Fix and improve file read, write handling in Obsidian

Fixes
- Fix to allow khoj to delete content in obsidian write mode
- Do not throw error when no edit blocks in write mode on obsidian
- Limit retries to fix invalid edit blocks in obsidian write mode

Improvements
- Only show 3 recent files as context in obsidian file read, write mode
- Persist open file access mode setting across restarts in obsidian
- Make khoj obsidian keyboard shortcuts toggle voice chat, chat history
- Do not show <SYSTEM> instructions in chat session title on obsidian

Closes #1209

src/interface/obsidian/src/chat_view.ts

@@ -1,9 +1,9 @@
 import { ItemView, MarkdownRenderer, Scope, WorkspaceLeaf, request, requestUrl, setIcon, Platform, TFile } from 'obsidian';
 import * as DOMPurify from 'isomorphic-dompurify';
-import { KhojSetting } from 'src/settings';
 import { KhojPaneView } from 'src/pane_view';
 import { KhojView, createCopyParentText, getLinkToEntry, pasteTextAtCursor } from 'src/utils';
 import { KhojSearchModal } from 'src/search_modal';
+import Khoj from 'src/main';
 import { FileInteractions, EditBlock } from 'src/interact_with_files';
 
 export interface ChatJsonResult {
@@ -67,12 +67,12 @@ interface Agent {
 
 export class KhojChatView extends KhojPaneView {
     result: string;
-    setting: KhojSetting;
     waitingForLocation: boolean;
     location: Location = { timezone: Intl.DateTimeFormat().resolvedOptions().timeZone };
     keyPressTimeout: NodeJS.Timeout | null = null;
     userMessages: string[] = [];  // Store user sent messages for input history cycling
     currentMessageIndex: number = -1;  // Track current message index in userMessages array
+    voiceChatActive: boolean = false; // Flag to track if voice chat is active
     private currentUserInput: string = ""; // Stores the current user input that is being typed in chat
     private startingMessage: string = this.getLearningMoment();
     chatMessageState: ChatMessageState;
@@ -101,10 +101,13 @@ export class KhojChatView extends KhojPaneView {
     // 2. Higher invalid edit blocks than tolerable
     private maxEditRetries: number = 1; // Maximum retries for edit blocks
 
-    constructor(leaf: WorkspaceLeaf, setting: KhojSetting) {
+    constructor(leaf: WorkspaceLeaf, plugin: Khoj) {
-        super(leaf, setting);
+        super(leaf, plugin);
         this.fileInteractions = new FileInteractions(this.app);
 
+        // Initialize file access mode from persisted settings
+        this.fileAccessMode = this.setting.fileAccessMode ?? 'read';
+
         this.waitingForLocation = true;
 
         fetch("https://ipapi.co/json")
@@ -129,7 +132,7 @@ export class KhojChatView extends KhojPaneView {
         this.scope = new Scope(this.app.scope);
         this.scope.register(["Ctrl", "Alt"], 'n', (_) => this.createNewConversation(this.currentAgent));
         this.scope.register(["Ctrl", "Alt"], 'o', async (_) => await this.toggleChatSessions());
-        this.scope.register(["Ctrl", "Alt"], 'v', (_) => this.speechToText(new KeyboardEvent('keydown')));
+        this.scope.register(["Ctrl", "Alt"], 'v', (_) => this.speechToText(this.voiceChatActive ? new KeyboardEvent('keyup') : new KeyboardEvent('keydown')));
         this.scope.register(["Ctrl"], 'f', (_) => new KhojSearchModal(this.app, this.setting).open());
         this.scope.register(["Ctrl"], 'r', (_) => { this.activateView(KhojView.SIMILAR); });
     }
@@ -272,29 +275,48 @@ export class KhojChatView extends KhojPaneView {
             text: "File Access",
             attr: {
                 class: "khoj-input-row-button clickable-icon",
-                title: "Toggle file access mode (Read Only)",
+                title: "Toggle open file access",
             },
         });
+        // Set initial icon based on persisted setting
+        switch (this.fileAccessMode) {
+            case 'none':
+                setIcon(fileAccessButton, "file-x");
+                fileAccessButton.title = "Toggle open file access (No Access)";
+                break;
+            case 'write':
+                setIcon(fileAccessButton, "file-edit");
+                fileAccessButton.title = "Toggle open file access (Read & Write)";
+                break;
+            case 'read':
+            default:
                 setIcon(fileAccessButton, "file-search");
-        fileAccessButton.addEventListener('click', () => {
+                fileAccessButton.title = "Toggle open file access (Read Only)";
+                break;
+        }
+        fileAccessButton.addEventListener('click', async () => {
             // Cycle through modes: none -> read -> write -> none
             switch (this.fileAccessMode) {
                 case 'none':
                     this.fileAccessMode = 'read';
                     setIcon(fileAccessButton, "file-search");
-                    fileAccessButton.title = "Toggle file access mode (Read Only)";
+                    fileAccessButton.title = "Toggle open file access (Read Only)";
                     break;
                 case 'read':
                     this.fileAccessMode = 'write';
                     setIcon(fileAccessButton, "file-edit");
-                    fileAccessButton.title = "Toggle file access mode (Read & Write)";
+                    fileAccessButton.title = "Toggle open file access (Read & Write)";
                     break;
                 case 'write':
                     this.fileAccessMode = 'none';
                     setIcon(fileAccessButton, "file-x");
-                    fileAccessButton.title = "Toggle file access mode (No Access)";
+                    fileAccessButton.title = "Toggle open file access (No Access)";
                     break;
             }
+
+            // Persist the updated mode to settings
+            this.setting.fileAccessMode = this.fileAccessMode;
+            await this.plugin.saveSettings();
         });
 
         let chatInput = inputRow.createEl("textarea", {
@@ -319,7 +341,7 @@ export class KhojChatView extends KhojPaneView {
             attr: {
                 id: "khoj-transcribe",
                 class: "khoj-transcribe khoj-input-row-button clickable-icon ",
-                title: "Start Voice Chat (Ctrl+Alt+V)",
+                title: "Hold to Voice Chat (Ctrl+Alt+V)",
             },
         })
         transcribe.addEventListener('mousedown', (event) => { this.startSpeechToText(event) });
@@ -1037,7 +1059,7 @@ export class KhojChatView extends KhojPaneView {
                     if (incomingConversationId == conversationId) {
                         conversationSessionEl.classList.add("selected-conversation");
                     }
-                    const conversationTitle = conversation["slug"] || `New conversation 🌱`;
+                    const conversationTitle = conversation["slug"].split("<SYSTEM>")[0].trim() || `New conversation 🌱`;
                     const conversationSessionTitleEl = conversationSessionEl.createDiv("conversation-session-title");
                     conversationSessionTitleEl.textContent = conversationTitle;
                     conversationSessionTitleEl.addEventListener('click', () => {
@@ -1190,7 +1212,7 @@ export class KhojChatView extends KhojPaneView {
             chatUrl += `&conversation_id=${chatBodyEl.dataset.conversationId}`;
         }
 
-        console.log("Fetching chat history from:", chatUrl);
+        console.debug("Fetching chat history from:", chatUrl);
 
         try {
             let response = await fetch(chatUrl, {
@@ -1199,7 +1221,7 @@ export class KhojChatView extends KhojPaneView {
             });
 
             let responseJson: any = await response.json();
-            console.log("Chat history response:", responseJson);
+            console.debug("Chat history response:", responseJson);
 
             chatBodyEl.dataset.conversationId = responseJson.conversation_id;
 
@@ -1221,7 +1243,7 @@ export class KhojChatView extends KhojPaneView {
 
                 // Update current agent from conversation history
                 if (responseJson.response.agent?.slug) {
-                    console.log("Found agent in conversation history:", responseJson.response.agent);
+                    console.debug("Found agent in conversation history:", responseJson.response.agent);
                     this.currentAgent = responseJson.response.agent.slug;
                     // Update the agent selector if it exists
                     const agentSelect = this.contentEl.querySelector('.khoj-header-agent-select') as HTMLSelectElement;
@@ -1352,19 +1374,26 @@ export class KhojChatView extends KhojPaneView {
             if (this.fileAccessMode === 'write') {
                 const editBlocks = this.parseEditBlocks(this.chatMessageState.rawResponse);
 
-                // Check for errors and retry if needed
-                if (editBlocks.length > 0 && editBlocks[0].hasError && this.editRetryCount < this.maxEditRetries) {
-                    await this.handleEditRetry(editBlocks[0]);
-                    return;
-                }
-
-                // Reset retry count on success
-                this.editRetryCount = 0;
-
-                // Apply edits if there are any
                 if (editBlocks.length > 0) {
+                    const firstBlock = editBlocks[0];
+                    if (firstBlock.hasError) {
+                        // Only retry if we have remaining attempts; do NOT reset counter on failure
+                        if (this.editRetryCount < this.maxEditRetries) {
+                            await this.handleEditRetry(firstBlock);
+                            return; // Wait for retry response
+                        } else {
+                            // Exhausted retries; surface error and do not attempt further automatic retries
+                            console.warn('[Khoj] Max edit retries reached. Aborting further retries.');
+                        }
+                    } else {
+                        // Successful parse => reset counter and apply edits
+                        this.editRetryCount = 0;
                         await this.applyEditBlocks(editBlocks);
                     }
+                } else {
+                    // No edit blocks => reset counter just in case
+                    this.editRetryCount = 0;
+                }
             }
 
             // Automatically respond with voice if the subscribed user has sent voice message
@@ -1720,6 +1749,7 @@ export class KhojChatView extends KhojPaneView {
 
         // Toggle recording
         if (!this.mediaRecorder || this.mediaRecorder.state === 'inactive' || event.type === 'touchstart' || event.type === 'mousedown' || event.type === 'keydown') {
+            this.voiceChatActive = true;
             navigator.mediaDevices
                 .getUserMedia({ audio: true })
                 ?.then(handleRecording)
@@ -1727,6 +1757,7 @@ export class KhojChatView extends KhojPaneView {
                     this.flashStatusInChatInput("⛔️ Failed to access microphone");
                 });
         } else if (this.mediaRecorder?.state === 'recording' || event.type === 'touchend' || event.type === 'touchcancel' || event.type === 'mouseup' || event.type === 'keyup') {
+            this.voiceChatActive = false;
             this.mediaRecorder.stop();
             this.mediaRecorder.stream.getTracks().forEach(track => track.stop());
             this.mediaRecorder = undefined;
@@ -2403,7 +2434,7 @@ export class KhojChatView extends KhojPaneView {
         // Add retry count
         retryBadge.createSpan({
             cls: "retry-count",
-            text: `Attempt ${this.editRetryCount}/3`
+            text: `Attempt ${this.editRetryCount}/${this.maxEditRetries}`
         });
 
         // Add error details as a tooltip
@@ -2418,7 +2449,7 @@ export class KhojChatView extends KhojPaneView {
         retryBadge.scrollIntoView({ behavior: "smooth", block: "center" });
 
         // Create a retry prompt for the LLM
-        const retryPrompt = `/general I noticed some issues with the edit block. Please fix the following and provide a corrected version (retry ${this.editRetryCount}/3):\n\n${errorDetails}\n\nPlease provide a new edit block that fixes these issues. Make sure to follow the exact format required.`;
+        const retryPrompt = `/general I noticed some issues with the edit block. Please fix the following and provide a corrected version (retry ${this.editRetryCount}/${this.maxEditRetries}):\n\n${errorDetails}\n\nPlease provide a new edit block that fixes these issues. Make sure to follow the exact format required.`;
 
         // Send retry request without displaying the user message
         await this.getChatResponse(retryPrompt, "", false, false);

src/interface/obsidian/src/interact_with_files.ts

@@ -1,4 +1,4 @@
-import { App, TFile } from 'obsidian';
+import { App, MarkdownView, TFile } from 'obsidian';
 import { diffWords } from 'diff';
 
 /**
@@ -55,6 +55,7 @@ export class FileInteractions {
     private app: App;
     private readonly EDIT_BLOCK_START = '<khoj_edit>';
     private readonly EDIT_BLOCK_END = '</khoj_edit>';
+    private readonly CONTEXT_FILES_LIMIT = 3;
 
     /**
      * Constructor for FileInteractions
@@ -65,6 +66,26 @@ export class FileInteractions {
         this.app = app;
     }
 
+    /**
+     * Get N open, recently viewed markdown files.
+     */
+    private getRecentActiveMarkdownFiles(N: number): TFile[] {
+        const seen = new Set<string>();
+        const recentActiveFiles = this.app.workspace.getLeavesOfType('markdown')
+            .sort((a, b) => (b as any).activeTime - (a as any).activeTime) // Sort by leaf activeTime (note: undocumented prop)
+            .map(leaf => (leaf.view as MarkdownView)?.file)
+            // Dedupe by file path
+            .filter((file): file is TFile => {
+                if (!file || seen.has(file.path)) return false;
+                seen.add(file.path);
+                return true;
+            })
+            .slice(0, N);
+
+        console.log(`Using ${recentActiveFiles.length} recently viewed md files for context: ${recentActiveFiles.map(file => file.path).join(', ')}`);
+        return recentActiveFiles;
+    }
+
     /**
      * Gets the content of all open files
      *
@@ -75,9 +96,9 @@ export class FileInteractions {
         // Only proceed if we have read or write access
         if (fileAccessMode === 'none') return '';
 
-        // Get all open markdown leaves
+        // Get recently viewed markdown files
-        const leaves = this.app.workspace.getLeavesOfType('markdown');
+        const recentFiles = this.getRecentActiveMarkdownFiles(this.CONTEXT_FILES_LIMIT);
-        if (leaves.length === 0) return '';
+        if (recentFiles.length === 0) return '';
 
         // Instructions in write access mode
         let editInstructions: string = '';
@@ -274,11 +295,7 @@ For context, the user is currently working on the following files:
 
 `;
 
-        for (const leaf of leaves) {
+        for (const file of recentFiles) {
-            const view = leaf.view as any;
-            const file = view?.file;
-            if (!file || file.extension !== 'md') continue;
-
             // Read file content
             let fileContent: string;
             try {
@@ -415,8 +432,16 @@ For context, the user is currently working on the following files:
             }
 
             // Try parse SEARCH/REPLACE format for complete edit blocks
-            // Regex: file_path\n<<<<<<< SEARCH\nsearch_content\n=======\nreplacement_content\n>>>>>>> REPLACE
+            // Supports empty SEARCH (new file / replace whole file) and empty REPLACE (deletion)
-            const newFormatRegex = /^([^\n]+)\n<<<<<<< SEARCH\n([\s\S]*?)\n=======\n([\s\S]*?)\n>>>>>>> REPLACE\s*$/;
+            // Regex structure:
+            //   file_path               (group 1)
+            //   <<<<<<< SEARCH          literal marker
+            //   search_content          (group 2, can be empty)
+            //   =======                 divider
+            //   replacement_content     (group 3, can be empty => deletion)
+            //   >>>>>>> REPLACE         end marker
+            // Note: The trailing newline before the end marker is optional to allow zero-length replacement
+            const newFormatRegex = /^([^\n]+)\n<<<<<<< SEARCH\n([\s\S]*?)\n=======\n([\s\S]*?)\n?>>>>>>> REPLACE\s*$/;
             const newFormatMatch = newFormatRegex.exec(cleanContent);
 
             let editData: EditBlock | null = null;
@@ -430,32 +455,25 @@ For context, the user is currently working on the following files:
 
             // Validate required fields
             let error: { type: 'missing_field' | 'invalid_format' | 'preprocessing' | 'unknown', message: string, details?: string } | null = null;
-            if (!editData) {
+            if (editData && !editData.file) {
-                error = {
-                    type: 'invalid_format',
-                    message: 'Invalid edit block format',
-                    details: 'The edit block does not match the expected format'
-                };
-            }
-            else if (!editData.file) {
                 error = {
                     type: 'missing_field',
                     message: 'Missing "file" field in edit block',
                     details: 'The "file" field is required and should contain the target file name'
                 };
             }
-            else if (editData.find === undefined || editData.find === null) {
+            else if (editData && (editData.find === undefined || editData.find === null)) {
                 error = {
                     type: 'missing_field',
                     message: 'Missing "find" field markers',
-                    details: 'The "find" field is required and should contain the content to find in the file'
+                    details: 'The "find" field is required. It should contain the content to find in the file or be empty for new files'
                 };
             }
-            else if (!editData.replace) {
+            else if (editData && editData.replace === undefined) {
                 error = {
                     type: 'missing_field',
                     message: 'Missing "replace" field in edit block',
-                    details: 'The "replace" field is required and should contain the replacement text'
+                    details: 'The "replace" field is required. It should contain the content to replace or be empty to indicate deletion'
                 };
             }
 
@@ -507,7 +525,7 @@ For context, the user is currently working on the following files:
             }
 
             if (!editData) {
-                console.error("No edit data parsed");
+                console.debug("No edit data parsed");
                 continue;
             }
 
@@ -684,10 +702,8 @@ For context, the user is currently working on the following files:
         // Track current content for each file as we apply edits
         const currentFileContents = new Map<string, string>();
 
-        // Get all open markdown files
+        // Get recently viewed markdown file(s) to edit
-        const files = this.app.workspace.getLeavesOfType('markdown')
+        const files = this.getRecentActiveMarkdownFiles(this.CONTEXT_FILES_LIMIT);
-            .map(leaf => (leaf.view as any)?.file)
-            .filter(file => file && file.extension === 'md');
 
         // Track success/failure for each edit
         const editResults: { block: EditBlock, success: boolean, error?: string }[] = [];
@@ -883,6 +899,10 @@ For context, the user is currently working on the following files:
 
             // Parse the block content
             const { editData, cleanContent, error, inProgress } = this.parseEditBlock(content, isComplete);
+            if (!editData && !error) {
+                // If no edit data and no error, skip this block
+                continue;
+            }
 
             // Escape content for HTML display
             const diff = diffWords(editData?.find || '', editData?.replace || '');
@@ -898,7 +918,7 @@ For context, the user is currently working on the following files:
             ).join('').trim();
 
             let htmlRender = '';
-            if (error || !editData) {
+            if (error) {
                 // Error block
                 console.error("Error parsing khoj-edit block:", error);
                 console.error("Content causing error:", content);
@@ -913,7 +933,7 @@ For context, the user is currently working on the following files:
                         <pre><code class="language-md error">${diffContent}</code></pre>
                     </div>
                 </details>`;
-            } else if (inProgress) {
+            } else if (editData && inProgress) {
                 // In-progress block
                 htmlRender = `<details class="khoj-edit-accordion in-progress">
                     <summary>📄 ${editData.file} <span class="khoj-edit-status">In Progress</span></summary>
@@ -921,7 +941,7 @@ For context, the user is currently working on the following files:
                         <pre><code class="language-md">${diffContent}</code></pre>
                     </div>
                 </details>`;
-            } else {
+            } else if (editData) {
                 // Success block
                 // Find the actual file that will be modified
                 const targetFile = this.findBestMatchingFile(editData.file, files);

src/interface/obsidian/src/main.ts

@@ -3,8 +3,8 @@ import { KhojSetting, KhojSettingTab, DEFAULT_SETTINGS } from 'src/settings'
 import { KhojSearchModal } from 'src/search_modal'
 import { KhojChatView } from 'src/chat_view'
 import { KhojSimilarView } from 'src/similar_view'
-import { updateContentIndex, canConnectToBackend, KhojView, jumpToPreviousView } from './utils';
+import { updateContentIndex, canConnectToBackend, KhojView } from 'src/utils';
-import { KhojPaneView } from './pane_view';
+import { KhojPaneView } from 'src/pane_view';
 
 
 export default class Khoj extends Plugin {
@@ -73,7 +73,7 @@ export default class Khoj extends Plugin {
                 this.activateView(KhojView.CHAT).then(() => {
                     const chatView = this.app.workspace.getActiveViewOfType(KhojChatView);
                     if (chatView) {
-                        chatView.toggleChatSessions(true);
+                        chatView.toggleChatSessions();
                     }
                 });
             }
@@ -88,8 +88,9 @@ export default class Khoj extends Plugin {
                 this.activateView(KhojView.CHAT).then(() => {
                     const chatView = this.app.workspace.getActiveViewOfType(KhojChatView);
                     if (chatView) {
-                        // Trigger speech to text functionality
+                        // Toggle speech to text functionality
-                        chatView.speechToText(new KeyboardEvent('keydown'));
+                        const toggleEvent = chatView.voiceChatActive ? 'keyup' : 'keydown';
+                        chatView.speechToText(new KeyboardEvent(toggleEvent));
                     }
                 });
             }
@@ -136,8 +137,8 @@ export default class Khoj extends Plugin {
         });
 
         // Register views
-        this.registerView(KhojView.CHAT, (leaf) => new KhojChatView(leaf, this.settings));
+        this.registerView(KhojView.CHAT, (leaf) => new KhojChatView(leaf, this));
-        this.registerView(KhojView.SIMILAR, (leaf) => new KhojSimilarView(leaf, this.settings));
+        this.registerView(KhojView.SIMILAR, (leaf) => new KhojSimilarView(leaf, this));
 
         // Create an icon in the left ribbon.
         this.addRibbonIcon('message-circle', 'Khoj', (_: MouseEvent) => {

src/interface/obsidian/src/pane_view.ts

@@ -1,14 +1,17 @@
 import { ItemView, WorkspaceLeaf } from 'obsidian';
 import { KhojSetting } from 'src/settings';
 import { KhojView, populateHeaderPane } from './utils';
+import Khoj from 'src/main';
 
 export abstract class KhojPaneView extends ItemView {
     setting: KhojSetting;
+    plugin: Khoj;
 
-    constructor(leaf: WorkspaceLeaf, setting: KhojSetting) {
+    constructor(leaf: WorkspaceLeaf, plugin: Khoj) {
         super(leaf);
 
-        this.setting = setting;
+        this.setting = plugin.settings;
+        this.plugin = plugin;
 
         // Register Modal Keybindings to send user message
         // this.scope.register([], 'Enter', async () => { await this.chat() });

src/interface/obsidian/src/settings.ts

@@ -38,6 +38,7 @@ export interface KhojSetting {
     syncFolders: string[];
     syncInterval: number;
     autoVoiceResponse: boolean;
+    fileAccessMode: 'none' | 'read' | 'write';
     selectedChatModelId: string | null; // Mirrors server's selected_chat_model_config
     availableChatModels: ModelOption[];
 }
@@ -58,6 +59,7 @@ export const DEFAULT_SETTINGS: KhojSetting = {
     syncFolders: [],
     syncInterval: 60,
     autoVoiceResponse: true,
+    fileAccessMode: 'read',
     selectedChatModelId: null, // Will be populated from server
     availableChatModels: [],
 }

src/interface/obsidian/src/similar_view.ts

@@ -1,7 +1,7 @@
 import { WorkspaceLeaf, TFile, MarkdownRenderer, Notice, setIcon } from 'obsidian';
-import { KhojSetting } from 'src/settings';
 import { KhojPaneView } from 'src/pane_view';
 import { KhojView, getLinkToEntry, supportedBinaryFileTypes } from 'src/utils';
+import Khoj from 'src/main';
 
 export interface SimilarResult {
     entry: string;
@@ -11,7 +11,6 @@ export interface SimilarResult {
 
 export class KhojSimilarView extends KhojPaneView {
     static iconName: string = "search";
-    setting: KhojSetting;
     currentController: AbortController | null = null;
     isLoading: boolean = false;
     loadingEl: HTMLElement;
@@ -21,9 +20,8 @@ export class KhojSimilarView extends KhojPaneView {
     fileWatcher: any;
     component: any;
 
-    constructor(leaf: WorkspaceLeaf, setting: KhojSetting) {
+    constructor(leaf: WorkspaceLeaf, plugin: Khoj) {
-        super(leaf, setting);
+        super(leaf, plugin);
-        this.setting = setting;
         this.component = this;
     }