feat: Add stdio transport support for Metals MCP server

metals-mcp/src/main/scala/scala/meta/internal/metals/mcp/McpLanguageClient.scala

@@ -59,7 +59,7 @@ class McpLanguageClient(workspace: AbsolutePath) extends MetalsLanguageClient {
   override def publishDiagnostics(
       diagnostics: PublishDiagnosticsParams
   ): Unit = {
-    // diagnotics are server via the compile request
+    // diagnostics are served via the compile request
   }
 
   override def showMessage(message: MessageParams): Unit = {
@@ -173,7 +173,7 @@ class McpLanguageClient(workspace: AbsolutePath) extends MetalsLanguageClient {
     }
   }
 
-  // Execute client command - no-op,
+  // Execute client command - no-op
   override def metalsExecuteClientCommand(
       params: ExecuteCommandParams
   ): Unit = {

metals-mcp/src/main/scala/scala/meta/internal/metals/mcp/StandaloneMcpService.scala

@@ -24,28 +24,32 @@ import scala.meta.io.AbsolutePath
  *
  * @param workspace The workspace root path
  * @param port Optional port for HTTP transport
+ * @param useStdio Whether to use stdio transport instead of HTTP
  * @param scheduledExecutor Scheduled executor for background tasks
  * @param client Client to generate config for (defaults to NoClient)
  * @param initialUserConfig Optional user configuration (e.g. from CLI); defaults to [[UserConfiguration.default]] if None
  */
 class StandaloneMcpService(
     workspace: AbsolutePath,
     port: Option[Int],
+    useStdio: Boolean,
     scheduledExecutor: ScheduledExecutorService,
     client: Client = NoClient,
     initialUserConfig: Option[UserConfiguration] = None,
 )(implicit ec: ExecutionContextExecutorService)
     extends Cancelable {
-  port match {
-    case Some(port) =>
-      McpConfig.writeConfig(
-        port,
-        workspace.filename,
-        workspace,
-        NoClient,
-        Set.empty,
-      )
-    case None => // random port will be assigned by the system
+  if (!useStdio) {
+    port match {
+      case Some(port) =>
+        McpConfig.writeConfig(
+          port,
+          workspace.filename,
+          workspace,
+          NoClient,
+          Set.empty,
+        )
+      case None => // random port will be assigned by the system
+    }
   }
   initialUserConfig.foreach(uc =>
     scribe.info(s"User configuration to use in MCP server: \n$uc")
@@ -139,21 +143,27 @@ class StandaloneMcpService(
   def start(): Unit = {
     scribe.info("Starting MCP server...")
     Await.result(projectMetalsLspService.initialized(), 10.minutes)
-    Await.result(projectMetalsLspService.startMcpServer(), 2.minutes)
+    if (useStdio) {
+      Await.result(projectMetalsLspService.startMcpStdioServer(), 2.minutes)
+    } else {
+      Await.result(projectMetalsLspService.startMcpServer(), 2.minutes)
+    }
     cancelables.add(projectMetalsLspService)
-    val createdPort =
-      McpConfig.readPort(workspace, workspace.filename, NoClient)
-    (createdPort, client) match {
-      case (_, NoClient) => // no client was set, nothing to do
-      case (Some(port), client) =>
-        McpConfig.writeConfig(
-          port,
-          workspace.filename,
-          workspace,
-          client,
-          Set.empty,
-        )
-      case (None, _) => scribe.error("No port was created")
+    if (!useStdio) {
+      val createdPort =
+        McpConfig.readPort(workspace, workspace.filename, NoClient)
+      (createdPort, client) match {
+        case (_, NoClient) => // no client was set, nothing to do
+        case (Some(port), client) =>
+          McpConfig.writeConfig(
+            port,
+            workspace.filename,
+            workspace,
+            client,
+            Set.empty,
+          )
+        case (None, _) => scribe.error("No port was created")
+      }
     }
     scribe.info("MCP server started successfully")
   }

metals-mcp/src/main/scala/scala/meta/metals/McpMain.scala

@@ -38,11 +38,12 @@ object McpMain {
     case object Http extends Transport
     case object Stdio extends Transport
 
-    def fromString(s: String): Option[Transport] = s.toLowerCase match {
-      case "http" => Some(Http)
-      case "stdio" => Some(Stdio)
-      case _ => None
-    }
+    def fromString(s: String): Option[Transport] =
+      s.toLowerCase match {
+        case "http" => Some(Http)
+        case "stdio" => Some(Stdio)
+        case _ => None
+      }
   }
 
   case class Config(
@@ -57,11 +58,12 @@ object McpMain {
     Client.allClients.flatMap(_.names).mkString(", ")
 
   // Skipped config keys that do not make sense in MCP context
-  private def skippedConfigKeys(key: String): Boolean = key match {
-    case "start-mcp-server" => true
-    case option if option.startsWith("inlay-hints.") => true
-    case _ => false
-  }
+  private def skippedConfigKeys(key: String): Boolean =
+    key match {
+      case "start-mcp-server" => true
+      case option if option.startsWith("inlay-hints.") => true
+      case _ => false
+    }
 
   /** Set of all config keys (kebab-case) for direct CLI parsing (e.g. --key value). */
   private val configKeys: Set[String] =
@@ -214,7 +216,7 @@ object McpMain {
          |Options:
          |  --workspace <path>      Path to the Scala project (required)
          |  --port <number>         HTTP port to listen on (default: auto-assign)
-         |  --transport <type>      Transport type: http (default) or stdio (reserved for future use)
+         |  --transport <type>      Transport type: http (default) or stdio
          |  --client <name>         Client to generate config for: $validClients
          |  --<key> [value]         UserConfiguration override. Use kebab-case (e.g. --java-home /path, --bloop-version 1.4.0).
          |                          For boolean options, value is optional: omit for true, or use --key true/false.
@@ -259,13 +261,22 @@ object McpMain {
         }
     }
 
+    val useStdio = config.transport == Transport.Stdio
+
+    // Warn about conflicting options
+    if (useStdio && config.port.isDefined) {
+      scribe.warn(
+        "--port is ignored when using stdio transport. Port option is only applicable to HTTP transport."
+      )
+    }
+
     val exec = Executors.newCachedThreadPool()
     implicit val ec: ExecutionContextExecutorService =
       ExecutionContext.fromExecutorService(exec)
     val sh = Executors.newSingleThreadScheduledExecutor()
-    if (config.transport == Transport.Stdio) {
+    if (useStdio) {
       val metalsLog = workspace.resolve(".metals/metals.log")
-      MetalsLogger.redirectSystemOut(metalsLog)
+      MetalsLogger.configureFileLogging(metalsLog)
     }
 
     scribe.info(
@@ -276,6 +287,7 @@ object McpMain {
     val service = new StandaloneMcpService(
       workspace,
       config.port,
+      useStdio,
       sh,
       config.client,
       userConfig,

metals/src/main/scala/scala/meta/internal/metals/ProjectMetalsLspService.scala

@@ -28,6 +28,7 @@ import scala.meta.internal.metals.mcp.McpQueryEngine
 import scala.meta.internal.metals.mcp.McpSymbolSearch
 import scala.meta.internal.metals.mcp.McpTestRunner
 import scala.meta.internal.metals.mcp.MetalsMcpServer
+import scala.meta.internal.metals.mcp.MetalsMcpStdioServer
 import scala.meta.internal.metals.mcp.ScalafixLlmRuleProvider
 import scala.meta.internal.metals.watcher.FileWatcherEvent
 import scala.meta.internal.metals.watcher.FileWatcherEvent.EventType
@@ -275,30 +276,62 @@ class ProjectMetalsLspService(
   )
 
   def startMcpServer(): Future[Unit] =
+    startMcpServer(useStdio = false)
+
+  def startMcpStdioServer(): Future[Unit] =
+    startMcpServer(useStdio = true)
+
+  private def startMcpServer(useStdio: Boolean): Future[Unit] =
     Future {
-      if (!isMcpServerRunning.getAndSet(true))
-        register(
-          new MetalsMcpServer(
-            queryEngine,
-            folder,
-            compilations,
-            () => focusedDocument,
-            diagnostics,
-            buildTargets,
-            mcpTestRunner,
-            userConfig.mcpClient.getOrElse(
-              initializeParams.getClientInfo().getName()
-            ),
-            getVisibleName,
-            languageClient,
-            connectionProvider,
-            scalaVersionSelector,
-            formattingProvider,
-            scalafixLlmRuleProvider,
-          )
-        ).run()
-    }.recover { case e: Exception =>
+      if (!isMcpServerRunning.getAndSet(true)) {
+        if (useStdio) {
+          register(
+            new MetalsMcpStdioServer(
+              queryEngine,
+              folder,
+              compilations,
+              () => focusedDocument,
+              diagnostics,
+              buildTargets,
+              mcpTestRunner,
+              userConfig.mcpClient.getOrElse(
+                initializeParams.getClientInfo().getName()
+              ),
+              getVisibleName,
+              languageClient,
+              connectionProvider,
+              scalaVersionSelector,
+              formattingProvider,
+              scalafixLlmRuleProvider,
+            )
+          ).run()
+        } else {
+          register(
+            new MetalsMcpServer(
+              queryEngine,
+              folder,
+              compilations,
+              () => focusedDocument,
+              diagnostics,
+              buildTargets,
+              mcpTestRunner,
+              userConfig.mcpClient.getOrElse(
+                initializeParams.getClientInfo().getName()
+              ),
+              getVisibleName,
+              languageClient,
+              connectionProvider,
+              scalaVersionSelector,
+              formattingProvider,
+              scalafixLlmRuleProvider,
+            )
+          ).run()
+        }
+      }
+    }.recoverWith { case e: Exception =>
+      isMcpServerRunning.set(false)
       scribe.error("Error starting MCP server", e)
+      Future.failed(e)
     }
 
   override def didChange(

metals/src/main/scala/scala/meta/internal/metals/logging/MetalsLogger.scala

@@ -74,6 +74,43 @@ object MetalsLogger {
     configureRootLogger(logfiles)
   }
 
+  def redirectLogsToFile(logfile: AbsolutePath): Unit = redirectLogsToFile(
+    List(logfile)
+  )
+
+  def redirectLogsToFile(logfiles: List[AbsolutePath]): Unit = {
+    logfiles.foreach(logfile =>
+      Files.createDirectories(logfile.toNIO.getParent)
+    )
+    configureRootLogger(logfiles)
+  }
+
+  def configureFileLogging(logfile: AbsolutePath): Unit = {
+    Files.createDirectories(logfile.toNIO.getParent)
+    configureFileLogging(List(logfile))
+  }
+
+  def configureFileLogging(logfiles: List[AbsolutePath]): Unit = {
+    logfiles.foreach(logfile =>
+      Files.createDirectories(logfile.toNIO.getParent)
+    )
+    logfiles
+      .foldLeft(
+        Logger.root
+          .clearModifiers()
+          .clearHandlers()
+      ) { (logger, logfile) =>
+        logger
+          .withHandler(
+            writer = newFileWriter(logfile),
+            formatter = defaultFormat,
+            minimumLevel = Some(level),
+            modifiers = List(MetalsFilter()),
+          )
+      }
+      .replace()
+  }
+
   private def configureRootLogger(logfile: List[AbsolutePath]): Unit = {
     logfile
       .foldLeft(

metals/src/main/scala/scala/meta/internal/metals/mcp/McpExceptions.scala

@@ -0,0 +1,43 @@
+package scala.meta.internal.metals.mcp
+
+object McpMessages {
+
+  object FindDep {
+
+    def versionMessage(completed: Option[String]): String = {
+      s"""|Latest version found: ${completed.getOrElse("none")}
+          |""".stripMargin
+    }
+
+    def dependencyReturnMessage(
+        key: String,
+        completed: Seq[String],
+    ): String = {
+      s"""|Tool managed to complete `$key` field and got potential values to use for it: ${completed.mkString(", ")}
+          |""".stripMargin
+    }
+
+    def noCompletionsFound: String =
+      "No completions found"
+  }
+}
+
+sealed trait IncorrectArgumentException extends Exception
+
+class MissingArgumentException(key: String)
+    extends Exception(s"Missing argument: $key")
+    with IncorrectArgumentException
+
+class IncorrectArgumentTypeException(key: String, expected: String)
+    extends Exception(s"Incorrect argument type for $key, expected: $expected")
+    with IncorrectArgumentException
+
+class InvalidSymbolTypeException(invalid: Seq[String], validTypes: String)
+    extends Exception(
+      s"Invalid symbol types: ${invalid.mkString(", ")}. Valid types are: $validTypes"
+    )
+    with IncorrectArgumentException
+
+object MissingFileInFocusException
+    extends Exception(s"Missing fileInFocus and failed to infer it.")
+    with IncorrectArgumentException