diff --git a/packages/flutter_tools/lib/src/base/context.dart b/packages/flutter_tools/lib/src/base/context.dart
index e830d6bc577..12d91564bc2 100644
--- a/packages/flutter_tools/lib/src/base/context.dart
+++ b/packages/flutter_tools/lib/src/base/context.dart
@@ -6,7 +6,7 @@ import 'dart:async';
 
 final AppContext _defaultContext = new AppContext();
 
-typedef void ErrorHandler(dynamic error);
+typedef void ErrorHandler(dynamic error, StackTrace stackTrace);
 
 /// A singleton for application functionality. This singleton can be different
 /// on a per-Zone basis.
@@ -17,6 +17,7 @@ AppContext get context {
 
 class AppContext {
   Map<Type, dynamic> _instances = <Type, dynamic>{};
+  Zone _zone;
 
   bool isSet(Type type) {
     if (_instances.containsKey(type))
@@ -30,7 +31,7 @@ class AppContext {
     if (_instances.containsKey(type))
       return _instances[type];
 
-    AppContext parent = _calcParent(Zone.current);
+    AppContext parent = _calcParent(_zone ?? Zone.current);
     return parent?.getVariable(type);
   }
 
@@ -58,11 +59,22 @@ class AppContext {
     }
   }
 
-  dynamic runInZone(dynamic method(), { ErrorHandler onError }) {
+  dynamic runInZone(dynamic method(), {
+    ZoneBinaryCallback<dynamic, dynamic, StackTrace> onError
+  }) {
     return runZoned(
-      method,
+      () => _run(method),
       zoneValues: <String, dynamic>{ 'context': this },
       onError: onError
     );
   }
+
+  dynamic _run(dynamic method()) async {
+    try {
+      _zone = Zone.current;
+      return await method();
+    } finally {
+      _zone = null;
+    }
+  }
 }
diff --git a/packages/flutter_tools/lib/src/base/logger.dart b/packages/flutter_tools/lib/src/base/logger.dart
index cbcc5161390..2ba170d6209 100644
--- a/packages/flutter_tools/lib/src/base/logger.dart
+++ b/packages/flutter_tools/lib/src/base/logger.dart
@@ -214,7 +214,6 @@ class AnsiTerminal {
   String writeBold(String str) => supportsColor ? '$_bold$str$_reset' : str;
 
   set singleCharMode(bool value) {
-    stdin.echoMode = !value;
     stdin.lineMode = !value;
   }
 
diff --git a/packages/flutter_tools/lib/src/base/utils.dart b/packages/flutter_tools/lib/src/base/utils.dart
index 7f9f5e48a9e..280c3935ae9 100644
--- a/packages/flutter_tools/lib/src/base/utils.dart
+++ b/packages/flutter_tools/lib/src/base/utils.dart
@@ -78,6 +78,13 @@ String getSizeAsMB(int bytesLength) {
   return '${(bytesLength / (1024 * 1024)).toStringAsFixed(1)}MB';
 }
 
+/// Return a relative path if [fullPath] is contained by the cwd, else return an
+/// absolute path.
+String getDisplayPath(String fullPath) {
+  String cwd = Directory.current.path + Platform.pathSeparator;
+  return fullPath.startsWith(cwd) ?  fullPath.substring(cwd.length) : fullPath;
+}
+
 /// A class to maintain a list of items, fire events when items are added or
 /// removed, and calculate a diff of changes when a new list of items is
 /// available.
diff --git a/packages/flutter_tools/lib/src/build_info.dart b/packages/flutter_tools/lib/src/build_info.dart
index 76b663211f1..c8d600e2fee 100644
--- a/packages/flutter_tools/lib/src/build_info.dart
+++ b/packages/flutter_tools/lib/src/build_info.dart
@@ -22,6 +22,16 @@ enum BuildMode {
 
 String getModeName(BuildMode mode) => getEnumName(mode);
 
+BuildMode getBuildModeForName(String mode) {
+  if (mode == 'debug')
+    return BuildMode.debug;
+  if (mode == 'profile')
+    return BuildMode.profile;
+  if (mode == 'release')
+    return BuildMode.release;
+  return null;
+}
+
 // Returns true if the selected build mode uses ahead-of-time compilation.
 bool isAotBuildMode(BuildMode mode) {
   return mode == BuildMode.profile || mode == BuildMode.release;
diff --git a/packages/flutter_tools/lib/src/commands/build_aot.dart b/packages/flutter_tools/lib/src/commands/build_aot.dart
index cc5148caff3..e5707de9b72 100644
--- a/packages/flutter_tools/lib/src/commands/build_aot.dart
+++ b/packages/flutter_tools/lib/src/commands/build_aot.dart
@@ -13,8 +13,8 @@ import '../base/utils.dart';
 import '../build_info.dart';
 import '../dart/sdk.dart';
 import '../globals.dart';
+import '../run.dart';
 import '../runner/flutter_command.dart';
-import 'run.dart';
 
 const String _kDefaultAotOutputDir = 'build/aot';
 
diff --git a/packages/flutter_tools/lib/src/commands/build_apk.dart b/packages/flutter_tools/lib/src/commands/build_apk.dart
index 38f576fd04f..08ee4ffac4d 100644
--- a/packages/flutter_tools/lib/src/commands/build_apk.dart
+++ b/packages/flutter_tools/lib/src/commands/build_apk.dart
@@ -10,17 +10,17 @@ import 'package:path/path.dart' as path;
 
 import '../android/android_sdk.dart';
 import '../base/file_system.dart' show ensureDirectoryExists;
-import '../base/os.dart';
 import '../base/logger.dart';
+import '../base/os.dart';
 import '../base/process.dart';
 import '../base/utils.dart';
 import '../build_info.dart';
 import '../flx.dart' as flx;
 import '../globals.dart';
+import '../run.dart';
 import '../runner/flutter_command.dart';
 import '../services.dart';
 import 'build_aot.dart';
-import 'run.dart';
 
 export '../android/android_device.dart' show AndroidDevice;
 
diff --git a/packages/flutter_tools/lib/src/commands/daemon.dart b/packages/flutter_tools/lib/src/commands/daemon.dart
index 247a4c3ac97..6b850f03c22 100644
--- a/packages/flutter_tools/lib/src/commands/daemon.dart
+++ b/packages/flutter_tools/lib/src/commands/daemon.dart
@@ -7,7 +7,6 @@ import 'dart:convert';
 import 'dart:io';
 
 import '../android/android_device.dart';
-import '../application_package.dart';
 import '../base/context.dart';
 import '../base/logger.dart';
 import '../build_info.dart';
@@ -15,10 +14,10 @@ import '../device.dart';
 import '../globals.dart';
 import '../ios/devices.dart';
 import '../ios/simulators.dart';
+import '../run.dart';
 import '../runner/flutter_command.dart';
-import 'run.dart';
 
-const String protocolVersion = '0.1.0';
+const String protocolVersion = '0.2.0';
 
 /// A server process command. This command will start up a long-lived server.
 /// It reads JSON-RPC based commands from stdin, executes them, and returns
@@ -73,14 +72,15 @@ class DaemonCommand extends FlutterCommand {
     return object;
   }
 
-  void _handleError(dynamic error) {
-    printError('Error from flutter daemon: $error');
+  dynamic _handleError(dynamic error, StackTrace stackTrace) {
+    printError('Error from flutter daemon: $error', stackTrace);
+    return null;
   }
 }
 
 typedef void DispatchComand(Map<String, dynamic> command);
 
-typedef Future<dynamic> CommandHandler(dynamic args);
+typedef Future<dynamic> CommandHandler(Map<String, dynamic> args);
 
 class Daemon {
   Daemon(Stream<Map<String, dynamic>> commandStream, this.sendCommand, {
@@ -137,7 +137,7 @@ class Daemon {
       if (_domainMap[prefix] == null)
         throw 'no domain for method: $method';
 
-      _domainMap[prefix].handleCommand(name, id, request['params']);
+      _domainMap[prefix].handleCommand(name, id, request['params'] ?? const <String, dynamic>{});
     } catch (error) {
       _send(<String, dynamic>{'id': id, 'error': _toJsonable(error)});
     }
@@ -168,7 +168,7 @@ abstract class Domain {
   @override
   String toString() => name;
 
-  void handleCommand(String command, dynamic id, dynamic args) {
+  void handleCommand(String command, dynamic id, Map<String, dynamic> args) {
     new Future<dynamic>.sync(() {
       if (_handlers.containsKey(command))
         return _handlers[command](args);
@@ -193,6 +193,33 @@ abstract class Domain {
 
   void _send(Map<String, dynamic> map) => daemon._send(map);
 
+  String _getStringArg(Map<String, dynamic> args, String name, { bool required: false }) {
+    if (required && !args.containsKey(name))
+      throw "$name is required";
+    dynamic val = args[name];
+    if (val != null && val is! String)
+      throw "$name is not a String";
+    return val;
+  }
+
+  bool _getBoolArg(Map<String, dynamic> args, String name, { bool required: false }) {
+    if (required && !args.containsKey(name))
+      throw "$name is required";
+    dynamic val = args[name];
+    if (val != null && val is! bool)
+      throw "$name is not a bool";
+    return val;
+  }
+
+  int _getIntArg(Map<String, dynamic> args, String name, { bool required: false }) {
+    if (required && !args.containsKey(name))
+      throw "$name is required";
+    dynamic val = args[name];
+    if (val != null && val is! int)
+      throw "$name is not an int";
+    return val;
+  }
+
   void dispose() { }
 }
 
@@ -222,11 +249,11 @@ class DaemonDomain extends Domain {
 
   StreamSubscription<LogMessage> _subscription;
 
-  Future<String> version(dynamic args) {
+  Future<String> version(Map<String, dynamic> args) {
     return new Future<String>.value(protocolVersion);
   }
 
-  Future<Null> shutdown(dynamic args) {
+  Future<Null> shutdown(Map<String, dynamic> args) {
     Timer.run(() => daemon.shutdown());
     return new Future<Null>.value();
   }
@@ -237,91 +264,149 @@ class DaemonDomain extends Domain {
   }
 }
 
-/// Return the device matching the deviceId field in the args.
-Future<Device> _getDevice(Daemon daemon, Map<String, dynamic> args) async {
-  if (args == null || args['deviceId'] is! String)
-    throw 'deviceId is required';
-
-  List<Device> devices = await daemon.deviceDomain.getDevices();
-  Device device = devices.firstWhere(
-    (Device device) => device.id == args['deviceId'],
-    orElse: () => null
-  );
-
-  if (device == null)
-    throw "device '${args['deviceId']}' not found";
-
-  return device;
-}
-
 /// This domain responds to methods like [start] and [stop].
 ///
-/// It'll be extended to fire events for when applications start, stop, and
-/// log data.
+/// It fires events for application start, stop, and stdout and stderr.
 class AppDomain extends Domain {
   AppDomain(Daemon daemon) : super(daemon, 'app') {
     registerHandler('start', start);
+    registerHandler('restart', restart);
     registerHandler('stop', stop);
     registerHandler('discover', discover);
   }
 
-  Future<dynamic> start(Map<String, dynamic> args) async {
-    Device device = await _getDevice(daemon, args);
+  static int _nextAppId = 0;
+
+  static String _getNextAppId() => 'app-${_nextAppId++}';
+
+  List<AppInstance> _apps = <AppInstance>[];
+
+  Future<Map<String, dynamic>> start(Map<String, dynamic> args) async {
+    String deviceId = _getStringArg(args, 'deviceId', required: true);
+    String projectDirectory = _getStringArg(args, 'projectDirectory', required: true);
+    bool startPaused = _getBoolArg(args, 'startPaused');
+    // TODO(devoncarew): Use the route param.
+    String route = _getStringArg(args, 'route'); // ignore: unused_local_variable
+    String mode = _getStringArg(args, 'mode');
+    String target = _getStringArg(args, 'target');
+
+    Device device = daemon.deviceDomain._getDevice(deviceId);
+    if (device == null)
+      throw "device '$deviceId' not found";
 
-    if (args['projectDirectory'] is! String)
-      throw "projectDirectory is required";
-    String projectDirectory = args['projectDirectory'];
     if (!FileSystemEntity.isDirectorySync(projectDirectory))
       throw "'$projectDirectory' does not exist";
 
+    BuildMode buildMode = getBuildModeForName(mode) ?? BuildMode.debug;
+    DebuggingOptions options;
+
+    switch (buildMode) {
+      case BuildMode.debug:
+      case BuildMode.profile:
+        options = new DebuggingOptions.enabled(buildMode, startPaused: startPaused);
+        break;
+      case BuildMode.release:
+        options = new DebuggingOptions.disabled(buildMode);
+        break;
+      default:
+        throw 'unhandle build mode: $buildMode';
+    }
+
     // We change the current working directory for the duration of the `start` command.
-    // TODO(devoncarew): Make flutter_tools work better with commands run from any directory.
     Directory cwd = Directory.current;
     Directory.current = new Directory(projectDirectory);
 
-    try {
-      int result = await startApp(
-        device,
-        stop: true,
-        target: args['target'],
-        route: args['route']
-      );
+    RunAndStayResident runner = new RunAndStayResident(
+      device,
+      target: target,
+      debuggingOptions: options,
+      usesTerminalUI: false
+    );
 
-      if (result != 0)
-        throw 'Error starting app: $result';
-    } finally {
-      Directory.current = cwd;
+    AppInstance app = new AppInstance(_getNextAppId(), runner);
+    _apps.add(app);
+    _sendAppEvent(app, 'start', <String, dynamic>{
+      'directory': projectDirectory,
+      'deviceId': deviceId
+    });
+
+    Completer<int> observatoryPortCompleter;
+
+    if (options.debuggingEnabled) {
+      observatoryPortCompleter = new Completer<int>();
+      observatoryPortCompleter.future.then((int port) {
+        _sendAppEvent(app, 'debugPort', <String, dynamic>{ 'port': port });
+      });
     }
 
-    return null;
+    app._runInZone(this, () {
+      runner.run(observatoryPortCompleter: observatoryPortCompleter).then((_) {
+        _sendAppEvent(app, 'stop');
+      }).catchError((dynamic error) {
+        _sendAppEvent(app, 'stop', <String, dynamic>{ 'error' : error.toString() });
+      }).whenComplete(() {
+        Directory.current = cwd;
+        _apps.remove(app);
+      });
+    });
+
+    return <String, dynamic>{ 'appId': app.id };
+  }
+
+  Future<bool> restart(Map<String, dynamic> args) async {
+    String appId = _getStringArg(args, 'appId', required: true);
+
+    AppInstance app = _getApp(appId);
+    if (app == null)
+      throw "app '$appId' not found";
+
+    return app._runInZone(this, () {
+      return app.restart();
+    });
   }
 
   Future<bool> stop(Map<String, dynamic> args) async {
-    Device device = await _getDevice(daemon, args);
+    String appId = _getStringArg(args, 'appId', required: true);
 
-    if (args['projectDirectory'] is! String)
-      throw "projectDirectory is required";
-    String projectDirectory = args['projectDirectory'];
-    if (!FileSystemEntity.isDirectorySync(projectDirectory))
-      throw "'$projectDirectory' does not exist";
+    AppInstance app = _getApp(appId);
+    if (app == null)
+      throw "app '$appId' not found";
 
-    Directory cwd = Directory.current;
-    Directory.current = new Directory(projectDirectory);
-
-    try {
-      ApplicationPackage app = command.applicationPackages.getPackageForPlatform(device.platform);
-      return device.stopApp(app);
-    } finally {
-      Directory.current = cwd;
-    }
+    return app.stop().timeout(new Duration(seconds: 5)).then((_) {
+      return true;
+    }).catchError((dynamic error) {
+      _sendAppEvent(app, 'log', <String, dynamic>{ 'log': '$error', 'error': true });
+      app.closeLogger();
+      _apps.remove(app);
+      return false;
+    });
   }
 
   Future<List<Map<String, dynamic>>> discover(Map<String, dynamic> args) async {
-    Device device = await _getDevice(daemon, args);
+    String deviceId = _getStringArg(args, 'deviceId', required: true);
+
+    Device device = daemon.deviceDomain._getDevice(deviceId);
+    if (device == null)
+      throw "device '$deviceId' not found";
+
     List<DiscoveredApp> apps = await device.discoverApps();
-    return apps.map((DiscoveredApp app) =>
-      <String, dynamic>{'id': app.id, 'observatoryDevicePort': app.observatoryPort}
-    ).toList();
+    return apps.map((DiscoveredApp app) {
+      return <String, dynamic>{
+        'id': app.id,
+        'observatoryDevicePort': app.observatoryPort
+      };
+    }).toList();
+  }
+
+  AppInstance _getApp(String id) {
+    return _apps.firstWhere((AppInstance app) => app.id == id, orElse: () => null);
+  }
+
+  void _sendAppEvent(AppInstance app, String name, [Map<String, dynamic> args]) {
+    Map<String, dynamic> eventArgs = <String, dynamic> { 'appId': app.id };
+    if (args != null)
+      eventArgs.addAll(args);
+    sendEvent('app.$name', eventArgs);
   }
 }
 
@@ -361,7 +446,7 @@ class DeviceDomain extends Domain {
 
   List<PollingDeviceDiscovery> _discoverers = <PollingDeviceDiscovery>[];
 
-  Future<List<Device>> getDevices([dynamic args]) {
+  Future<List<Device>> getDevices([Map<String, dynamic> args]) {
     List<Device> devices = _discoverers.expand((PollingDeviceDiscovery discoverer) {
       return discoverer.devices;
     }).toList();
@@ -369,56 +454,59 @@ class DeviceDomain extends Domain {
   }
 
   /// Enable device events.
-  Future<Null> enable(dynamic args) {
-    for (PollingDeviceDiscovery discoverer in _discoverers) {
+  Future<Null> enable(Map<String, dynamic> args) {
+    for (PollingDeviceDiscovery discoverer in _discoverers)
       discoverer.startPolling();
-    }
     return new Future<Null>.value();
   }
 
   /// Disable device events.
-  Future<Null> disable(dynamic args) {
-    for (PollingDeviceDiscovery discoverer in _discoverers) {
+  Future<Null> disable(Map<String, dynamic> args) {
+    for (PollingDeviceDiscovery discoverer in _discoverers)
       discoverer.stopPolling();
-    }
     return new Future<Null>.value();
   }
 
   /// Forward a host port to a device port.
   Future<Map<String, dynamic>> forward(Map<String, dynamic> args) async {
-    Device device = await _getDevice(daemon, args);
+    String deviceId = _getStringArg(args, 'deviceId', required: true);
+    int devicePort = _getIntArg(args, 'devicePort', required: true);
+    int hostPort = _getIntArg(args, 'hostPort');
 
-    if (args['devicePort'] is! int)
-      throw 'devicePort is required';
-    int devicePort = args['devicePort'];
-
-    int hostPort = args['hostPort'];
+    Device device = daemon.deviceDomain._getDevice(deviceId);
+    if (device == null)
+      throw "device '$deviceId' not found";
 
     hostPort = await device.portForwarder.forward(devicePort, hostPort: hostPort);
 
-    return <String, dynamic>{'hostPort': hostPort};
+    return <String, dynamic>{ 'hostPort': hostPort };
   }
 
   /// Removes a forwarded port.
   Future<Null> unforward(Map<String, dynamic> args) async {
-    Device device = await _getDevice(daemon, args);
+    String deviceId = _getStringArg(args, 'deviceId', required: true);
+    int devicePort = _getIntArg(args, 'devicePort', required: true);
+    int hostPort = _getIntArg(args, 'hostPort', required: true);
 
-    if (args['devicePort'] is! int)
-      throw 'devicePort is required';
-    int devicePort = args['devicePort'];
+    Device device = daemon.deviceDomain._getDevice(deviceId);
+    if (device == null)
+      throw "device '$deviceId' not found";
 
-    if (args['hostPort'] is! int)
-      throw 'hostPort is required';
-    int hostPort = args['hostPort'];
-
-    device.portForwarder.unforward(new ForwardedPort(hostPort, devicePort));
+    return device.portForwarder.unforward(new ForwardedPort(hostPort, devicePort));
   }
 
   @override
   void dispose() {
-    for (PollingDeviceDiscovery discoverer in _discoverers) {
+    for (PollingDeviceDiscovery discoverer in _discoverers)
       discoverer.dispose();
-    }
+  }
+
+  /// Return the device matching the deviceId field in the args.
+  Device _getDevice(String deviceId) {
+    List<Device> devices = _discoverers.expand((PollingDeviceDiscovery discoverer) {
+      return discoverer.devices;
+    }).toList();
+    return devices.firstWhere((Device device) => device.id == deviceId, orElse: () => null);
   }
 }
 
@@ -465,6 +553,75 @@ class NotifyingLogger extends Logger {
   }
 }
 
+/// A running application, started by this daemon.
+class AppInstance {
+  AppInstance(this.id, [this.runner]);
+
+  final String id;
+  final RunAndStayResident runner;
+
+  _AppRunLogger _logger;
+
+  Future<bool> restart() => runner.restart();
+
+  Future<Null> stop() => runner.stop();
+
+  void closeLogger() {
+    _logger.close();
+  }
+
+  dynamic _runInZone(AppDomain domain, dynamic method()) {
+    if (_logger == null)
+      _logger = new _AppRunLogger(domain, this);
+
+    AppContext appContext = new AppContext();
+    appContext[Logger] = _logger;
+    return appContext.runInZone(method);
+  }
+}
+
+/// A [Logger] which sends log messages to a listening daemon client.
+class _AppRunLogger extends Logger {
+  _AppRunLogger(this.domain, this.app);
+
+  AppDomain domain;
+  final AppInstance app;
+
+  @override
+  void printError(String message, [StackTrace stackTrace]) {
+    if (stackTrace != null) {
+      domain?._sendAppEvent(app, 'log', <String, dynamic>{
+        'log': message,
+        'stackTrace': stackTrace.toString(),
+        'error': true
+      });
+    } else {
+      domain?._sendAppEvent(app, 'log', <String, dynamic>{
+        'log': message,
+        'error': true
+      });
+    }
+  }
+
+  @override
+  void printStatus(String message, { bool emphasis: false }) {
+    domain?._sendAppEvent(app, 'log', <String, dynamic>{ 'log': message });
+  }
+
+  @override
+  void printTrace(String message) { }
+
+  @override
+  Status startProgress(String message) {
+    printStatus(message);
+    return new Status();
+  }
+
+  void close() {
+    domain = null;
+  }
+}
+
 class LogMessage {
   final String level;
   final String message;
diff --git a/packages/flutter_tools/lib/src/commands/drive.dart b/packages/flutter_tools/lib/src/commands/drive.dart
index 3bf2d90d039..9cc65aa535d 100644
--- a/packages/flutter_tools/lib/src/commands/drive.dart
+++ b/packages/flutter_tools/lib/src/commands/drive.dart
@@ -20,6 +20,7 @@ import '../dart/sdk.dart';
 import '../device.dart';
 import '../globals.dart';
 import '../ios/simulators.dart' show SimControl, IOSSimulatorUtils;
+import '../run.dart';
 import 'build_apk.dart' as build_apk;
 import 'run.dart';
 
diff --git a/packages/flutter_tools/lib/src/commands/run.dart b/packages/flutter_tools/lib/src/commands/run.dart
index bb0b4000abb..91925abb6ec 100644
--- a/packages/flutter_tools/lib/src/commands/run.dart
+++ b/packages/flutter_tools/lib/src/commands/run.dart
@@ -5,16 +5,14 @@
 import 'dart:async';
 import 'dart:io';
 
-import 'package:path/path.dart' as path;
-
 import '../application_package.dart';
 import '../base/common.dart';
-import '../base/logger.dart';
 import '../base/utils.dart';
 import '../build_info.dart';
 import '../device.dart';
 import '../globals.dart';
 import '../observatory.dart';
+import '../run.dart';
 import '../runner/flutter_command.dart';
 import 'build_apk.dart';
 import 'install.dart';
@@ -112,15 +110,16 @@ class RunCommand extends RunCommandBase {
     }
 
     if (argResults['resident']) {
-      _RunAndStayResident runner = new _RunAndStayResident(
+      RunAndStayResident runner = new RunAndStayResident(
         deviceForCommand,
         target: target,
-        debuggingOptions: options,
-        buildMode: getBuildMode()
+        debuggingOptions: options
       );
 
       return runner.run(traceStartup: traceStartup, benchmark: argResults['benchmark']);
     } else {
+      // TODO(devoncarew): Remove this path and support the `--no-resident` option
+      // using the `RunAndStayResident` class.
       return startApp(
         deviceForCommand,
         target: target,
@@ -160,7 +159,7 @@ Future<int> startApp(
 
   if (package == null) {
     String message = 'No application found for ${device.platform}.';
-    String hint = _getMissingPackageHintForPlatform(device.platform);
+    String hint = getMissingPackageHintForPlatform(device.platform);
     if (hint != null)
       message += '\n$hint';
     printError(message);
@@ -211,7 +210,7 @@ Future<int> startApp(
   if (traceStartup != null)
     platformArgs['trace-startup'] = traceStartup;
 
-  printStatus('Running ${_getDisplayPath(mainPath)} on ${device.name}...');
+  printStatus('Running ${getDisplayPath(mainPath)} on ${device.name}...');
 
   LaunchResult result = await device.startApp(
     package,
@@ -229,7 +228,7 @@ Future<int> startApp(
   } else if (traceStartup) {
     try {
       Observatory observatory = await Observatory.connect(result.observatoryPort);
-      await _downloadStartupTrace(observatory);
+      await downloadStartupTrace(observatory);
     } catch (error) {
       printError('Error connecting to observatory: $error');
       return 1;
@@ -237,345 +236,7 @@ Future<int> startApp(
   }
 
   if (benchmark)
-    _writeBenchmark(stopwatch);
+    writeRunBenchmarkFile(stopwatch);
 
   return result.started ? 0 : 2;
 }
-
-/// Given the value of the --target option, return the path of the Dart file
-/// where the app's main function should be.
-String findMainDartFile([String target]) {
-  if (target == null)
-    target = '';
-  String targetPath = path.absolute(target);
-  if (FileSystemEntity.isDirectorySync(targetPath))
-    return path.join(targetPath, 'lib', 'main.dart');
-  else
-    return targetPath;
-}
-
-String _getMissingPackageHintForPlatform(TargetPlatform platform) {
-  switch (platform) {
-    case TargetPlatform.android_arm:
-    case TargetPlatform.android_x64:
-      return 'Is your project missing an android/AndroidManifest.xml?';
-    case TargetPlatform.ios:
-      return 'Is your project missing an ios/Info.plist?';
-    default:
-      return null;
-  }
-}
-
-/// Return a relative path if [fullPath] is contained by the cwd, else return an
-/// absolute path.
-String _getDisplayPath(String fullPath) {
-  String cwd = Directory.current.path + Platform.pathSeparator;
-  return fullPath.startsWith(cwd) ?  fullPath.substring(cwd.length) : fullPath;
-}
-
-class _RunAndStayResident {
-  _RunAndStayResident(
-    this.device, {
-    this.target,
-    this.debuggingOptions,
-    this.buildMode : BuildMode.debug
-  });
-
-  final Device device;
-  final String target;
-  final DebuggingOptions debuggingOptions;
-  final BuildMode buildMode;
-
-  Completer<int> _exitCompleter;
-  StreamSubscription<String> _loggingSubscription;
-
-  Observatory observatory;
-
-  /// Start the app and keep the process running during its lifetime.
-  Future<int> run({ bool traceStartup: false, bool benchmark: false }) {
-    // Don't let uncaught errors kill the process.
-    return runZoned(() {
-      return _run(traceStartup: traceStartup, benchmark: benchmark);
-    }, onError: (dynamic error) {
-      printError('Exception from flutter run: $error');
-    });
-  }
-
-  Future<int> _run({ bool traceStartup: false, bool benchmark: false }) async {
-    String mainPath = findMainDartFile(target);
-    if (!FileSystemEntity.isFileSync(mainPath)) {
-      String message = 'Tried to run $mainPath, but that file does not exist.';
-      if (target == null)
-        message += '\nConsider using the -t option to specify the Dart file to start.';
-      printError(message);
-      return 1;
-    }
-
-    ApplicationPackage package = getApplicationPackageForPlatform(device.platform);
-
-    if (package == null) {
-      String message = 'No application found for ${device.platform}.';
-      String hint = _getMissingPackageHintForPlatform(device.platform);
-      if (hint != null)
-        message += '\n$hint';
-      printError(message);
-      return 1;
-    }
-
-    Stopwatch startTime = new Stopwatch()..start();
-
-    // TODO(devoncarew): We shouldn't have to do type checks here.
-    if (device is AndroidDevice) {
-      printTrace('Running build command.');
-
-      int result = await buildApk(
-        device.platform,
-        target: target,
-        buildMode: buildMode
-      );
-
-      if (result != 0)
-        return result;
-    }
-
-    // TODO(devoncarew): Move this into the device.startApp() impls.
-    if (package != null) {
-      printTrace("Stopping app '${package.name}' on ${device.name}.");
-      // We don't wait for the stop command to complete.
-      device.stopApp(package);
-    }
-
-    // Allow any stop commands from above to start work.
-    await new Future<Duration>.delayed(Duration.ZERO);
-
-    // TODO(devoncarew): This fails for ios devices - we haven't built yet.
-    if (device is AndroidDevice) {
-      printTrace('Running install command.');
-      if (!(installApp(device, package)))
-        return 1;
-    }
-
-    Map<String, dynamic> platformArgs;
-    if (traceStartup != null)
-      platformArgs = <String, dynamic>{ 'trace-startup': traceStartup };
-
-    printStatus('Running ${_getDisplayPath(mainPath)} on ${device.name}...');
-
-    _loggingSubscription = device.logReader.logLines.listen((String line) {
-      if (!line.contains('Observatory listening on http') && !line.contains('Diagnostic server listening on http'))
-        printStatus(line);
-    });
-
-    LaunchResult result = await device.startApp(
-      package,
-      buildMode,
-      mainPath: mainPath,
-      debuggingOptions: debuggingOptions,
-      platformArgs: platformArgs
-    );
-
-    if (!result.started) {
-      printError('Error running application on ${device.name}.');
-      await _loggingSubscription.cancel();
-      return 2;
-    }
-
-    startTime.stop();
-
-    _exitCompleter = new Completer<int>();
-
-    // Connect to observatory.
-    if (debuggingOptions.debuggingEnabled) {
-      observatory = await Observatory.connect(result.observatoryPort);
-      printTrace('Connected to observatory port: ${result.observatoryPort}.');
-
-      observatory.populateIsolateInfo();
-      observatory.onExtensionEvent.listen((Event event) {
-        printTrace(event.toString());
-      });
-      observatory.onIsolateEvent.listen((Event event) {
-        printTrace(event.toString());
-      });
-
-      if (benchmark)
-        await observatory.waitFirstIsolate;
-
-      // Listen for observatory connection close.
-      observatory.done.whenComplete(() {
-        _handleExit();
-      });
-    }
-
-    printStatus('Application running.');
-
-    if (observatory != null && traceStartup) {
-      printStatus('Downloading startup trace info...');
-
-      await _downloadStartupTrace(observatory);
-
-      _handleExit();
-    } else {
-      if (!logger.quiet)
-        _printHelp();
-
-      terminal.singleCharMode = true;
-
-      terminal.onCharInput.listen((String code) {
-        String lower = code.toLowerCase();
-
-        if (lower == 'h' || code == AnsiTerminal.KEY_F1) {
-          // F1, help
-          _printHelp();
-        } else if (lower == 'r' || code == AnsiTerminal.KEY_F5) {
-          // F5, refresh
-          _handleRefresh(package, result, mainPath);
-        } else if (lower == 'q' || code == AnsiTerminal.KEY_F10) {
-          // F10, exit
-          _handleExit();
-        }
-      });
-
-      ProcessSignal.SIGINT.watch().listen((ProcessSignal signal) {
-        _handleExit();
-      });
-      ProcessSignal.SIGTERM.watch().listen((ProcessSignal signal) {
-        _handleExit();
-      });
-    }
-
-    if (benchmark) {
-      await new Future<Null>.delayed(new Duration(seconds: 4));
-
-      // Touch the file.
-      File mainFile = new File(mainPath);
-      mainFile.writeAsBytesSync(mainFile.readAsBytesSync());
-
-      Stopwatch restartTime = new Stopwatch()..start();
-      bool restarted = await _handleRefresh(package, result, mainPath);
-      restartTime.stop();
-      _writeBenchmark(startTime, restarted ? restartTime : null);
-      await new Future<Null>.delayed(new Duration(seconds: 2));
-      _handleExit();
-    }
-
-    return _exitCompleter.future.then((int exitCode) async {
-      try {
-        if (observatory != null && !observatory.isClosed) {
-          if (observatory.isolates.isNotEmpty) {
-            observatory.flutterExit(observatory.firstIsolateId);
-            // The Dart WebSockets API does not have a flush() method.
-            await new Future<Null>.delayed(new Duration(milliseconds: 100));
-          }
-        }
-      } catch (error) {
-        stderr.writeln(error.toString());
-      }
-
-      return exitCode;
-    });
-  }
-
-  void _printHelp() {
-    printStatus('Type "h" or F1 for help, "r" or F5 to restart the app, and "q", F10, or ctrl-c to quit.');
-  }
-
-  Future<bool> _handleRefresh(ApplicationPackage package, LaunchResult result, String mainPath) async {
-    if (observatory == null) {
-      printError('Debugging is not enabled.');
-      return false;
-    } else {
-      Status status = logger.startProgress('Re-starting application...');
-
-      Future<Event> extensionAddedEvent = observatory.onExtensionEvent
-        .where((Event event) => event.extensionKind == 'Flutter.FrameworkInitialization')
-        .first;
-
-      bool restartResult = await device.restartApp(
-        package,
-        result,
-        mainPath: mainPath,
-        observatory: observatory
-      );
-
-      status.stop(showElapsedTime: true);
-
-      if (restartResult) {
-        // TODO(devoncarew): We should restore the route here.
-
-        await extensionAddedEvent;
-      }
-
-      return restartResult;
-    }
-  }
-
-  void _handleExit() {
-    terminal.singleCharMode = false;
-
-    if (!_exitCompleter.isCompleted) {
-      _loggingSubscription?.cancel();
-      printStatus('Application finished.');
-      _exitCompleter.complete(0);
-    }
-  }
-}
-
-Future<Null> _downloadStartupTrace(Observatory observatory) async {
-  Tracing tracing = new Tracing(observatory);
-
-  Map<String, dynamic> timeline = await tracing.stopTracingAndDownloadTimeline(
-    waitForFirstFrame: true
-  );
-
-  int extractInstantEventTimestamp(String eventName) {
-    List<Map<String, dynamic>> events = timeline['traceEvents'];
-    Map<String, dynamic> event = events.firstWhere(
-      (Map<String, dynamic> event) => event['name'] == eventName, orElse: () => null
-    );
-    return event == null ? null : event['ts'];
-  }
-
-  int engineEnterTimestampMicros = extractInstantEventTimestamp(kFlutterEngineMainEnterEventName);
-  int frameworkInitTimestampMicros = extractInstantEventTimestamp(kFrameworkInitEventName);
-  int firstFrameTimestampMicros = extractInstantEventTimestamp(kFirstUsefulFrameEventName);
-
-  if (engineEnterTimestampMicros == null) {
-    printError('Engine start event is missing in the timeline. Cannot compute startup time.');
-    return null;
-  }
-
-  if (firstFrameTimestampMicros == null) {
-    printError('First frame event is missing in the timeline. Cannot compute startup time.');
-    return null;
-  }
-
-  File traceInfoFile = new File('build/start_up_info.json');
-  int timeToFirstFrameMicros = firstFrameTimestampMicros - engineEnterTimestampMicros;
-  Map<String, dynamic> traceInfo = <String, dynamic>{
-    'engineEnterTimestampMicros': engineEnterTimestampMicros,
-    'timeToFirstFrameMicros': timeToFirstFrameMicros,
-  };
-
-  if (frameworkInitTimestampMicros != null) {
-    traceInfo['timeToFrameworkInitMicros'] = frameworkInitTimestampMicros - engineEnterTimestampMicros;
-    traceInfo['timeAfterFrameworkInitMicros'] = firstFrameTimestampMicros - frameworkInitTimestampMicros;
-  }
-
-  traceInfoFile.writeAsStringSync(toPrettyJson(traceInfo));
-
-  printStatus('Time to first frame: ${timeToFirstFrameMicros ~/ 1000}ms.');
-  printStatus('Saved startup trace info in ${traceInfoFile.path}.');
-}
-
-void _writeBenchmark(Stopwatch startTime, [Stopwatch restartTime]) {
-  final String benchmarkOut = 'refresh_benchmark.json';
-  Map<String, dynamic> data = <String, dynamic>{
-    'start': startTime.elapsedMilliseconds,
-    'time': (restartTime ?? startTime).elapsedMilliseconds // time and restart are the same
-  };
-  if (restartTime != null)
-    data['restart'] = restartTime.elapsedMilliseconds;
-
-  new File(benchmarkOut).writeAsStringSync(toPrettyJson(data));
-  printStatus('Run benchmark written to $benchmarkOut ($data).');
-}
diff --git a/packages/flutter_tools/lib/src/commands/run_mojo.dart b/packages/flutter_tools/lib/src/commands/run_mojo.dart
index b3cc0bb062c..67da3832388 100644
--- a/packages/flutter_tools/lib/src/commands/run_mojo.dart
+++ b/packages/flutter_tools/lib/src/commands/run_mojo.dart
@@ -11,8 +11,8 @@ import '../base/process.dart';
 import '../build_info.dart';
 import '../flx.dart' as flx;
 import '../globals.dart';
+import '../run.dart';
 import '../runner/flutter_command.dart';
-import 'run.dart';
 
 const String _kDefaultBundlePath = 'build/app.flx';
 
diff --git a/packages/flutter_tools/lib/src/commands/stop.dart b/packages/flutter_tools/lib/src/commands/stop.dart
index 630ecb110c8..123c2a935c5 100644
--- a/packages/flutter_tools/lib/src/commands/stop.dart
+++ b/packages/flutter_tools/lib/src/commands/stop.dart
@@ -5,6 +5,7 @@
 import 'dart:async';
 
 import '../application_package.dart';
+import '../build_info.dart';
 import '../device.dart';
 import '../globals.dart';
 import '../runner/flutter_command.dart';
@@ -23,6 +24,11 @@ class StopCommand extends FlutterCommand {
   Future<int> runInProject() async {
     Device device = deviceForCommand;
     ApplicationPackage app = applicationPackages.getPackageForPlatform(device.platform);
+    if (app == null) {
+      String platformName = getNameForTargetPlatform(device.platform);
+      printError('No Flutter application for $platformName found in the current directory.');
+      return 1;
+    }
     printStatus('Stopping apps on ${device.name}.');
     return await device.stopApp(app) ? 0 : 1;
   }
diff --git a/packages/flutter_tools/lib/src/commands/test.dart b/packages/flutter_tools/lib/src/commands/test.dart
index 53df9c20447..9ad502afe1c 100644
--- a/packages/flutter_tools/lib/src/commands/test.dart
+++ b/packages/flutter_tools/lib/src/commands/test.dart
@@ -8,6 +8,7 @@ import 'dart:io';
 import 'package:path/path.dart' as path;
 import 'package:test/src/executable.dart' as executable; // ignore: implementation_imports
 
+import '../dart/package_map.dart';
 import '../globals.dart';
 import '../runner/flutter_command.dart';
 import '../test/flutter_platform.dart' as loader;
@@ -58,6 +59,7 @@ class TestCommand extends FlutterCommand {
     try {
       if (testDirectory != null) {
         printTrace('switching to directory $testDirectory to run tests');
+        PackageMap.globalPackagesPath = path.normalize(path.absolute(PackageMap.globalPackagesPath));
         Directory.current = testDirectory;
       }
       printTrace('running test package with arguments: $testArgs');
diff --git a/packages/flutter_tools/lib/src/commands/trace.dart b/packages/flutter_tools/lib/src/commands/trace.dart
index 9d90983fdb2..674940a62a5 100644
--- a/packages/flutter_tools/lib/src/commands/trace.dart
+++ b/packages/flutter_tools/lib/src/commands/trace.dart
@@ -147,3 +147,52 @@ class Tracing {
     return timeline.response;
   }
 }
+
+/// Download the startup trace information from the given observatory client and
+/// store it to build/start_up_info.json.
+Future<Null> downloadStartupTrace(Observatory observatory) async {
+  Tracing tracing = new Tracing(observatory);
+
+  Map<String, dynamic> timeline = await tracing.stopTracingAndDownloadTimeline(
+    waitForFirstFrame: true
+  );
+
+  int extractInstantEventTimestamp(String eventName) {
+    List<Map<String, dynamic>> events = timeline['traceEvents'];
+    Map<String, dynamic> event = events.firstWhere(
+      (Map<String, dynamic> event) => event['name'] == eventName, orElse: () => null
+    );
+    return event == null ? null : event['ts'];
+  }
+
+  int engineEnterTimestampMicros = extractInstantEventTimestamp(kFlutterEngineMainEnterEventName);
+  int frameworkInitTimestampMicros = extractInstantEventTimestamp(kFrameworkInitEventName);
+  int firstFrameTimestampMicros = extractInstantEventTimestamp(kFirstUsefulFrameEventName);
+
+  if (engineEnterTimestampMicros == null) {
+    printError('Engine start event is missing in the timeline. Cannot compute startup time.');
+    return null;
+  }
+
+  if (firstFrameTimestampMicros == null) {
+    printError('First frame event is missing in the timeline. Cannot compute startup time.');
+    return null;
+  }
+
+  File traceInfoFile = new File('build/start_up_info.json');
+  int timeToFirstFrameMicros = firstFrameTimestampMicros - engineEnterTimestampMicros;
+  Map<String, dynamic> traceInfo = <String, dynamic>{
+    'engineEnterTimestampMicros': engineEnterTimestampMicros,
+    'timeToFirstFrameMicros': timeToFirstFrameMicros,
+  };
+
+  if (frameworkInitTimestampMicros != null) {
+    traceInfo['timeToFrameworkInitMicros'] = frameworkInitTimestampMicros - engineEnterTimestampMicros;
+    traceInfo['timeAfterFrameworkInitMicros'] = firstFrameTimestampMicros - frameworkInitTimestampMicros;
+  }
+
+  traceInfoFile.writeAsStringSync(toPrettyJson(traceInfo));
+
+  printStatus('Time to first frame: ${timeToFirstFrameMicros ~/ 1000}ms.');
+  printStatus('Saved startup trace info in ${traceInfoFile.path}.');
+}
diff --git a/packages/flutter_tools/lib/src/dart/package_map.dart b/packages/flutter_tools/lib/src/dart/package_map.dart
index 6c4252878d1..2e0705c0078 100644
--- a/packages/flutter_tools/lib/src/dart/package_map.dart
+++ b/packages/flutter_tools/lib/src/dart/package_map.dart
@@ -17,6 +17,14 @@ Map<String, Uri> _parse(String packagesPath) {
 class PackageMap {
   PackageMap(this.packagesPath);
 
+  static String get globalPackagesPath => _globalPackagesPath ?? kPackagesFileName;
+
+  static set globalPackagesPath(String value) {
+    _globalPackagesPath = value;
+  }
+
+  static String _globalPackagesPath;
+
   final String packagesPath;
 
   Map<String, Uri> get map {
@@ -26,8 +34,6 @@ class PackageMap {
   }
   Map<String, Uri> _map;
 
-  static PackageMap instance;
-
   String checkValid() {
     if (FileSystemEntity.isFileSync(packagesPath))
       return null;
diff --git a/packages/flutter_tools/lib/src/device.dart b/packages/flutter_tools/lib/src/device.dart
index fc96d64ae38..5d96756d790 100644
--- a/packages/flutter_tools/lib/src/device.dart
+++ b/packages/flutter_tools/lib/src/device.dart
@@ -321,7 +321,7 @@ abstract class DevicePortForwarder {
   /// Forward [hostPort] on the host to [devicePort] on the device.
   /// If [hostPort] is null, will auto select a host port.
   /// Returns a Future that completes with the host port.
-  Future<int> forward(int devicePort, { int hostPort: null });
+  Future<int> forward(int devicePort, { int hostPort });
 
   /// Stops forwarding [forwardedPort].
   Future<Null> unforward(ForwardedPort forwardedPort);
diff --git a/packages/flutter_tools/lib/src/flx.dart b/packages/flutter_tools/lib/src/flx.dart
index e4309938148..77457598e1d 100644
--- a/packages/flutter_tools/lib/src/flx.dart
+++ b/packages/flutter_tools/lib/src/flx.dart
@@ -46,7 +46,7 @@ Future<int> createSnapshot({
   final List<String> args = <String>[
     tools.getHostToolPath(HostTool.SkySnapshot),
     mainPath,
-    '--packages=${PackageMap.instance.packagesPath}',
+    '--packages=${path.absolute(PackageMap.globalPackagesPath)}',
     '--snapshot=$snapshotPath'
   ];
   if (depfilePath != null)
diff --git a/packages/flutter_tools/lib/src/run.dart b/packages/flutter_tools/lib/src/run.dart
new file mode 100644
index 00000000000..7d95e0cd596
--- /dev/null
+++ b/packages/flutter_tools/lib/src/run.dart
@@ -0,0 +1,338 @@
+// Copyright 2016 The Chromium Authors. All rights reserved.
+// Use of this source code is governed by a BSD-style license that can be
+// found in the LICENSE file.
+
+import 'dart:async';
+import 'dart:io';
+
+import 'package:path/path.dart' as path;
+
+import 'application_package.dart';
+import 'base/logger.dart';
+import 'base/utils.dart';
+import 'build_info.dart';
+import 'commands/build_apk.dart';
+import 'commands/install.dart';
+import 'commands/trace.dart';
+import 'device.dart';
+import 'globals.dart';
+import 'observatory.dart';
+
+/// Given the value of the --target option, return the path of the Dart file
+/// where the app's main function should be.
+String findMainDartFile([String target]) {
+  if (target == null)
+    target = '';
+  String targetPath = path.absolute(target);
+  if (FileSystemEntity.isDirectorySync(targetPath))
+    return path.join(targetPath, 'lib', 'main.dart');
+  else
+    return targetPath;
+}
+
+// TODO: split out the cli part of the UI from this class
+
+class RunAndStayResident {
+  RunAndStayResident(
+    this.device, {
+    this.target,
+    this.debuggingOptions,
+    this.usesTerminalUI: true
+  });
+
+  final Device device;
+  final String target;
+  final DebuggingOptions debuggingOptions;
+  final bool usesTerminalUI;
+
+  ApplicationPackage _package;
+  String _mainPath;
+  LaunchResult _result;
+
+  Completer<int> _exitCompleter = new Completer<int>();
+  StreamSubscription<String> _loggingSubscription;
+
+  Observatory observatory;
+
+  /// Start the app and keep the process running during its lifetime.
+  Future<int> run({
+    bool traceStartup: false,
+    bool benchmark: false,
+    Completer<int> observatoryPortCompleter
+  }) {
+    // Don't let uncaught errors kill the process.
+    return runZoned(() {
+      return _run(
+        traceStartup: traceStartup,
+        benchmark: benchmark,
+        observatoryPortCompleter: observatoryPortCompleter
+      );
+    }, onError: (dynamic error, StackTrace stackTrace) {
+      printError('Exception from flutter run: $error', stackTrace);
+    });
+  }
+
+  Future<bool> restart() async {
+    if (observatory == null) {
+      printError('Debugging is not enabled.');
+      return false;
+    } else {
+      Status status = logger.startProgress('Re-starting application...');
+
+      Future<Event> extensionAddedEvent = observatory.onExtensionEvent
+        .where((Event event) => event.extensionKind == 'Flutter.FrameworkInitialization')
+        .first;
+
+      bool restartResult = await device.restartApp(
+        _package,
+        _result,
+        mainPath: _mainPath,
+        observatory: observatory
+      );
+
+      status.stop(showElapsedTime: true);
+
+      if (restartResult) {
+        // TODO(devoncarew): We should restore the route here.
+        await extensionAddedEvent;
+      }
+
+      return restartResult;
+    }
+  }
+
+  Future<Null> stop() {
+    _stopLogger();
+    return _stopApp();
+  }
+
+  Future<int> _run({
+    bool traceStartup: false,
+    bool benchmark: false,
+    Completer<int> observatoryPortCompleter
+  }) async {
+    _mainPath = findMainDartFile(target);
+    if (!FileSystemEntity.isFileSync(_mainPath)) {
+      String message = 'Tried to run $_mainPath, but that file does not exist.';
+      if (target == null)
+        message += '\nConsider using the -t option to specify the Dart file to start.';
+      printError(message);
+      return 1;
+    }
+
+    _package = getApplicationPackageForPlatform(device.platform);
+
+    if (_package == null) {
+      String message = 'No application found for ${device.platform}.';
+      String hint = getMissingPackageHintForPlatform(device.platform);
+      if (hint != null)
+        message += '\n$hint';
+      printError(message);
+      return 1;
+    }
+
+    Stopwatch startTime = new Stopwatch()..start();
+
+    // TODO(devoncarew): We shouldn't have to do type checks here.
+    if (device is AndroidDevice) {
+      printTrace('Running build command.');
+
+      int result = await buildApk(
+        device.platform,
+        target: target,
+        buildMode: debuggingOptions.buildMode
+      );
+
+      if (result != 0)
+        return result;
+    }
+
+    // TODO(devoncarew): Move this into the device.startApp() impls.
+    if (_package != null) {
+      printTrace("Stopping app '${_package.name}' on ${device.name}.");
+      // We don't wait for the stop command to complete.
+      device.stopApp(_package);
+    }
+
+    // Allow any stop commands from above to start work.
+    await new Future<Duration>.delayed(Duration.ZERO);
+
+    // TODO(devoncarew): This fails for ios devices - we haven't built yet.
+    if (device is AndroidDevice) {
+      printTrace('Running install command.');
+      if (!(installApp(device, _package)))
+        return 1;
+    }
+
+    Map<String, dynamic> platformArgs;
+    if (traceStartup != null)
+      platformArgs = <String, dynamic>{ 'trace-startup': traceStartup };
+
+    printStatus('Running ${getDisplayPath(_mainPath)} on ${device.name}...');
+
+    _loggingSubscription = device.logReader.logLines.listen((String line) {
+      if (!line.contains('Observatory listening on http') && !line.contains('Diagnostic server listening on http'))
+        printStatus(line);
+    });
+
+    _result = await device.startApp(
+      _package,
+      debuggingOptions.buildMode,
+      mainPath: _mainPath,
+      debuggingOptions: debuggingOptions,
+      platformArgs: platformArgs
+    );
+
+    if (!_result.started) {
+      printError('Error running application on ${device.name}.');
+      await _loggingSubscription.cancel();
+      return 2;
+    }
+
+    startTime.stop();
+
+    if (observatoryPortCompleter != null && _result.hasObservatory)
+      observatoryPortCompleter.complete(_result.observatoryPort);
+
+    // Connect to observatory.
+    if (debuggingOptions.debuggingEnabled) {
+      observatory = await Observatory.connect(_result.observatoryPort);
+      printTrace('Connected to observatory port: ${_result.observatoryPort}.');
+
+      observatory.populateIsolateInfo();
+      observatory.onExtensionEvent.listen((Event event) {
+        printTrace(event.toString());
+      });
+      observatory.onIsolateEvent.listen((Event event) {
+        printTrace(event.toString());
+      });
+
+      if (benchmark)
+        await observatory.waitFirstIsolate;
+
+      // Listen for observatory connection close.
+      observatory.done.whenComplete(() {
+        if (!_exitCompleter.isCompleted) {
+          printStatus('Application finished.');
+          _exitCompleter.complete(0);
+        }
+      });
+    }
+
+    printStatus('Application running.');
+
+    if (observatory != null && traceStartup) {
+      printStatus('Downloading startup trace info...');
+
+      await downloadStartupTrace(observatory);
+
+      if (!_exitCompleter.isCompleted)
+        _exitCompleter.complete(0);
+    } else {
+      if (usesTerminalUI) {
+        if (!logger.quiet)
+          _printHelp();
+
+        terminal.singleCharMode = true;
+        terminal.onCharInput.listen((String code) {
+          String lower = code.toLowerCase();
+
+          if (lower == 'h' || code == AnsiTerminal.KEY_F1) {
+            // F1, help
+            _printHelp();
+          } else if (lower == 'r' || code == AnsiTerminal.KEY_F5) {
+            // F5, restart
+            restart();
+          } else if (lower == 'q' || code == AnsiTerminal.KEY_F10) {
+            // F10, exit
+            _stopApp();
+          }
+        });
+      }
+
+      ProcessSignal.SIGINT.watch().listen((ProcessSignal signal) {
+        _resetTerminal();
+        _stopLogger();
+        _stopApp();
+      });
+      ProcessSignal.SIGTERM.watch().listen((ProcessSignal signal) {
+        _resetTerminal();
+        _stopLogger();
+        _stopApp();
+      });
+    }
+
+    if (benchmark) {
+      await new Future<Null>.delayed(new Duration(seconds: 4));
+
+      // Touch the file.
+      File mainFile = new File(_mainPath);
+      mainFile.writeAsBytesSync(mainFile.readAsBytesSync());
+
+      Stopwatch restartTime = new Stopwatch()..start();
+      bool restarted = await restart();
+      restartTime.stop();
+      writeRunBenchmarkFile(startTime, restarted ? restartTime : null);
+      await new Future<Null>.delayed(new Duration(seconds: 2));
+      stop();
+    }
+
+    return _exitCompleter.future.then((int exitCode) async {
+      _resetTerminal();
+      _stopLogger();
+      return exitCode;
+    });
+  }
+
+  void _printHelp() {
+    printStatus('Type "h" or F1 for help, "r" or F5 to restart the app, and "q", F10, or ctrl-c to quit.');
+  }
+
+  void _stopLogger() {
+    _loggingSubscription?.cancel();
+  }
+
+  void _resetTerminal() {
+    if (usesTerminalUI)
+      terminal.singleCharMode = false;
+  }
+
+  Future<Null> _stopApp() {
+    if (observatory != null && !observatory.isClosed) {
+      if (observatory.isolates.isNotEmpty) {
+        observatory.flutterExit(observatory.firstIsolateId);
+        return new Future<Null>.delayed(new Duration(milliseconds: 100));
+      }
+    }
+
+    if (!_exitCompleter.isCompleted)
+      _exitCompleter.complete(0);
+
+    return new Future<Null>.value();
+  }
+}
+
+String getMissingPackageHintForPlatform(TargetPlatform platform) {
+  switch (platform) {
+    case TargetPlatform.android_arm:
+    case TargetPlatform.android_x64:
+      return 'Is your project missing an android/AndroidManifest.xml?';
+    case TargetPlatform.ios:
+      return 'Is your project missing an ios/Info.plist?';
+    default:
+      return null;
+  }
+}
+
+void writeRunBenchmarkFile(Stopwatch startTime, [Stopwatch restartTime]) {
+  final String benchmarkOut = 'refresh_benchmark.json';
+  Map<String, dynamic> data = <String, dynamic>{
+    'start': startTime.elapsedMilliseconds,
+    'time': (restartTime ?? startTime).elapsedMilliseconds // time and restart are the same
+  };
+  if (restartTime != null)
+    data['restart'] = restartTime.elapsedMilliseconds;
+
+  new File(benchmarkOut).writeAsStringSync(toPrettyJson(data));
+  printStatus('Run benchmark written to $benchmarkOut ($data).');
+}
diff --git a/packages/flutter_tools/lib/src/runner/flutter_command.dart b/packages/flutter_tools/lib/src/runner/flutter_command.dart
index 2917a5a4f84..cb476b5dfe3 100644
--- a/packages/flutter_tools/lib/src/runner/flutter_command.dart
+++ b/packages/flutter_tools/lib/src/runner/flutter_command.dart
@@ -193,7 +193,7 @@ abstract class FlutterCommand extends Command {
 
     // Validate the current package map only if we will not be running "pub get" later.
     if (!(_usesPubOption && argResults['pub'])) {
-      String error = PackageMap.instance.checkValid();
+      String error = new PackageMap(PackageMap.globalPackagesPath).checkValid();
       if (error != null) {
         printError(error);
         return false;
diff --git a/packages/flutter_tools/lib/src/runner/flutter_command_runner.dart b/packages/flutter_tools/lib/src/runner/flutter_command_runner.dart
index 98f176b859f..18a79b045f4 100644
--- a/packages/flutter_tools/lib/src/runner/flutter_command_runner.dart
+++ b/packages/flutter_tools/lib/src/runner/flutter_command_runner.dart
@@ -148,9 +148,8 @@ class FlutterCommandRunner extends CommandRunner {
     if (!_checkFlutterCopy())
       return new Future<int>.value(1);
 
-    PackageMap.instance = new PackageMap(path.normalize(path.absolute(
-      globalResults.wasParsed('packages') ? globalResults['packages'] : kPackagesFileName
-    )));
+    if (globalResults.wasParsed('packages'))
+      PackageMap.globalPackagesPath = path.normalize(path.absolute(globalResults['packages']));
 
     // See if the user specified a specific device.
     deviceManager.specifiedDeviceId = globalResults['device-id'];
@@ -191,7 +190,7 @@ class FlutterCommandRunner extends CommandRunner {
 
     if (engineSourcePath == null && globalResults['local-engine'] != null) {
       try {
-        Uri engineUri = PackageMap.instance.map[kFlutterEnginePackageName];
+        Uri engineUri = new PackageMap(PackageMap.globalPackagesPath).map[kFlutterEnginePackageName];
         engineSourcePath = path.dirname(path.dirname(path.dirname(path.dirname(engineUri.path))));
         bool dirExists = FileSystemEntity.isDirectorySync(path.join(engineSourcePath, 'out'));
         if (engineSourcePath == '/' || engineSourcePath.isEmpty || !dirExists)
diff --git a/packages/flutter_tools/lib/src/services.dart b/packages/flutter_tools/lib/src/services.dart
index 7f8b3818b4f..2fe5947794f 100644
--- a/packages/flutter_tools/lib/src/services.dart
+++ b/packages/flutter_tools/lib/src/services.dart
@@ -30,7 +30,7 @@ Future<Null> parseServiceConfigs(
 ) async {
   Map<String, Uri> packageMap;
   try {
-    packageMap = PackageMap.instance.map;
+    packageMap = new PackageMap(PackageMap.globalPackagesPath).map;
   } on FormatException catch(e) {
     printTrace('Invalid ".packages" file while parsing service configs:\n$e');
     return;
diff --git a/packages/flutter_tools/lib/src/test/flutter_platform.dart b/packages/flutter_tools/lib/src/test/flutter_platform.dart
index 43d3401ea71..d3e6ecbd7e1 100644
--- a/packages/flutter_tools/lib/src/test/flutter_platform.dart
+++ b/packages/flutter_tools/lib/src/test/flutter_platform.dart
@@ -15,6 +15,7 @@ import 'package:test/src/runner/plugin/platform.dart'; // ignore: implementation
 import 'package:test/src/runner/plugin/hack_register_platform.dart' as hack; // ignore: implementation_imports
 
 import '../dart/package_map.dart';
+import '../globals.dart';
 
 final String _kSkyShell = Platform.environment['SKY_SHELL'];
 const String _kHost = '127.0.0.1';
@@ -46,12 +47,15 @@ Future<_ServerInfo> _startServer() async {
 
 Future<Process> _startProcess(String mainPath, { String packages }) {
   assert(shellPath != null || _kSkyShell != null); // Please provide the path to the shell in the SKY_SHELL environment variable.
-  return Process.start(shellPath ?? _kSkyShell, <String>[
+  String executable = shellPath ?? _kSkyShell;
+  List<String> arguments = <String>[
     '--enable-checked-mode',
     '--non-interactive',
     '--packages=$packages',
-    mainPath,
-  ], environment: <String, String>{ 'FLUTTER_TEST': 'true' });
+    mainPath
+  ];
+  printTrace('$executable ${arguments.join(' ')}');
+  return Process.start(executable, arguments, environment: <String, String>{ 'FLUTTER_TEST': 'true' });
 }
 
 void _attachStandardStreams(Process process) {
@@ -102,7 +106,7 @@ void main() {
 ''');
 
     Process process = await _startProcess(
-      listenerFile.path, packages: PackageMap.instance.packagesPath
+      listenerFile.path, packages: PackageMap.globalPackagesPath
     );
 
     _attachStandardStreams(process);
diff --git a/packages/flutter_tools/test/context_test.dart b/packages/flutter_tools/test/context_test.dart
index 8141909618a..51e5464deeb 100644
--- a/packages/flutter_tools/test/context_test.dart
+++ b/packages/flutter_tools/test/context_test.dart
@@ -14,7 +14,7 @@ void main() {
       BufferLogger mockLogger = new BufferLogger();
       context[Logger] = mockLogger;
 
-      context.runInZone(() {
+      await context.runInZone(() {
         printError('foo bar');
       });
 
@@ -28,7 +28,7 @@ void main() {
       BufferLogger mockLogger = new BufferLogger();
       context[Logger] = mockLogger;
 
-      context.runInZone(() {
+      await context.runInZone(() {
         printStatus('foo bar');
       });
 
@@ -42,7 +42,7 @@ void main() {
       BufferLogger mockLogger = new BufferLogger();
       context[Logger] = mockLogger;
 
-      context.runInZone(() {
+      await context.runInZone(() {
         printTrace('foo bar');
       });
 
diff --git a/packages/flutter_tools/test/daemon_test.dart b/packages/flutter_tools/test/daemon_test.dart
index 23032e30fd9..0780514e88d 100644
--- a/packages/flutter_tools/test/daemon_test.dart
+++ b/packages/flutter_tools/test/daemon_test.dart
@@ -94,6 +94,44 @@ void main() {
       });
     });
 
+    _testUsingContext('daemon.start', () async {
+      DaemonCommand command = new DaemonCommand();
+      applyMocksToCommand(command);
+
+      StreamController<Map<String, dynamic>> commands = new StreamController<Map<String, dynamic>>();
+      StreamController<Map<String, dynamic>> responses = new StreamController<Map<String, dynamic>>();
+      daemon = new Daemon(
+        commands.stream,
+        (Map<String, dynamic> result) => responses.add(result),
+        daemonCommand: command,
+        notifyingLogger: notifyingLogger
+      );
+
+      commands.add(<String, dynamic>{ 'id': 0, 'method': 'app.start' });
+      Map<String, dynamic> response = await responses.stream.where(_notEvent).first;
+      expect(response['id'], 0);
+      expect(response['error'], contains('deviceId is required'));
+    });
+
+    _testUsingContext('daemon.restart', () async {
+      DaemonCommand command = new DaemonCommand();
+      applyMocksToCommand(command);
+
+      StreamController<Map<String, dynamic>> commands = new StreamController<Map<String, dynamic>>();
+      StreamController<Map<String, dynamic>> responses = new StreamController<Map<String, dynamic>>();
+      daemon = new Daemon(
+        commands.stream,
+        (Map<String, dynamic> result) => responses.add(result),
+        daemonCommand: command,
+        notifyingLogger: notifyingLogger
+      );
+
+      commands.add(<String, dynamic>{ 'id': 0, 'method': 'app.restart' });
+      Map<String, dynamic> response = await responses.stream.where(_notEvent).first;
+      expect(response['id'], 0);
+      expect(response['error'], contains('appId is required'));
+    });
+
     _testUsingContext('daemon.stop', () async {
       DaemonCommand command = new DaemonCommand();
       applyMocksToCommand(command);
@@ -110,7 +148,7 @@ void main() {
       commands.add(<String, dynamic>{ 'id': 0, 'method': 'app.stop' });
       Map<String, dynamic> response = await responses.stream.where(_notEvent).first;
       expect(response['id'], 0);
-      expect(response['error'], contains('deviceId is required'));
+      expect(response['error'], contains('appId is required'));
     });
 
     _testUsingContext('device.getDevices', () async {
diff --git a/packages/flutter_tools/tool/daemon_client.dart b/packages/flutter_tools/tool/daemon_client.dart
index f11fc0f0a95..2cf2cd6d25d 100644
--- a/packages/flutter_tools/tool/daemon_client.dart
+++ b/packages/flutter_tools/tool/daemon_client.dart
@@ -12,7 +12,7 @@ Process daemon;
 //   version: print version
 //   shutdown: terminate the server
 //   start: start an app
-//   stopAll: stop any running app
+//   stop: stop a running app
 //   devices: list devices
 
 Future<Null> main() async {
@@ -27,18 +27,44 @@ Future<Null> main() async {
 
   stdout.write('> ');
   stdin.transform(UTF8.decoder).transform(const LineSplitter()).listen((String line) {
+    List<String> words = line.split(' ');
+
     if (line == 'version' || line == 'v') {
       _send(<String, dynamic>{'method': 'daemon.version'});
     } else if (line == 'shutdown' || line == 'q') {
       _send(<String, dynamic>{'method': 'daemon.shutdown'});
-    } else if (line == 'start') {
-      _send(<String, dynamic>{'method': 'app.start'});
-    } else if (line == 'stopAll') {
-      _send(<String, dynamic>{'method': 'app.stopAll'});
+    } else if (words.first == 'start') {
+      _send(<String, dynamic>{
+        'method': 'app.start',
+        'params': <String, dynamic> {
+          'deviceId': words[1],
+          'projectDirectory': words[2]
+        }
+      });
+    } else if (words.first == 'stop') {
+      if (words.length > 1) {
+        _send(<String, dynamic>{
+          'method': 'app.stop',
+          'params': <String, dynamic> { 'appId': words[1] }
+        });
+      } else {
+        _send(<String, dynamic>{'method': 'app.stop'});
+      }
+    } else if (words.first == 'restart') {
+      if (words.length > 1) {
+        _send(<String, dynamic>{
+          'method': 'app.restart',
+          'params': <String, dynamic> { 'appId': words[1] }
+        });
+      } else {
+        _send(<String, dynamic>{'method': 'app.restart'});
+      }
     } else if (line == 'devices') {
       _send(<String, dynamic>{'method': 'device.getDevices'});
+    } else if (line == 'enable') {
+      _send(<String, dynamic>{'method': 'device.enable'});
     } else {
-      print('command not understood: $line');
+      _send(<String, dynamic>{'method': line.trim()});
     }
     stdout.write('> ');
   });