fix: support multi-folder workspace for codebase indexing

- Update CodeIndexManager.getInstance() to use active workspace folder instead of always using first folder
- Add handleWorkspaceFolderChange() method to ClineProvider to re-initialize code index when workspace changes
- Integrate workspace change detection in WorkspaceTracker to trigger code index updates
- This ensures codebase index corresponds to the currently active workspace folder

Fixes #6197

Author: roomote

src/core/webview/ClineProvider.ts

@@ -1825,6 +1825,58 @@ export class ClineProvider
 		return this.mcpHub
 	}
 
+	/**
+	 * Handle workspace folder change by re-initializing the CodeIndexManager
+	 * This ensures the code index corresponds to the currently active workspace folder
+	 */
+	public async handleWorkspaceFolderChange() {
+		if (!this.codeIndexManager) {
+			return
+		}
+
+		try {
+			// Dispose of the old code index status subscription
+			if (this.codeIndexStatusSubscription) {
+				this.codeIndexStatusSubscription.dispose()
+				this.codeIndexStatusSubscription = undefined
+			}
+
+			// Get a new instance of CodeIndexManager for the current workspace
+			const newManager = CodeIndexManager.getInstance(this.context)
+			if (!newManager) {
+				this.log("No workspace folder available for code index")
+				return
+			}
+
+			// Re-initialize the manager
+			await newManager.initialize(this.contextProxy)
+
+			// Re-subscribe to status updates
+			this.codeIndexStatusSubscription = newManager.onProgressUpdate((update: IndexProgressUpdate) => {
+				this.postMessageToWebview({
+					type: "indexingStatusUpdate",
+					values: update,
+				})
+			})
+			if (this.webviewDisposables && this.codeIndexStatusSubscription) {
+				this.webviewDisposables.push(this.codeIndexStatusSubscription)
+			}
+
+			// Update the reference
+			;(this as any).codeIndexManager = newManager
+
+			// Send the current status to the webview
+			this.postMessageToWebview({
+				type: "indexingStatusUpdate",
+				values: newManager.getCurrentStatus(),
+			})
+
+			this.log(`Code index re-initialized for workspace: ${getWorkspacePath()}`)
+		} catch (error) {
+			this.log(`Failed to re-initialize code index: ${error}`)
+		}
+	}
+
 	/**
 	 * Check if the current state is compliant with MDM policy
 	 * @returns true if compliant, false if blocked

src/integrations/workspace/WorkspaceTracker.ts

@@ -97,11 +97,16 @@ class WorkspaceTracker {
 		}
 		this.resetTimer = setTimeout(async () => {
 			if (this.prevWorkSpacePath !== this.cwd) {
-				await this.providerRef.deref()?.postMessageToWebview({
-					type: "workspaceUpdated",
-					filePaths: [],
-					openedTabs: this.getOpenedTabsInfo(),
-				})
+				const provider = this.providerRef.deref()
+				if (provider) {
+					await provider.postMessageToWebview({
+						type: "workspaceUpdated",
+						filePaths: [],
+						openedTabs: this.getOpenedTabsInfo(),
+					})
+					// Trigger code index re-initialization for the new workspace
+					await provider.handleWorkspaceFolderChange()
+				}
 				this.filePaths.clear()
 				this.prevWorkSpacePath = this.cwd
 				this.initializeFilePaths()

src/services/code-index/__tests__/manager.spec.ts

@@ -13,6 +13,9 @@ vi.mock("vscode", () => ({
 			},
 		],
 	},
+	window: {
+		activeTextEditor: undefined,
+	},
 }))
 
 // Mock only the essential dependencies

src/services/code-index/manager.ts

@@ -29,17 +29,14 @@ export class CodeIndexManager {
 	private _cacheManager: CacheManager | undefined
 
 	public static getInstance(context: vscode.ExtensionContext): CodeIndexManager | undefined {
-		// Use first workspace folder consistently
-		const workspaceFolders = vscode.workspace.workspaceFolders
-		if (!workspaceFolders || workspaceFolders.length === 0) {
+		// Get the workspace path based on the active editor or current context
+		const workspacePath = getWorkspacePath()
+		if (!workspacePath) {
 			return undefined
 		}
 
-		// Always use the first workspace folder for consistency across all indexing operations.
-		// This ensures that the same workspace context is used throughout the indexing pipeline,
-		// preventing path resolution errors in multi-workspace scenarios.
-		const workspacePath = workspaceFolders[0].uri.fsPath
-
+		// Use the workspace folder of the active editor to support multi-folder workspaces.
+		// This ensures that the codebase index corresponds to the folder the user is currently working in.
 		if (!CodeIndexManager.instances.has(workspacePath)) {
 			CodeIndexManager.instances.set(workspacePath, new CodeIndexManager(workspacePath, context))
 		}