Add symbol extraction, inline CodeLens, restore undo, native diff, and fixes

CHANGELOG.md

@@ -6,6 +6,33 @@ format is based on [Keep a Changelog](https://keepachangelog.com/).
 ## [Unreleased]
 
 ### Added
+- **Symbol extraction.** Captured changes now record the functions/classes they
+  touched (via VS Code's document symbol provider), so symbol history, the
+  clickable symbol tags, and symbol-aware search actually work. Also records the
+  active function/class for each change.
+- **Inline history CodeLens.** Unobtrusive lenses above a file ("N changes in
+  history") and its functions/classes ("k versions"), gated by
+  `codeHistorian.ui.showInlineHistory`. Click to jump to the file or symbol
+  history.
+- **Undo a restore.** Restoring now offers a one-click Undo via a native
+  notification (backed by the existing backup mechanism).
+- **Native diff actions.** "Compare with current" opens VS Code's diff editor
+  (file now ↔ before this change); "Open diff" shows the change's unified diff
+  with syntax highlighting.
+- **`codeHistorian.debug` setting** to opt into verbose DEBUG logging.
+- DB-layer integration tests (compression, BM25 ranking, bookmarks, retention,
+  symbol/file lookup) running against sql.js in Node.
+
+### Fixed
+- **Duplicate embeddings.** Changes were embedded before their rows were
+  inserted, leaving `embedding_id` NULL and causing re-embedding (a duplicate
+  vector) on every restart. Embedding now happens after the flush.
+- **File history** used an absolute path against relative-path records and
+  returned nothing; it now matches correctly.
+- API keys and full settings are no longer written to the output channel, and
+  the output panel no longer pops open on every settings save.
+
+### Added (previously)
 - **Zero-config built-in embeddings.** A new `local` embedding provider (now the
   default) produces deterministic vectors with no API key, model download, or
   local server, so semantic search works on first run.

README.md

@@ -48,10 +48,17 @@
 
 ### ⏪ **Code Restoration**
 - Restore any previous version of your code with one click
-- Preview changes before restoring
+- **One-click Undo** after a restore
+- Preview changes, or open them in VS Code's native diff editor
+  (*Compare with current* / *Open diff*)
 - Automatic backup creation before restoration
 - Works seamlessly with your existing git workflow
 
+### 🔎 **Inline History (CodeLens)**
+- *"N changes in history"* above a file and *"k versions"* above each
+  function/class — click to jump straight to that file's or symbol's history
+- Toggle with `codeHistorian.ui.showInlineHistory`
+
 ### 📊 **Visual Timeline**
 - Beautiful, modern timeline view of all changes
 - **Multiple view modes**: Timeline, Cards, or Compact list

package.json

@@ -400,7 +400,12 @@
         "codeHistorian.ui.showInlineHistory": {
           "type": "boolean",
           "default": true,
-          "description": "Show inline history decorations in editor"
+          "description": "Show inline history CodeLens above files and functions"
+        },
+        "codeHistorian.debug": {
+          "type": "boolean",
+          "default": false,
+          "description": "Enable verbose DEBUG logging in the Code Historian output channel"
         }
       }
     },

src/constants.ts

@@ -389,6 +389,7 @@ export const WEBVIEW_IDS = {
 // Event names
 export const EVENTS = {
   CHANGE_CAPTURED: 'change:captured',
+  CHANGES_FLUSHED: 'changes:flushed',
   SESSION_STARTED: 'session:started',
   SESSION_ENDED: 'session:ended',
   SEARCH_COMPLETED: 'search:completed',

src/database/metadata.ts

@@ -170,7 +170,7 @@
    * Save database to file
    */
   private saveToFile(): void {
     if (!this.db) return;
 
     try {
       const data = this.db.export();
@@ -195,7 +195,7 @@
    * Create database tables
    */
   private createTables(): void {
     if (!this.db) throw new Error('Database not initialized');
 
     // Changes table
     this.db.run(`
@@ -284,7 +284,7 @@
    * Create database indexes for faster queries
    */
   private createIndexes(): void {
     if (!this.db) throw new Error('Database not initialized');
 
     const indexes = [
       `CREATE INDEX IF NOT EXISTS idx_changes_timestamp ON ${TABLES.CHANGES}(timestamp)`,
@@ -312,7 +312,7 @@
    * Insert a change record
    */
   insertChange(change: ChangeRecord): void {
     if (!this.db) throw new Error('Database not initialized');
 
     // Compress large diffs to save disk space. We then store an empty `diff`
     // column and reconstruct it on read. Small diffs stay as plain text so
@@ -372,7 +372,7 @@
    * Insert multiple changes
    */
   insertChanges(changes: ChangeRecord[]): void {
     if (!this.db) throw new Error('Database not initialized');
     if (changes.length === 0) {
       return;
     }
@@ -396,7 +396,7 @@
    * Get a change by ID
    */
   getChange(id: string): ChangeRecord | null {
     if (!this.db) throw new Error('Database not initialized');
 
     const results = this.db.exec(
       `SELECT * FROM ${TABLES.CHANGES} WHERE id = ?`,
@@ -419,7 +419,7 @@
     limit: number = 100,
     offset: number = 0
   ): ChangeRecord[] {
     if (!this.db) throw new Error('Database not initialized');
 
     let query = `SELECT * FROM ${TABLES.CHANGES} WHERE workspace_id = ?`;
     const params: unknown[] = [workspaceId];
@@ -488,7 +488,7 @@
     query: string,
     limit: number = 50
   ): Array<{ change: ChangeRecord; rank: number }> {
     if (!this.db) throw new Error('Database not initialized');
 
     // Build an OR of LIKE clauses across query terms to gather candidates.
     const terms = query
@@ -573,12 +573,32 @@
     return result;
   }
 
+  /**
+   * Get changes for a specific file by its workspace-relative path (exact match).
+   */
+  getChangesForFile(workspaceId: string, relativePath: string, limit: number = 100): ChangeRecord[] {
+    if (!this.db) throw new Error('Database not initialized');
+
+    const results = this.db.exec(
+      `SELECT * FROM ${TABLES.CHANGES}
+       WHERE workspace_id = ? AND file_path = ?
+       ORDER BY timestamp DESC
+       LIMIT ?`,
+      [workspaceId, relativePath, limit]
+    );
+
+    if (results.length === 0) {
+      return [];
+    }
+    return results[0].values.map(row => this.resultToChangeRecord(results[0].columns, row));
+  }
+
   /**
    * Find the history of a specific symbol (function/class/variable name).
    * Matches the stored `symbols` JSON array and the searchable text.
    */
   getSymbolHistory(workspaceId: string, symbol: string, limit: number = 100): ChangeRecord[] {
     if (!this.db) throw new Error('Database not initialized');
 
     // Match the symbol as a JSON array element (e.g. "getUser") or anywhere in
     // the searchable text. The leading/trailing quote keeps it reasonably

src/extension.ts

@@ -12,10 +12,11 @@ import { EmbeddingService } from './services/embedding';
 import { SearchEngine } from './services/search';
 import { LLMOrchestrator } from './services/llm';
 import { RestorationEngine } from './services/restoration';
+import { HistoryCodeLensProvider } from './services/codeLens';
 import { ChatParticipant } from './chat/participant';
 import { WebviewProvider } from './webview/provider';
 import { logger, LogLevel } from './utils/logger';
-import { generateWorkspaceId } from './utils';
+import { generateWorkspaceId, getRelativePath } from './utils';
 import { eventEmitter } from './utils/events';
 import { secrets } from './services/secrets';
 import { LOCAL_EMBEDDING_DIMENSIONS } from './services/localEmbedding';
@@ -36,6 +37,7 @@ let embeddingService: EmbeddingService;
 let searchEngine: SearchEngine;
 let llmOrchestrator: LLMOrchestrator;
 let restorationEngine: RestorationEngine;
+let codeLensProvider: HistoryCodeLensProvider | undefined;
 let _chatParticipant: ChatParticipant;
 let webviewProvider: WebviewProvider;
 let currentSession: Session | null = null;
@@ -77,8 +79,9 @@ export async function activate(context: vscode.ExtensionContext): Promise<void>
   context.subscriptions.push(outputChannel);
   logger.initialize(outputChannel);
 
-  // Enable debug logging to help diagnose issues
-  logger.setLevel(LogLevel.DEBUG);
+  // Default to INFO; set codeHistorian.debug to surface DEBUG diagnostics.
+  const debugEnabled = vscode.workspace.getConfiguration(EXTENSION_ID).get<boolean>('debug', false);
+  logger.setLevel(debugEnabled ? LogLevel.DEBUG : LogLevel.INFO);
 
   logger.info('Activating Code Historian extension');
 
@@ -228,22 +231,32 @@ async function initializeServices(context: vscode.ExtensionContext): Promise<voi
   // Initialize restoration engine
   restorationEngine = new RestorationEngine(workspaceRoot, metadataDb, storagePath);
 
+  // Register the inline-history CodeLens provider.
+  codeLensProvider = new HistoryCodeLensProvider(metadataDb, workspaceId, workspaceRoot);
+  context.subscriptions.push(
+    vscode.languages.registerCodeLensProvider({ scheme: 'file' }, codeLensProvider),
+    codeLensProvider
+  );
+
   // Initialize capture engine
   const captureConfig = getCaptureConfig();
   captureEngine = new CaptureEngine(context, workspaceRoot, metadataDb, captureConfig);
 
-  // Connect capture engine to embedding service via events
-  // When a change is captured, process it to generate embeddings
+  // Connect capture engine to embedding service via events.
+  // We embed on CHANGES_FLUSHED (after the rows are inserted) rather than on
+  // CHANGE_CAPTURED. Embedding earlier would call updateEmbeddingId() before the
+  // row exists, leaving embedding_id NULL and causing the change to be
+  // re-embedded (a duplicate vector) on every restart.
   context.subscriptions.push(
-    eventEmitter.on(EVENTS.CHANGE_CAPTURED, async change => {
+    eventEmitter.on(EVENTS.CHANGES_FLUSHED, async (changes: ChangeRecord[]) => {
       try {
-        // Only process if embedding service is configured
         if (embeddingService.isConfigured()) {
-          await embeddingService.processChange(change);
-          logger.debug(`Generated embedding for change: ${change.id}`);
+          await embeddingService.processChanges(changes);
+          // Refresh CodeLens so new history shows up inline.
+          codeLensProvider?.refresh();
         }
       } catch (error) {
-        logger.warn(`Failed to generate embedding for change ${change.id}:`, error as Error);
+        logger.warn('Failed to generate embeddings for flushed changes:', error as Error);
         // Don't throw - embedding failure shouldn't block capture
       }
     })
@@ -306,19 +319,17 @@ function registerCommands(context: vscode.ExtensionContext): void {
         return;
       }
 
-      const changes = metadataDb.getChanges(
-        workspaceId,
-        {
-          filePatterns: [fileUri.fsPath],
-        },
-        100
-      );
+      const workspaceRoot = vscode.workspace.workspaceFolders?.[0]?.uri.fsPath || '';
+      const relativePath = getRelativePath(fileUri.fsPath, workspaceRoot);
+      const changes = metadataDb.getChangesForFile(workspaceId, relativePath, 200);
 
       if (changes.length === 0) {
         vscode.window.showInformationMessage('No history found for this file');
         return;
       }
 
+      await vscode.commands.executeCommand('workbench.view.extension.codeHistorian');
+
       // Show results in webview
       webviewProvider.postMessage({
         type: 'searchResults',
@@ -415,22 +426,27 @@ function registerCommands(context: vscode.ExtensionContext): void {
 
   // Show symbol history command — time-travel a single function/class/variable
   context.subscriptions.push(
-    vscode.commands.registerCommand(COMMANDS.SHOW_SYMBOL_HISTORY, async () => {
-      // Default to the word under the cursor, if any.
-      const editor = vscode.window.activeTextEditor;
-      let defaultSymbol = '';
-      if (editor) {
-        const range = editor.document.getWordRangeAtPosition(editor.selection.active);
-        if (range) {
-          defaultSymbol = editor.document.getText(range);
+    vscode.commands.registerCommand(COMMANDS.SHOW_SYMBOL_HISTORY, async (symbolArg?: string) => {
+      let symbol = typeof symbolArg === 'string' ? symbolArg : undefined;
+
+      // No argument (invoked from palette/context menu): prompt, defaulting to
+      // the word under the cursor.
+      if (!symbol) {
+        const editor = vscode.window.activeTextEditor;
+        let defaultSymbol = '';
+        if (editor) {
+          const range = editor.document.getWordRangeAtPosition(editor.selection.active);
+          if (range) {
+            defaultSymbol = editor.document.getText(range);
+          }
         }
-      }
 
-      const symbol = await vscode.window.showInputBox({
-        prompt: 'Show history for symbol (function, class, or variable name)',
-        placeHolder: 'e.g. parseConfig',
-        value: defaultSymbol,
-      });
+        symbol = await vscode.window.showInputBox({
+          prompt: 'Show history for symbol (function, class, or variable name)',
+          placeHolder: 'e.g. parseConfig',
+          value: defaultSymbol,
+        });
+      }
 
       if (!symbol) {
         return;
@@ -637,6 +653,24 @@ async function handleWebviewMessage(message: WebviewToExtensionMessage): Promise
 
           if (result.success) {
             await webviewProvider.sendToast('success', `Restored ${result.linesRestored} line(s)`);
+            codeLensProvider?.refresh();
+
+            // Offer a one-click Undo via a native notification when a backup
+            // was created.
+            if (result.backupId) {
+              const backupId = result.backupId;
+              void vscode.window
+                .showInformationMessage(`Restored ${result.linesRestored} line(s).`, 'Undo')
+                .then(async choice => {
+                  if (choice === 'Undo') {
+                    const undone = await restorationEngine.undoRestoration(backupId);
+                    await webviewProvider.sendToast(
+                      undone ? 'info' : 'error',
+                      undone ? 'Restore undone' : 'Could not undo restore'
+                    );
+                  }
+                });
+            }
           } else {
             await webviewProvider.sendToast('error', `Restoration failed: ${result.error}`);
           }
@@ -647,18 +681,39 @@ async function handleWebviewMessage(message: WebviewToExtensionMessage): Promise
         break;
       }
 
+      case 'compareWithCurrent': {
+        // Reuse the restoration preview, which opens VS Code's native diff
+        // editor (current file ↔ the file as it was before this change).
+        try {
+          await restorationEngine.previewRestoration(message.data.changeId);
+        } catch (error) {
+          await webviewProvider.sendToast(
+            'error',
+            `Cannot compare: ${(error as Error).message}`
+          );
+        }
+        break;
+      }
+
+      case 'openDiff': {
+        try {
+          await restorationEngine.openDiff(message.data.changeId);
+        } catch (error) {
+          await webviewProvider.sendToast('error', `Cannot open diff: ${(error as Error).message}`);
+        }
+        break;
+      }
+
       case 'getSettings': {
         await webviewProvider.postMessage({ type: 'settings', data: getCurrentSettings() });
         break;
       }
 
       case 'updateSettings': {
-        logger.info('Received updateSettings from webview:', JSON.stringify(message.data, null, 2));
-        logger.show(); // Show the output channel for debugging
+        // Note: settings payloads can contain API keys, so we don't log them.
         await updateSettings(message.data);
         // Send back the confirmed settings from VS Code configuration
         const confirmedSettings = getCurrentSettings();
-        logger.info('Sending back confirmed settings:', JSON.stringify(confirmedSettings, null, 2));
         await webviewProvider.postMessage({ type: 'settings', data: confirmedSettings });
         await webviewProvider.sendToast('success', 'Settings saved');
         break;
@@ -1172,8 +1227,6 @@ function getCurrentSettings(): SettingsData {
 async function updateSettings(settings: Partial<SettingsData>): Promise<void> {
   const config = vscode.workspace.getConfiguration(EXTENSION_ID);
 
-  logger.info('updateSettings called with:', JSON.stringify(settings, null, 2));
-
   // Capture settings
   if (settings.capture) {
     if (settings.capture.enabled !== undefined) {
@@ -1303,7 +1356,6 @@ async function updateSettings(settings: Partial<SettingsData>): Promise<void> {
     // Using a small delay to ensure VS Code has updated the configuration
     await new Promise(resolve => setTimeout(resolve, 100));
     const llmConfig = getLLMConfig();
-    logger.info('LLM config after save:', JSON.stringify(llmConfig));
     llmOrchestrator.updateConfig(llmConfig);
   }
 
@@ -1332,12 +1384,7 @@ async function updateSettings(settings: Partial<SettingsData>): Promise<void> {
   // Wait for VS Code configuration to fully propagate
   await new Promise(resolve => setTimeout(resolve, 200));
 
-  // Log the final settings after all updates
-  const finalSettings = getCurrentSettings();
-  logger.info(
-    'Settings saved successfully. Final settings:',
-    JSON.stringify(finalSettings, null, 2)
-  );
+  logger.info('Settings saved');
 }
 
 /**