fix: use tool-specific subdirectories for .env files to prevent overwrites

Author: roomote

packages/core/src/custom-tools/custom-tool-registry.ts

@@ -236,16 +236,22 @@ export class CustomToolRegistry {
 
 	/**
 	 * Clear the TypeScript compilation cache (both in-memory and on disk).
+	 * This removes all tool-specific subdirectories and their contents.
 	 */
 	clearCache(): void {
 		this.tsCache.clear()
 
 		if (fs.existsSync(this.cacheDir)) {
 			try {
-				const files = fs.readdirSync(this.cacheDir)
-				for (const file of files) {
-					if (file.endsWith(".mjs")) {
-						fs.unlinkSync(path.join(this.cacheDir, file))
+				const entries = fs.readdirSync(this.cacheDir, { withFileTypes: true })
+				for (const entry of entries) {
+					const entryPath = path.join(this.cacheDir, entry.name)
+					if (entry.isDirectory()) {
+						// Remove tool-specific subdirectory and all its contents.
+						fs.rmSync(entryPath, { recursive: true, force: true })
+					} else if (entry.name.endsWith(".mjs")) {
+						// Also clean up any legacy flat .mjs files from older cache format.
+						fs.unlinkSync(entryPath)
 					}
 				}
 			} catch (error) {
@@ -282,11 +288,13 @@ export class CustomToolRegistry {
 			return import(`file://${cachedPath}`)
 		}
 
-		// Ensure cache directory exists.
-		fs.mkdirSync(this.cacheDir, { recursive: true })
-
 		const hash = createHash("sha256").update(cacheKey).digest("hex").slice(0, 16)
-		const tempFile = path.join(this.cacheDir, `${hash}.mjs`)
+
+		// Use a tool-specific subdirectory to avoid .env file conflicts between tools.
+		const toolCacheDir = path.join(this.cacheDir, hash)
+		fs.mkdirSync(toolCacheDir, { recursive: true })
+
+		const tempFile = path.join(toolCacheDir, "bundle.mjs")
 
 		// Check if we have a cached version on disk (from a previous run/instance).
 		if (fs.existsSync(tempFile)) {
@@ -322,34 +330,37 @@ export class CustomToolRegistry {
 			this.extensionPath,
 		)
 
-		// Copy .env files from the tool's source directory to the cache directory.
-		// This allows tools that use dotenv with __dirname to find their .env files.
-		this.copyEnvFiles(toolDir)
+		// Copy .env files from the tool's source directory to the tool-specific cache directory.
+		// This allows tools that use dotenv with __dirname to find their .env files,
+		// while ensuring different tools' .env files don't overwrite each other.
+		this.copyEnvFiles(toolDir, toolCacheDir)
 
 		this.tsCache.set(cacheKey, tempFile)
 		return import(`file://${tempFile}`)
 	}
 
 	/**
-	 * Copy .env files from the tool's source directory to the cache directory.
-	 * This allows tools that use dotenv with __dirname to find their .env files.
+	 * Copy .env files from the tool's source directory to the tool-specific cache directory.
+	 * This allows tools that use dotenv with __dirname to find their .env files,
+	 * while ensuring different tools' .env files don't overwrite each other.
 	 *
 	 * @param toolDir - The directory containing the tool source files
+	 * @param destDir - The tool-specific cache directory to copy .env files to
 	 */
-	private copyEnvFiles(toolDir: string): void {
+	private copyEnvFiles(toolDir: string, destDir: string): void {
 		try {
 			const files = fs.readdirSync(toolDir)
 			const envFiles = files.filter((f) => f === ".env" || f.startsWith(".env."))
 
 			for (const envFile of envFiles) {
 				const srcPath = path.join(toolDir, envFile)
-				const destPath = path.join(this.cacheDir, envFile)
+				const destPath = path.join(destDir, envFile)
 
 				// Only copy if source is a file (not a directory).
 				const stat = fs.statSync(srcPath)
 				if (stat.isFile()) {
 					fs.copyFileSync(srcPath, destPath)
-					console.log(`[CustomToolRegistry] copied ${envFile} to cache directory`)
+					console.log(`[CustomToolRegistry] copied ${envFile} to tool cache directory`)
 				}
 			}
 		} catch (error) {