fix(filesystem): only apply MCP roots when no CLI directories are provided

src/everything/resources/templates.ts

@@ -25,7 +25,7 @@ export const RESOURCE_TYPES: string[] = [
  * The completion logic matches the input against available resource types.
  */
 export const resourceTypeCompleter = completable(
-  z.string().describe("Type of resource to fetch"),
+  z.string().describe("Type of resource — must be 'Text' or 'Blob'"),
   (value: string) => {
     return RESOURCE_TYPES.filter((t) => t.startsWith(value));
   }

src/everything/tools/get-env.ts

@@ -6,26 +6,50 @@ const name = "get-env";
 const config = {
   title: "Print Environment Tool",
   description:
-    "Returns all environment variables, helpful for debugging MCP server configuration",
-  inputSchema: {},
+    "Returns the value of a specific environment variable, helpful for debugging MCP server configuration",
+  inputSchema: {
+    type: "object",
+    properties: {
+      key: {
+        type: "string",
+        description:
+          "The name of the environment variable to retrieve (e.g., 'PATH', 'HOME', 'USER')",
+      },
+    },
+    required: ["key"],
+  },
 };
 
 /**
  * Registers the 'get-env' tool.
  *
- * The registered tool Retrieves and returns the environment variables
- * of the current process as a JSON-formatted string encapsulated in a text response.
+ * The registered tool retrieves and returns the value of a specific
+ * environment variable from the current process.
  *
  * @param {McpServer} server - The McpServer instance where the tool will be registered.
  * @returns {void}
  */
 export const registerGetEnvTool = (server: McpServer) => {
   server.registerTool(name, config, async (args): Promise<CallToolResult> => {
+    const { key } = args as { key: string };
+    const value = process.env[key];
+
+    if (value === undefined) {
+      return {
+        content: [
+          {
+            type: "text",
+            text: `Environment variable '${key}' is not set.`,
+          },
+        ],
+      };
+    }
+
     return {
       content: [
         {
           type: "text",
-          text: JSON.stringify(process.env, null, 2),
+          text: `${key}=${value}`,
         },
       ],
     };

src/filesystem/index.ts

@@ -717,7 +717,10 @@ async function updateAllowedDirectoriesFromRoots(requestedRoots: Root[]) {
 // Handles dynamic roots updates during runtime, when client sends "roots/list_changed" notification, server fetches the updated roots and replaces all allowed directories with the new roots.
 server.server.setNotificationHandler(RootsListChangedNotificationSchema, async () => {
   try {
-    // Request the updated roots list from the client
+    // Only update from MCP roots if no CLI directories were set
+    if (allowedDirectories.length > 0) {
+      return;
+    }
     const response = await server.server.listRoots();
     if (response && 'roots' in response) {
       await updateAllowedDirectoriesFromRoots(response.roots);
@@ -731,7 +734,10 @@ server.server.setNotificationHandler(RootsListChangedNotificationSchema, async (
 server.server.oninitialized = async () => {
   const clientCapabilities = server.server.getClientCapabilities();
 
-  if (clientCapabilities?.roots) {
+  if (clientCapabilities?.roots && allowedDirectories.length === 0) {
+    // Only fetch and apply MCP roots when no CLI directories were provided.
+    // CLI arguments take precedence over MCP roots since they are explicitly
+    // specified by the server operator.
     try {
       const response = await server.server.listRoots();
       if (response && 'roots' in response) {
@@ -744,7 +750,7 @@ server.server.oninitialized = async () => {
     }
   } else {
     if (allowedDirectories.length > 0) {
-      console.error("Client does not support MCP Roots, using allowed directories set from server args:", allowedDirectories);
+      console.error("Client does not support MCP Roots, or CLI directories provided. Using allowed directories from server args:", allowedDirectories);
     }else{
       throw new Error(`Server cannot operate: No allowed directories available. Server was started without command-line directories and client either does not support MCP roots protocol or provided empty roots. Please either: 1) Start server with directory arguments, or 2) Use a client that supports MCP roots protocol and provides valid root directories.`);
     }