(hover: none) {
     #khoj-chat-body.abbr[title] {
         position: relative;
-        padding-left: 4px;  /* space references out to ease tapping */
+        padding-left: 4px;
+        /* space references out to ease tapping */
     }
+
     #khoj-chat-body.abbr[title]:focus:after {
         content: attr(title);
 
         /* position tooltip */
         position: absolute;
-        left: 16px;  /* open tooltip to right of ref link, instead of on top of it */
+        left: 16px;
+        /* open tooltip to right of ref link, instead of on top of it */
         width: auto;
-        z-index: 1;  /* show tooltip above chat messages */
+        z-index: 1;
+        /* show tooltip above chat messages */
 
         /* style tooltip */
         background-color: var(--background-secondary);
@@ -410,11 +455,11 @@ div.selected-conversation {
     white-space: normal;
 }
 
-.khoj-result-entry > * {
+.khoj-result-entry>* {
     font-size: var(--font-ui-medium);
 }
 
-.khoj-result-entry > p {
+.khoj-result-entry>p {
     margin-top: 0.2em;
     margin-bottom: 0.2em;
 }
@@ -440,9 +485,11 @@ div.khoj-header {
 a.khoj-nav {
     -webkit-app-region: no-drag;
 }
+
 div.khoj-nav {
     -webkit-app-region: no-drag;
 }
+
 nav.khoj-nav {
     display: grid;
     grid-auto-flow: column;
@@ -470,24 +517,30 @@ div.khoj-logo {
     justify-self: center;
     margin: 0;
 }
+
 .khoj-nav a:hover {
     background-color: var(--background-modifier-active-hover);
     color: var(--main-text-color);
 }
+
 a.khoj-nav-selected {
     background-color: var(--background-modifier-active-hover);
 }
+
 #similar-nav-icon-svg,
 .khoj-nav-icon {
     width: 24px;
     height: 24px;
 }
+
 .khoj-nav-icon-chat {
     background-image: var(--chat-icon);
 }
+
 .khoj-nav-icon-search {
     background-image: var(--search-icon);
 }
+
 span.khoj-nav-item-text {
     padding-left: 8px;
 }
@@ -507,12 +560,14 @@ button.chat-action-button {
     margin-top: 8px;
     float: right;
 }
+
 button.chat-action-button span {
     cursor: pointer;
     display: inline-block;
     position: relative;
     transition: 0.5s;
 }
+
 button.chat-action-button:hover {
     background-color: var(--background-modifier-active-hover);
     color: var(--text-normal);
@@ -534,6 +589,7 @@ img.copy-icon {
     box-sizing: border-box;
     animation: rotation 1s linear infinite;
 }
+
 .loader::after {
     content: '';
     box-sizing: border-box;
@@ -552,6 +608,7 @@ img.copy-icon {
     0% {
         transform: rotate(0deg);
     }
+
     100% {
         transform: rotate(360deg);
     }
@@ -564,6 +621,7 @@ img.copy-icon {
     width: 60px;
     height: 32px;
 }
+
 .lds-ellipsis div {
     position: absolute;
     top: 12px;
@@ -573,42 +631,52 @@ img.copy-icon {
     background: var(--color-base-70);
     animation-timing-function: cubic-bezier(0, 1, 1, 0);
 }
+
 .lds-ellipsis div:nth-child(1) {
     left: 8px;
     animation: lds-ellipsis1 0.6s infinite;
 }
+
 .lds-ellipsis div:nth-child(2) {
     left: 8px;
     animation: lds-ellipsis2 0.6s infinite;
 }
+
 .lds-ellipsis div:nth-child(3) {
     left: 32px;
     animation: lds-ellipsis2 0.6s infinite;
 }
+
 .lds-ellipsis div:nth-child(4) {
     left: 56px;
     animation: lds-ellipsis3 0.6s infinite;
 }
+
 @keyframes lds-ellipsis1 {
     0% {
         transform: scale(0);
     }
+
     100% {
         transform: scale(1);
     }
 }
+
 @keyframes lds-ellipsis3 {
     0% {
         transform: scale(1);
     }
+
     100% {
         transform: scale(0);
     }
 }
+
 @keyframes lds-ellipsis2 {
     0% {
         transform: translate(0, 0);
     }
+
     100% {
         transform: translate(24px, 0);
     }
@@ -633,15 +701,18 @@ img.copy-icon {
     border-radius: 50%;
     animation: pulse 3s ease-in-out infinite;
 }
+
 @keyframes pulse {
     0% {
         transform: scale(1);
         opacity: 1;
     }
+
     50% {
         transform: scale(1.2);
         opacity: 0.2;
     }
+
     100% {
         transform: scale(1);
         opacity: 1;
@@ -649,9 +720,15 @@ img.copy-icon {
 }
 
 @keyframes spin {
-    0% { transform: rotate(0deg); }
-    100% { transform: rotate(360deg); }
+    0% {
+        transform: rotate(0deg);
+    }
+
+    100% {
+        transform: rotate(360deg);
+    }
 }
+
 @media only screen and (max-width: 600px) {
     div.khoj-header {
         display: grid;
@@ -665,10 +742,65 @@ img.copy-icon {
         grid-gap: 0px;
         justify-content: space-between;
     }
+
     a.khoj-nav {
         padding: 0 16px;
     }
+
     span.khoj-nav-item-text {
         display: none;
     }
 }
+
+/* Folder list styles */
+.folder-list {
+    list-style: none;
+    padding: 0;
+    margin: 8px 0;
+}
+
+.folder-list-item {
+    display: flex;
+    align-items: center;
+    justify-content: space-between;
+    padding: 6px 12px;
+    margin: 4px 0;
+    background: var(--background-secondary);
+    border-radius: 4px;
+    min-height: 32px;
+}
+
+.folder-list-remove {
+    background: none;
+    border: none;
+    color: #ff5555;
+    cursor: pointer;
+    font-size: 18px;
+    width: 24px;
+    height: 24px;
+    display: flex;
+    align-items: center;
+    justify-content: center;
+    margin-left: 8px;
+    padding: 0;
+    border-radius: 4px;
+    opacity: 0.7;
+    transition: all 0.2s ease;
+}
+
+.folder-list-remove:hover {
+    opacity: 1;
+    background-color: rgba(255, 85, 85, 0.1);
+}
+
+.folder-list-empty {
+    color: var(--text-muted);
+    font-style: italic;
+    padding: 6px 0;
+}
+
+/* Folder suggestion modal styles */
+.folder-suggest-item {
+    padding: 4px 8px;
+    display: block;
+}
\ No newline at end of file

From 7d28b46ca7631be860f5c3b4c25da7c033f9417a Mon Sep 17 00:00:00 2001
From: Henri Jamet <42291955+hjamet@users.noreply.github.com>
Date: Sun, 29 Dec 2024 13:23:08 +0100
Subject: [PATCH 3/5] Implement sync interval setting and enhance
 synchronization timer in Khoj plugin

- Added a new setting for users to configure the sync interval in minutes, allowing for more flexible automatic synchronization.
- Introduced methods to start and restart the synchronization timer based on the configured interval.
- Updated the synchronization logic to use the user-defined interval instead of a fixed 60 minutes.
- Improved code readability and organization by refactoring the sync timer logic.
---
 src/interface/obsidian/src/main.ts     | 32 +++++++++++++++++++++-----
 src/interface/obsidian/src/settings.ts | 24 +++++++++++++++++++
 2 files changed, 50 insertions(+), 6 deletions(-)

diff --git a/src/interface/obsidian/src/main.ts b/src/interface/obsidian/src/main.ts
index f5f80cfc4..bb4eecbd5 100644
--- a/src/interface/obsidian/src/main.ts
+++ b/src/interface/obsidian/src/main.ts
@@ -43,8 +43,8 @@ export default class Khoj extends Plugin {
                     this.app.vault,
                     this.settings,
                     this.settings.lastSync,
-                    false, // regenerate = false pour ne synchroniser que les nouvelles modifications
-                    true  // userTriggered = true pour afficher une notification
+                    false,
+                    true
                 );
             }
         });
@@ -59,12 +59,32 @@ export default class Khoj extends Plugin {
         // Add a settings tab so the user can configure khoj
         this.addSettingTab(new KhojSettingTab(this.app, this));
 
-        // Add scheduled job to update index every 60 minutes
+        // Démarrer le timer de synchronisation
+        this.startSyncTimer();
+    }
+
+    // Méthode pour démarrer le timer de synchronisation
+    private startSyncTimer() {
+        // Nettoyer l'ancien timer s'il existe
+        if (this.indexingTimer) {
+            clearInterval(this.indexingTimer);
+        }
+
+        // Démarrer un nouveau timer avec l'intervalle configuré
         this.indexingTimer = setInterval(async () => {
             if (this.settings.autoConfigure) {
-                this.settings.lastSync = await updateContentIndex(this.app.vault, this.settings, this.settings.lastSync);
+                this.settings.lastSync = await updateContentIndex(
+                    this.app.vault,
+                    this.settings,
+                    this.settings.lastSync
+                );
             }
-        }, 60 * 60 * 1000);
+        }, this.settings.syncInterval * 60 * 1000); // Convertir les minutes en millisecondes
+    }
+
+    // Méthode publique pour redémarrer le timer (appelée depuis les paramètres)
+    public restartSyncTimer() {
+        this.startSyncTimer();
     }
 
     async loadSettings() {
@@ -77,7 +97,7 @@ export default class Khoj extends Plugin {
     }
 
     async saveSettings() {
-        this.saveData(this.settings);
+        await this.saveData(this.settings);
     }
 
     async onunload() {
diff --git a/src/interface/obsidian/src/settings.ts b/src/interface/obsidian/src/settings.ts
index 62467b88a..54dbb812b 100644
--- a/src/interface/obsidian/src/settings.ts
+++ b/src/interface/obsidian/src/settings.ts
@@ -26,6 +26,7 @@ export interface KhojSetting {
     syncFileType: SyncFileTypes;
     userInfo: UserInfo | null;
     syncFolders: string[];
+    syncInterval: number;
 }
 
 export const DEFAULT_SETTINGS: KhojSetting = {
@@ -42,6 +43,7 @@ export const DEFAULT_SETTINGS: KhojSetting = {
     },
     userInfo: null,
     syncFolders: [],
+    syncInterval: 60,
 }
 
 export class KhojSettingTab extends PluginSettingTab {
@@ -158,6 +160,28 @@ export class KhojSettingTab extends PluginSettingTab {
                     await this.plugin.saveSettings();
                 }));
 
+        // Add setting for sync interval
+        const syncIntervalValues = [1, 5, 10, 20, 30, 45, 60, 120, 1440];
+        new Setting(containerEl)
+            .setName('Sync Interval')
+            .setDesc('Minutes between automatic synchronizations')
+            .addDropdown(dropdown => dropdown
+                .addOptions(Object.fromEntries(
+                    syncIntervalValues.map(value => [
+                        value.toString(),
+                        value === 1 ? '1 minute' :
+                            value === 1440 ? '24 hours' :
+                                `${value} minutes`
+                    ])
+                ))
+                .setValue(this.plugin.settings.syncInterval.toString())
+                .onChange(async (value) => {
+                    this.plugin.settings.syncInterval = parseInt(value);
+                    await this.plugin.saveSettings();
+                    // Redémarrer le timer avec le nouvel intervalle
+                    this.plugin.restartSyncTimer();
+                }));
+
         // Add setting to manage sync folders
         const syncFoldersContainer = containerEl.createDiv('sync-folders-container');
         const foldersSetting = new Setting(syncFoldersContainer)

From 1aff78a969deb83a70232bc3352c02c24ae45c1b Mon Sep 17 00:00:00 2001
From: Henri Jamet <42291955+hjamet@users.noreply.github.com>
Date: Sun, 29 Dec 2024 16:19:42 +0100
Subject: [PATCH 4/5] Enhance Khoj plugin search functionality and loading
 indicators

- Added visual loading indicators to the search modal for improved user experience during search operations.
- Implemented logic to check if search results correspond to files in the vault, with color-coded results for better clarity.
- Refactored the getSuggestions method to handle loading states and abort previous requests if necessary.
- Updated CSS styles to support new loading animations and result file status indicators.
- Improved the renderSuggestion method to display file status and provide feedback for files not in the vault.
---
 src/interface/obsidian/src/search_modal.ts | 164 ++++++++++++++++++---
 src/interface/obsidian/styles.css          |  55 +++++++
 2 files changed, 195 insertions(+), 24 deletions(-)

diff --git a/src/interface/obsidian/src/search_modal.ts b/src/interface/obsidian/src/search_modal.ts
index 60b4accbc..0e1093ed9 100644
--- a/src/interface/obsidian/src/search_modal.ts
+++ b/src/interface/obsidian/src/search_modal.ts
@@ -1,4 +1,4 @@
-import { App, SuggestModal, request, MarkdownRenderer, Instruction, Platform } from 'obsidian';
+import { App, SuggestModal, request, MarkdownRenderer, Instruction, Platform, Notice } from 'obsidian';
 import { KhojSetting } from 'src/settings';
 import { supportedBinaryFileTypes, createNoteAndCloseModal, getFileFromPath, getLinkToEntry, supportedImageFilesTypes } from 'src/utils';
 
@@ -13,6 +13,9 @@ export class KhojSearchModal extends SuggestModal<SearchResult> {
     find_similar_notes: boolean;
     query: string = "";
     app: App;
+    currentController: AbortController | null = null;  // Pour annuler les requêtes
+    isLoading: boolean = false;
+    loadingEl: HTMLElement;
 
     constructor(app: App, setting: KhojSetting, find_similar_notes: boolean = false) {
         super(app);
@@ -23,6 +26,24 @@ export class KhojSearchModal extends SuggestModal<SearchResult> {
         // Hide input element in Similar Notes mode
         this.inputEl.hidden = this.find_similar_notes;
 
+        // Create loading element
+        this.loadingEl = createDiv({ cls: "search-loading" });
+        const spinnerEl = this.loadingEl.createDiv({ cls: "search-loading-spinner" });
+
+        this.loadingEl.style.position = "absolute";
+        this.loadingEl.style.top = "50%";
+        this.loadingEl.style.left = "50%";
+        this.loadingEl.style.transform = "translate(-50%, -50%)";
+        this.loadingEl.style.zIndex = "1000";
+        this.loadingEl.style.display = "none";
+
+        // Ajouter l'élément au modal
+        this.modalEl.appendChild(this.loadingEl);
+
+        // Customize empty state message
+        // @ts-ignore - Accès à la propriété privée pour personnaliser le message
+        this.emptyStateText = "";
+
         // Register Modal Keybindings to Rerank Results
         this.scope.register(['Mod'], 'Enter', async () => {
             // Re-rank when explicitly triggered by user
@@ -66,6 +87,101 @@ export class KhojSearchModal extends SuggestModal<SearchResult> {
         this.setPlaceholder('Search with Khoj...');
     }
 
+    // Check if the file exists in the vault
+    private isFileInVault(filePath: string): boolean {
+        // Normalize the path to handle different separators
+        const normalizedPath = filePath.replace(/\\/g, '/');
+
+        // Check if the file exists in the vault
+        return this.app.vault.getFiles().some(file =>
+            file.path === normalizedPath
+        );
+    }
+
+    async getSuggestions(query: string): Promise<SearchResult[]> {
+        // Ne pas afficher le chargement si la requête est vide
+        if (!query.trim()) {
+            this.isLoading = false;
+            this.updateLoadingState();
+            return [];
+        }
+
+        // Show loading state
+        this.isLoading = true;
+        this.updateLoadingState();
+
+        // Cancel previous request if it exists
+        if (this.currentController) {
+            this.currentController.abort();
+        }
+
+        try {
+            // Create a new controller for this request
+            this.currentController = new AbortController();
+
+            // Setup Query Khoj backend for search results
+            let encodedQuery = encodeURIComponent(query);
+            let searchUrl = `${this.setting.khojUrl}/api/search?q=${encodedQuery}&n=${this.setting.resultsCount}&r=${this.rerank}&client=obsidian`;
+            let headers = {
+                'Authorization': `Bearer ${this.setting.khojApiKey}`,
+            }
+
+            // Get search results from Khoj backend
+            const response = await fetch(searchUrl, {
+                headers: headers,
+                signal: this.currentController.signal
+            });
+
+            if (!response.ok) {
+                throw new Error(`HTTP error! status: ${response.status}`);
+            }
+
+            const data = await response.json();
+
+            // Parse search results
+            let results = data
+                .filter((result: any) =>
+                    !this.find_similar_notes || !result.additional.file.endsWith(this.app.workspace.getActiveFile()?.path)
+                )
+                .map((result: any) => {
+                    return {
+                        entry: result.entry,
+                        file: result.additional.file,
+                        inVault: this.isFileInVault(result.additional.file)
+                    } as SearchResult & { inVault: boolean };
+                })
+                .sort((a: SearchResult & { inVault: boolean }, b: SearchResult & { inVault: boolean }) => {
+                    if (a.inVault === b.inVault) return 0;
+                    return a.inVault ? -1 : 1;
+                });
+
+            this.query = query;
+
+            // Hide loading state only on successful completion
+            this.isLoading = false;
+            this.updateLoadingState();
+
+            return results;
+        } catch (error) {
+            // Ignore cancellation errors and keep loading state
+            if (error.name === 'AbortError') {
+                // When cancelling, we don't want to render anything
+                return undefined as any;
+            }
+
+            // For other errors, hide loading state
+            console.error('Search error:', error);
+            this.isLoading = false;
+            this.updateLoadingState();
+            return [];
+        }
+    }
+
+    private updateLoadingState() {
+        // Show or hide loading element
+        this.loadingEl.style.display = this.isLoading ? "block" : "none";
+    }
+
     async onOpen() {
         if (this.find_similar_notes) {
             // If markdown file is currently active
@@ -86,25 +202,7 @@ export class KhojSearchModal extends SuggestModal<SearchResult> {
         }
     }
 
-    async getSuggestions(query: string): Promise<SearchResult[]> {
-        // Setup Query Khoj backend for search results
-        let encodedQuery = encodeURIComponent(query);
-        let searchUrl = `${this.setting.khojUrl}/api/search?q=${encodedQuery}&n=${this.setting.resultsCount}&r=${this.rerank}&client=obsidian`;
-        let headers = { 'Authorization': `Bearer ${this.setting.khojApiKey}` }
-
-        // Get search results from Khoj backend
-        let response = await request({ url: `${searchUrl}`, headers: headers });
-
-        // Parse search results
-        let results = JSON.parse(response)
-            .filter((result: any) => !this.find_similar_notes || !result.additional.file.endsWith(this.app.workspace.getActiveFile()?.path))
-            .map((result: any) => { return { entry: result.entry, file: result.additional.file } as SearchResult; });
-
-        this.query = query;
-        return results;
-    }
-
-    async renderSuggestion(result: SearchResult, el: HTMLElement) {
+    async renderSuggestion(result: SearchResult & { inVault: boolean }, el: HTMLElement) {
         // Max number of lines to render
         let lines_to_render = 8;
 
@@ -112,13 +210,25 @@ export class KhojSearchModal extends SuggestModal<SearchResult> {
         let os_path_separator = result.file.includes('\\') ? '\\' : '/';
         let filename = result.file.split(os_path_separator).pop();
 
-        // Show filename of each search result for context
-        el.createEl("div",{ cls: 'khoj-result-file' }).setText(filename ?? "");
+        // Show filename of each search result for context with appropriate color
+        const fileEl = el.createEl("div", {
+            cls: `khoj-result-file ${result.inVault ? 'in-vault' : 'not-in-vault'}`
+        });
+        fileEl.setText(filename ?? "");
+
+        // Add a visual indication for files not in vault
+        if (!result.inVault) {
+            fileEl.createSpan({
+                text: " (not in vault)",
+                cls: "khoj-result-file-status"
+            });
+        }
+
         let result_el = el.createEl("div", { cls: 'khoj-result-entry' })
 
         let resultToRender = "";
         let fileExtension = filename?.split(".").pop() ?? "";
-        if (supportedImageFilesTypes.includes(fileExtension) && filename) {
+        if (supportedImageFilesTypes.includes(fileExtension) && filename && result.inVault) {
             let linkToEntry: string = filename;
             let imageFiles = this.app.vault.getFiles().filter(file => supportedImageFilesTypes.includes(fileExtension));
             // Find vault file of chosen search result
@@ -140,7 +250,13 @@ export class KhojSearchModal extends SuggestModal<SearchResult> {
         MarkdownRenderer.renderMarkdown(resultToRender, result_el, result.file, null);
     }
 
-    async onChooseSuggestion(result: SearchResult, _: MouseEvent | KeyboardEvent) {
+    async onChooseSuggestion(result: SearchResult & { inVault: boolean }, _: MouseEvent | KeyboardEvent) {
+        // Only open files that are in the vault
+        if (!result.inVault) {
+            new Notice("This file is not in your vault");
+            return;
+        }
+
         // Get all markdown, pdf and image files in vault
         const mdFiles = this.app.vault.getMarkdownFiles();
         const binaryFiles = this.app.vault.getFiles().filter(file => supportedBinaryFileTypes.includes(file.extension));
diff --git a/src/interface/obsidian/styles.css b/src/interface/obsidian/styles.css
index 35573b0c4..728c064f9 100644
--- a/src/interface/obsidian/styles.css
+++ b/src/interface/obsidian/styles.css
@@ -443,6 +443,14 @@ div.selected-conversation {
     font-weight: 600;
 }
 
+.khoj-result-file.in-vault {
+    color: var(--color-green);
+}
+
+.khoj-result-file.not-in-vault {
+    color: var(--color-blue);
+}
+
 .khoj-result-entry {
     color: var(--text-muted);
     margin-left: 2em;
@@ -803,4 +811,51 @@ img.copy-icon {
 .folder-suggest-item {
     padding: 4px 8px;
     display: block;
+}
+
+/* Animation de chargement */
+.khoj-loading {
+    display: flex;
+    justify-content: center;
+    align-items: center;
+    padding: 20px;
+}
+
+.khoj-loading-spinner {
+    width: 24px;
+    height: 24px;
+    border: 3px solid var(--background-modifier-border);
+    border-top: 3px solid var(--text-accent);
+    border-radius: 50%;
+    animation: khoj-spin 1s linear infinite;
+}
+
+@keyframes khoj-spin {
+    0% {
+        transform: rotate(0deg);
+    }
+
+    100% {
+        transform: rotate(360deg);
+    }
+}
+
+/* Research Spinner */
+.search-loading-spinner {
+    width: 24px;
+    height: 24px;
+    border: 3px solid var(--background-modifier-border);
+    border-top: 3px solid var(--text-accent);
+    border-radius: 50%;
+    animation: search-spin 0.8s linear infinite;
+}
+
+@keyframes search-spin {
+    0% {
+        transform: rotate(0deg);
+    }
+
+    100% {
+        transform: rotate(360deg);
+    }
 }
\ No newline at end of file

From f42b0cb08c425c7d67a7d99e13ac433ffc096853 Mon Sep 17 00:00:00 2001
From: Henri Jamet <henri.jamet@unil.ch>
Date: Wed, 8 Jan 2025 09:31:43 +0100
Subject: [PATCH 5/5] Refactor comments and CSS for improved clarity in Khoj
 plugin

- Translated comments from French to English for better accessibility and understanding.
- Updated CSS comment for loading animation to reflect the change in language.
- Enhanced code readability by ensuring consistent language usage across multiple files.
- Improved user experience by clarifying the purpose of various functions and settings in the codebase.
---
 src/interface/obsidian/src/main.ts         | 12 ++++++------
 src/interface/obsidian/src/search_modal.ts |  8 ++++----
 src/interface/obsidian/src/settings.ts     |  6 +++---
 src/interface/obsidian/src/utils.ts        |  4 ++--
 src/interface/obsidian/styles.css          |  2 +-
 5 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/src/interface/obsidian/src/main.ts b/src/interface/obsidian/src/main.ts
index bb4eecbd5..a75d6040c 100644
--- a/src/interface/obsidian/src/main.ts
+++ b/src/interface/obsidian/src/main.ts
@@ -59,18 +59,18 @@ export default class Khoj extends Plugin {
         // Add a settings tab so the user can configure khoj
         this.addSettingTab(new KhojSettingTab(this.app, this));
 
-        // Démarrer le timer de synchronisation
+        // Start the sync timer
         this.startSyncTimer();
     }
 
-    // Méthode pour démarrer le timer de synchronisation
+    // Method to start the sync timer
     private startSyncTimer() {
-        // Nettoyer l'ancien timer s'il existe
+        // Clean up the old timer if it exists
         if (this.indexingTimer) {
             clearInterval(this.indexingTimer);
         }
 
-        // Démarrer un nouveau timer avec l'intervalle configuré
+        // Start a new timer with the configured interval
         this.indexingTimer = setInterval(async () => {
             if (this.settings.autoConfigure) {
                 this.settings.lastSync = await updateContentIndex(
@@ -79,10 +79,10 @@ export default class Khoj extends Plugin {
                     this.settings.lastSync
                 );
             }
-        }, this.settings.syncInterval * 60 * 1000); // Convertir les minutes en millisecondes
+        }, this.settings.syncInterval * 60 * 1000); // Convert minutes to milliseconds
     }
 
-    // Méthode publique pour redémarrer le timer (appelée depuis les paramètres)
+    // Public method to restart the timer (called from settings)
     public restartSyncTimer() {
         this.startSyncTimer();
     }
diff --git a/src/interface/obsidian/src/search_modal.ts b/src/interface/obsidian/src/search_modal.ts
index 0e1093ed9..fdf727016 100644
--- a/src/interface/obsidian/src/search_modal.ts
+++ b/src/interface/obsidian/src/search_modal.ts
@@ -13,7 +13,7 @@ export class KhojSearchModal extends SuggestModal<SearchResult> {
     find_similar_notes: boolean;
     query: string = "";
     app: App;
-    currentController: AbortController | null = null;  // Pour annuler les requêtes
+    currentController: AbortController | null = null;  // To cancel requests
     isLoading: boolean = false;
     loadingEl: HTMLElement;
 
@@ -37,11 +37,11 @@ export class KhojSearchModal extends SuggestModal<SearchResult> {
         this.loadingEl.style.zIndex = "1000";
         this.loadingEl.style.display = "none";
 
-        // Ajouter l'élément au modal
+        // Add the element to the modal
         this.modalEl.appendChild(this.loadingEl);
 
         // Customize empty state message
-        // @ts-ignore - Accès à la propriété privée pour personnaliser le message
+        // @ts-ignore - Access to private property to customize the message
         this.emptyStateText = "";
 
         // Register Modal Keybindings to Rerank Results
@@ -99,7 +99,7 @@ export class KhojSearchModal extends SuggestModal<SearchResult> {
     }
 
     async getSuggestions(query: string): Promise<SearchResult[]> {
-        // Ne pas afficher le chargement si la requête est vide
+        // Do not show loading if the query is empty
         if (!query.trim()) {
             this.isLoading = false;
             this.updateLoadingState();
diff --git a/src/interface/obsidian/src/settings.ts b/src/interface/obsidian/src/settings.ts
index 54dbb812b..15bc5b01c 100644
--- a/src/interface/obsidian/src/settings.ts
+++ b/src/interface/obsidian/src/settings.ts
@@ -178,7 +178,7 @@ export class KhojSettingTab extends PluginSettingTab {
                 .onChange(async (value) => {
                     this.plugin.settings.syncInterval = parseInt(value);
                     await this.plugin.saveSettings();
-                    // Redémarrer le timer avec le nouvel intervalle
+                    // Restart the timer with the new interval
                     this.plugin.restartSyncTimer();
                 }));
 
@@ -311,13 +311,13 @@ class FolderSuggestModal extends SuggestModal<string> {
         const folders = new Set<string>();
         folders.add(''); // Root folder
 
-        // Récupérer tous les fichiers et extraire les chemins des dossiers
+        // Get all files and extract folder paths
         this.app.vault.getAllLoadedFiles().forEach(file => {
             const folderPath = file.parent?.path;
             if (folderPath) {
                 folders.add(folderPath);
 
-                // Ajouter aussi tous les dossiers parents
+                // Also add all parent folders
                 let parent = folderPath;
                 while (parent.includes('/')) {
                     parent = parent.substring(0, parent.lastIndexOf('/'));
diff --git a/src/interface/obsidian/src/utils.ts b/src/interface/obsidian/src/utils.ts
index b0dbf61f6..27903af4c 100644
--- a/src/interface/obsidian/src/utils.ts
+++ b/src/interface/obsidian/src/utils.ts
@@ -74,9 +74,9 @@ export async function updateContentIndex(vault: Vault, setting: KhojSetting, las
         })
         // Filter files based on specified folders
         .filter(file => {
-            // Si aucun dossier n'est spécifié, synchroniser tous les fichiers
+            // If no folders are specified, sync all files
             if (setting.syncFolders.length === 0) return true;
-            // Sinon, vérifier si le fichier est dans un des dossiers spécifiés
+            // Otherwise, check if the file is in one of the specified folders
             return setting.syncFolders.some(folder =>
                 file.path.startsWith(folder + '/') || file.path === folder
             );
diff --git a/src/interface/obsidian/styles.css b/src/interface/obsidian/styles.css
index 728c064f9..23113c906 100644
--- a/src/interface/obsidian/styles.css
+++ b/src/interface/obsidian/styles.css
@@ -813,7 +813,7 @@ img.copy-icon {
     display: block;
 }
 
-/* Animation de chargement */
+/* Loading animation */
 .khoj-loading {
     display: flex;
     justify-content: center;