fix: update remaining files to use vscode-aware wrapper functions

- Update custom-system-prompt.ts to use async getSystemPromptFilePath
- Update ClineProvider.ts to handle async change
- Update MarketplaceManager.ts to use getProjectRooDirectoryForCwd wrapper
- Update webviewMessageHandler.ts to use wrapper (already done)

This ensures all .roo path constructions properly check for workspace folders

Author: roomote

src/core/prompts/sections/custom-system-prompt.ts

@@ -2,6 +2,7 @@ import fs from "fs/promises"
 import path from "path"
 import { Mode } from "../../../shared/modes"
 import { fileExistsAtPath } from "../../../utils/fs"
+import { getProjectRooDirectoryForCwd } from "../../../services/roo-config/wrapper"
 
 export type PromptVariables = {
 	workspace?: string
@@ -45,16 +46,17 @@ async function safeReadFile(filePath: string): Promise<string> {
 /**
  * Get the path to a system prompt file for a specific mode
  */
-export function getSystemPromptFilePath(cwd: string, mode: Mode): string {
-	return path.join(cwd, ".roo", `system-prompt-${mode}`)
+export async function getSystemPromptFilePath(cwd: string, mode: Mode): Promise<string> {
+	const rooDir = await getProjectRooDirectoryForCwd(cwd)
+	return path.join(rooDir, `system-prompt-${mode}`)
 }
 
 /**
  * Loads custom system prompt from a file at .roo/system-prompt-[mode slug]
  * If the file doesn't exist, returns an empty string
  */
 export async function loadSystemPromptFile(cwd: string, mode: Mode, variables: PromptVariables): Promise<string> {
-	const filePath = getSystemPromptFilePath(cwd, mode)
+	const filePath = await getSystemPromptFilePath(cwd, mode)
 	const rawContent = await safeReadFile(filePath)
 	if (!rawContent) {
 		return ""
@@ -67,7 +69,7 @@ export async function loadSystemPromptFile(cwd: string, mode: Mode, variables: P
  * Ensures the .roo directory exists, creating it if necessary
  */
 export async function ensureRooDirectory(cwd: string): Promise<void> {
-	const rooDir = path.join(cwd, ".roo")
+	const rooDir = await getProjectRooDirectoryForCwd(cwd)
 
 	// Check if directory already exists
 	if (await fileExistsAtPath(rooDir)) {

src/core/webview/ClineProvider.ts

@@ -1538,7 +1538,7 @@ export class ClineProvider
 	 * Checks if there is a file-based system prompt override for the given mode
 	 */
 	async hasFileBasedSystemPromptOverride(mode: Mode): Promise<boolean> {
-		const promptFilePath = getSystemPromptFilePath(this.cwd, mode)
+		const promptFilePath = await getSystemPromptFilePath(this.cwd, mode)
 		return await fileExistsAtPath(promptFilePath)
 	}
 

src/services/marketplace/MarketplaceManager.ts

@@ -12,6 +12,7 @@ import { GlobalFileNames } from "../../shared/globalFileNames"
 import { ensureSettingsDirectoryExists } from "../../utils/globalContext"
 import { t } from "../../i18n"
 import type { CustomModesManager } from "../../core/config/CustomModesManager"
+import { getProjectRooDirectoryForCwd } from "../../services/roo-config/wrapper"
 
 import { RemoteConfigLoader } from "./RemoteConfigLoader"
 import { SimpleInstaller } from "./SimpleInstaller"
@@ -270,7 +271,8 @@ export class MarketplaceManager {
 			}
 
 			// Check MCPs in .roo/mcp.json
-			const projectMcpPath = path.join(workspaceFolder.uri.fsPath, ".roo", "mcp.json")
+			const rooDir = await getProjectRooDirectoryForCwd(workspaceFolder.uri.fsPath)
+			const projectMcpPath = path.join(rooDir, "mcp.json")
 			try {
 				const content = await fs.readFile(projectMcpPath, "utf-8")
 				const data = JSON.parse(content)

src/services/roo-config/__tests__/index.spec.ts

@@ -35,16 +35,12 @@ vi.mock("vscode", () => ({
 	},
 }))
 
-import {
-	getGlobalRooDirectory,
-	getProjectRooDirectoryForCwd,
-	directoryExists,
-	fileExists,
-	readFileIfExists,
-	getRooDirectoriesForCwd,
-	loadConfiguration,
-} from "../index"
+import { getGlobalRooDirectory, directoryExists, fileExists, readFileIfExists, loadConfiguration } from "../index"
 import { findWorkspaceWithRoo } from "../vscode-utils"
+import { getProjectRooDirectoryForCwd, getRooDirectoriesForCwd, setVscodeUtils } from "../wrapper"
+
+// Initialize the wrapper with vscode utilities for testing
+setVscodeUtils({ findWorkspaceWithRoo })
 
 describe("RooConfigService", () => {
 	beforeEach(() => {

src/services/roo-config/wrapper.ts

@@ -1,5 +1,10 @@
 import * as path from "path"
-import { getProjectRooDirectoryForCwd as getProjectRooDirectoryBase } from "./index"
+import {
+	getProjectRooDirectoryForCwd as getProjectRooDirectoryBase,
+	getGlobalRooDirectory,
+	getRooDirectoriesForCwd as getRooDirectoriesBase,
+	loadConfiguration as loadConfigurationBase,
+} from "./index"
 
 // This will be set by the extension during activation
 let vscodeUtils: { findWorkspaceWithRoo: () => any } | undefined
@@ -28,3 +33,68 @@ export function getProjectRooDirectoryForCwd(cwd: string): string {
 	// Fall back to base implementation
 	return getProjectRooDirectoryBase(cwd)
 }
+
+/**
+ * Gets the ordered list of .roo directories to check (global first, then project-local)
+ * This wrapper uses the vscode-aware getProjectRooDirectoryForCwd
+ */
+export function getRooDirectoriesForCwd(cwd: string): string[] {
+	const directories: string[] = []
+
+	// Add global directory first
+	directories.push(getGlobalRooDirectory())
+
+	// Add project-local directory second (using wrapper version)
+	directories.push(getProjectRooDirectoryForCwd(cwd))
+
+	return directories
+}
+
+/**
+ * Loads configuration from multiple .roo directories with project overriding global
+ * This wrapper uses the vscode-aware getProjectRooDirectoryForCwd
+ */
+export async function loadConfiguration(
+	relativePath: string,
+	cwd: string,
+): Promise<{
+	global: string | null
+	project: string | null
+	merged: string
+}> {
+	// Use the wrapper version of getProjectRooDirectoryForCwd
+	const globalDir = getGlobalRooDirectory()
+	const projectDir = getProjectRooDirectoryForCwd(cwd)
+
+	const globalFilePath = path.join(globalDir, relativePath)
+	const projectFilePath = path.join(projectDir, relativePath)
+
+	// Import readFileIfExists from index
+	const { readFileIfExists } = await import("./index")
+
+	// Read global configuration
+	const globalContent = await readFileIfExists(globalFilePath)
+
+	// Read project-local configuration
+	const projectContent = await readFileIfExists(projectFilePath)
+
+	// Merge configurations - project overrides global
+	let merged = ""
+
+	if (globalContent) {
+		merged += globalContent
+	}
+
+	if (projectContent) {
+		if (merged) {
+			merged += "\n\n# Project-specific rules (override global):\n\n"
+		}
+		merged += projectContent
+	}
+
+	return {
+		global: globalContent,
+		project: projectContent,
+		merged: merged || "",
+	}
+}