diff --git a/.appveyor.yml b/.appveyor.yml
new file mode 100644
index 000000000..a0d3292f1
--- /dev/null
+++ b/.appveyor.yml
@@ -0,0 +1,23 @@
+build: off
+
+init:
+  - git config --global core.autocrlf input
+
+install:
+  - cinst jdk8 -params 'installdir=C:\\jdk8'
+  - SET JAVA_HOME=C:\jdk8
+  - SET PATH=C:\jdk8\bin;%PATH%
+
+  - ps: |
+      Add-Type -AssemblyName System.IO.Compression.FileSystem
+      if (!(Test-Path -Path "C:\sbt" )) {
+        (new-object System.Net.WebClient).DownloadFile(
+          'https://github.com/sbt/sbt/releases/download/v1.0.4/sbt-1.0.4.zip',
+          'C:\sbt-bin.zip'
+        )
+        [System.IO.Compression.ZipFile]::ExtractToDirectory("C:\sbt-bin.zip", "C:\sbt")
+      }
+  - SET PATH=C:\sbt\sbt\bin;%PATH%
+  - SET SBT_OPTS=-XX:MaxPermSize=2g -Xmx4g -Dfile.encoding=UTF8
+test_script:
+  - sbt "scripted actions/* server/*"
diff --git a/build.sbt b/build.sbt
index f9fe5937b..8a8643f45 100644
--- a/build.sbt
+++ b/build.sbt
@@ -34,6 +34,7 @@ def buildLevelSettings: Seq[Setting[_]] =
       scmInfo := Some(ScmInfo(url("https://github.com/sbt/sbt"), "git@github.com:sbt/sbt.git")),
       resolvers += Resolver.mavenLocal,
       scalafmtOnCompile := true,
+      scalafmtOnCompile in Sbt := false,
       scalafmtVersion := "1.3.0",
     ))
 
@@ -328,8 +329,7 @@ lazy val commandProj = (project in file("main-command"))
   .settings(
     testedBaseSettings,
     name := "Command",
-    libraryDependencies ++= Seq(launcherInterface, sjsonNewScalaJson.value, templateResolverApi,
-      jna, jnaPlatform),
+    libraryDependencies ++= Seq(launcherInterface, sjsonNewScalaJson.value, templateResolverApi),
     managedSourceDirectories in Compile +=
       baseDirectory.value / "src" / "main" / "contraband-scala",
     sourceManaged in (Compile, generateContrabands) := baseDirectory.value / "src" / "main" / "contraband-scala",
@@ -481,10 +481,9 @@ lazy val sbtIgnoredProblems = {
 }
 
 def runNpm(command: String, base: File, log: sbt.internal.util.ManagedLogger) = {
-  val npm = if (sbt.internal.util.Util.isWindows) "npm.cmd" else "npm"
   import scala.sys.process._
   try {
-    val exitCode = Process(s"$npm $command", Option(base)) ! log
+    val exitCode = Process(s"npm $command", Option(base)) ! log
     if (exitCode != 0) throw new Exception("Process returned exit code: " + exitCode)
   } catch {
     case e: java.io.IOException => log.warn("failed to run npm " + e.getMessage)
diff --git a/main-actions/src/main/scala/sbt/compiler/Eval.scala b/main-actions/src/main/scala/sbt/compiler/Eval.scala
index a075f61a8..a9d97246a 100644
--- a/main-actions/src/main/scala/sbt/compiler/Eval.scala
+++ b/main-actions/src/main/scala/sbt/compiler/Eval.scala
@@ -485,12 +485,10 @@ private[sbt] object Eval {
   def filesModifiedBytes(fs: Array[File]): Array[Byte] =
     if (fs eq null) filesModifiedBytes(Array[File]()) else seqBytes(fs)(fileModifiedBytes)
   def fileModifiedBytes(f: File): Array[Byte] =
-    (if (f.isDirectory) filesModifiedBytes(f listFiles classDirFilter)
+    (if (f.isDirectory)
+       filesModifiedBytes(f listFiles classDirFilter)
      else
-       bytes(
-         try IO.getModifiedTime(f)
-         catch { case _: java.io.FileNotFoundException => 0L })) ++
-      bytes(f.getAbsolutePath)
+       bytes(IO.getModifiedTimeOrZero(f))) ++ bytes(f.getAbsolutePath)
   def fileExistsBytes(f: File): Array[Byte] =
     bytes(f.exists) ++
       bytes(f.getAbsolutePath)
diff --git a/main-command/src/main/java/sbt/internal/NGWin32NamedPipeLibrary.java b/main-command/src/main/java/sbt/internal/NGWin32NamedPipeLibrary.java
index ba535691f..dd4d8f15a 100644
--- a/main-command/src/main/java/sbt/internal/NGWin32NamedPipeLibrary.java
+++ b/main-command/src/main/java/sbt/internal/NGWin32NamedPipeLibrary.java
@@ -29,7 +29,7 @@ import com.sun.jna.ptr.IntByReference;
 
 import com.sun.jna.win32.W32APIOptions;
 
-public interface NGWin32NamedPipeLibrary extends WinNT {
+public interface NGWin32NamedPipeLibrary extends Library, WinNT {
     int PIPE_ACCESS_DUPLEX = 3;
     int PIPE_UNLIMITED_INSTANCES = 255;
     int FILE_FLAG_FIRST_PIPE_INSTANCE = 524288;
diff --git a/main-command/src/main/scala/sbt/internal/server/Server.scala b/main-command/src/main/scala/sbt/internal/server/Server.scala
index 4fb8a7cb4..521c8d399 100644
--- a/main-command/src/main/scala/sbt/internal/server/Server.scala
+++ b/main-command/src/main/scala/sbt/internal/server/Server.scala
@@ -97,7 +97,7 @@ private[sbt] object Server {
             case Failure(e) => ()
             case Success(socket) =>
               socket.close()
-              throw new IOException("sbt server is already running.")
+              throw new AlreadyRunningException()
           }
         } else ()
       }
@@ -210,3 +210,5 @@ private[sbt] case class ServerConnection(
     }
   }
 }
+
+private[sbt] class AlreadyRunningException extends IOException("sbt server is already running.")
diff --git a/main/src/main/scala/sbt/Defaults.scala b/main/src/main/scala/sbt/Defaults.scala
index 9471fa8c9..0b82ce8ea 100755
--- a/main/src/main/scala/sbt/Defaults.scala
+++ b/main/src/main/scala/sbt/Defaults.scala
@@ -2318,7 +2318,7 @@ object Classpaths {
         case Some(period) =>
           val fullUpdateOutput = cacheDirectory / "out"
           val now = System.currentTimeMillis
-          val diff = now - IO.getModifiedTime(fullUpdateOutput)
+          val diff = now - IO.getModifiedTimeOrZero(fullUpdateOutput)
           val elapsedDuration = new FiniteDuration(diff, TimeUnit.MILLISECONDS)
           fullUpdateOutput.exists() && elapsedDuration > period
       }
diff --git a/main/src/main/scala/sbt/Main.scala b/main/src/main/scala/sbt/Main.scala
index 7732d2323..75401eacd 100644
--- a/main/src/main/scala/sbt/Main.scala
+++ b/main/src/main/scala/sbt/Main.scala
@@ -128,6 +128,9 @@ object StandardMain {
   def initialState(configuration: xsbti.AppConfiguration,
                    initialDefinitions: Seq[Command],
                    preCommands: Seq[String]): State = {
+    // This is to workaround https://github.com/sbt/io/issues/110
+    sys.props.put("jna.nosys", "true")
+
     import BasicCommandStrings.isEarlyCommand
     val userCommands = configuration.arguments.map(_.trim)
     val (earlyCommands, normalCommands) = (preCommands ++ userCommands).partition(isEarlyCommand)
diff --git a/main/src/main/scala/sbt/internal/CommandExchange.scala b/main/src/main/scala/sbt/internal/CommandExchange.scala
index 443c9642c..33fbfa986 100644
--- a/main/src/main/scala/sbt/internal/CommandExchange.scala
+++ b/main/src/main/scala/sbt/internal/CommandExchange.scala
@@ -10,7 +10,7 @@ package internal
 
 import java.io.IOException
 import java.util.concurrent.ConcurrentLinkedQueue
-import java.util.concurrent.atomic.AtomicInteger
+import java.util.concurrent.atomic._
 import scala.collection.mutable.ListBuffer
 import scala.annotation.tailrec
 import BasicKeys.{
@@ -26,7 +26,7 @@ import sjsonnew.JsonFormat
 import sjsonnew.shaded.scalajson.ast.unsafe._
 import scala.concurrent.Await
 import scala.concurrent.duration.Duration
-import scala.util.{ Success, Failure }
+import scala.util.{ Success, Failure, Try }
 import sbt.io.syntax._
 import sbt.io.{ Hash, IO }
 import sbt.internal.server._
@@ -48,6 +48,7 @@ private[sbt] final class CommandExchange {
 
   private val lock = new AnyRef {}
   private var server: Option[ServerInstance] = None
+  private val firstInstance: AtomicBoolean = new AtomicBoolean(true)
   private var consoleChannel: Option[ConsoleChannel] = None
   private val commandQueue: ConcurrentLinkedQueue[Exec] = new ConcurrentLinkedQueue()
   private val channelBuffer: ListBuffer[CommandChannel] = new ListBuffer()
@@ -131,7 +132,8 @@ private[sbt] final class CommandExchange {
       subscribe(channel)
     }
     server match {
-      case Some(_) => // do nothing
+      case Some(_)                    => // do nothing
+      case None if !firstInstance.get => // there's another server
       case _ =>
         val portfile = (new File(".")).getAbsoluteFile / "project" / "target" / "active.json"
         val h = Hash.halfHashString(IO.toURI(portfile).toString)
@@ -148,15 +150,27 @@ private[sbt] final class CommandExchange {
                            socketfile,
                            pipeName)
         val x = Server.start(connection, onIncomingSocket, s.log)
-        Await.ready(x.ready, Duration("10s"))
+
+        // don't throw exception when it times out
+        val d = "10s"
+        Try(Await.ready(x.ready, Duration(d)))
         x.ready.value match {
           case Some(Success(_)) =>
             // rememeber to shutdown only when the server comes up
             server = Some(x)
+          case Some(Failure(e: AlreadyRunningException)) =>
+            s.log.warn(
+              "sbt server could not start because there's another instance of sbt running on this build.")
+            s.log.warn("Running multiple instances is unsupported")
+            server = None
+            firstInstance.set(false)
           case Some(Failure(e)) =>
             s.log.error(e.toString)
             server = None
-          case None => // this won't happen because we awaited
+          case None =>
+            s.log.warn(s"sbt server could not start in $d")
+            server = None
+            firstInstance.set(false)
         }
     }
     s
@@ -190,6 +204,7 @@ private[sbt] final class CommandExchange {
       case xs =>
         lock.synchronized {
           channelBuffer --= xs
+          ()
         }
     }
   }
@@ -228,6 +243,7 @@ private[sbt] final class CommandExchange {
       case xs =>
         lock.synchronized {
           channelBuffer --= xs
+          ()
         }
     }
   }
@@ -269,6 +285,7 @@ private[sbt] final class CommandExchange {
       case xs =>
         lock.synchronized {
           channelBuffer --= xs
+          ()
         }
     }
   }
@@ -310,6 +327,7 @@ private[sbt] final class CommandExchange {
       case xs =>
         lock.synchronized {
           channelBuffer --= xs
+          ()
         }
     }
   }
diff --git a/main/src/main/scala/sbt/internal/LibraryManagement.scala b/main/src/main/scala/sbt/internal/LibraryManagement.scala
index 66fa494c1..28a40c5c7 100644
--- a/main/src/main/scala/sbt/internal/LibraryManagement.scala
+++ b/main/src/main/scala/sbt/internal/LibraryManagement.scala
@@ -121,7 +121,7 @@ private[sbt] object LibraryManagement {
   }
 
   private[this] def fileUptodate(file: File, stamps: Map[File, Long]): Boolean =
-    stamps.get(file).forall(_ == IO.getModifiedTime(file))
+    stamps.get(file).forall(_ == IO.getModifiedTimeOrZero(file))
 
   private[sbt] def transitiveScratch(
       lm: DependencyResolution,
diff --git a/notes/1.1.0.markdown b/notes/1.1.0.markdown
index 07d8a4a4a..29ed283f7 100644
--- a/notes/1.1.0.markdown
+++ b/notes/1.1.0.markdown
@@ -1,12 +1,19 @@
+### Changes since RC-2
+
+- Provides workaround for `File#lastModified()` losing millisecond-precision by using native code when possible. [io#92](https://github.com/sbt/io/pull/92)/[io#106](https://github.com/sbt/io/pull/106) by [@cunei][@cunei]
+- Fixes `IO.relativize` not working with relative path. [io#108](https://github.com/sbt/io/pull/108) by [@dwijnand][@dwijnand]
+- Fixes `ClasspathFilter` that was causing `Class.forName` to not work in `run`. [zinc#473](https://github.com/sbt/zinc/pull/473) / [#3736](https://github.com/sbt/sbt/issues/3736) / [#3733](https://github.com/sbt/sbt/issues/3733) / [#3647](https://github.com/sbt/sbt/issues/3647) / [#3608](https://github.com/sbt/sbt/issues/3608) by [@ravwojdyla][@ravwojdyla]
+- Fixes JNA version mixup. [#3837](https://github.com/sbt/sbt/pull/3837) by [@eed3si9n][@eed3si9n]
+- Fixes warning message when multiple instances are detected. [#3828](https://github.com/sbt/sbt/pull/3828) by [@eed3si9n][@eed3si9n]
+
 ### Changes since RC-1
 
 - Fixes Java compilation causing `NullPointerException` by making PositionImpl thread-safe. [zinc#465](https://github.com/sbt/zinc/pull/465) by [@eed3si9n][@eed3si9n]
-- Restores Scala 2.13.0-M1 support. #461 by @dwijnand
+- Restores Scala 2.13.0-M1 support. #461 by [@dwijnand][@dwijnand]
 - Fixes `PollingWatchService` by preventing concurrent modification of `keysWithEvents` map. [io#90](https://github.com/sbt/io/pull/90) by [@mechkg][@mechkg], which fixes `~` related issues [#3687](https://github.com/sbt/sbt/issues/3687), [#3695](https://github.com/sbt/sbt/issues/3695), and [#3775](https://github.com/sbt/sbt/issues/3775).
 - Fixed server spewing out debug level logs. [#3791](https://github.com/sbt/sbt/pull/3791) by [@eed3si9n][@eed3si9n]
 - Fixes the encoding of Unix-like file path to use `file:///`. [#3805](https://github.com/sbt/sbt/pull/3805) by [@eed3si9n][@eed3si9n]
 - Fixes Log4J2 initialization error during startup. [#3814](https://github.com/sbt/sbt/pull/3814) by [@dwijnand][@dwijnand]
-- Provides workaround for `File#lastModified()` losing millisecond-precision by using native code when possible. [io#92](https://github.com/sbt/io/pull/92) by [@cunei][@cunei]
 
 ### Features, fixes, changes with compatibility implications
 
@@ -148,6 +155,7 @@ This allows you to define scripted tests that track the minimum supported sbt ve
   [@raboof]: https://github.com/raboof
   [@jilen]: https://github.com/jilen
   [@mechkg]: https://github.com/mechkg
+  [@ravwojdyla]: https://github.com/ravwojdyla
   [vscode-sbt-scala]: https://marketplace.visualstudio.com/items?itemName=lightbend.vscode-sbt-scala
   [1812]: https://github.com/sbt/sbt/issues/1812
   [3524]: https://github.com/sbt/sbt/pull/3524
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index f8e14429f..f8d470ccd 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -12,10 +12,10 @@ object Dependencies {
   val baseScalaVersion = scala212
 
   // sbt modules
-  private val ioVersion = "1.1.2"
-  private val utilVersion = "1.1.1"
-  private val lmVersion = "1.1.1"
-  private val zincVersion = "1.1.0-RC3"
+  private val ioVersion = "1.1.3"
+  private val utilVersion = "1.1.2"
+  private val lmVersion = "1.1.2"
+  private val zincVersion = "1.1.0"
 
   private val sbtIO = "org.scala-sbt" %% "io" % ioVersion
 
@@ -106,8 +106,6 @@ object Dependencies {
   val specs2 = "org.specs2" %% "specs2-junit" % "4.0.1"
   val junit = "junit" % "junit" % "4.11"
   val templateResolverApi = "org.scala-sbt" % "template-resolver" % "0.1"
-  val jna = "net.java.dev.jna" % "jna" % "4.1.0"
-  val jnaPlatform = "net.java.dev.jna" % "jna-platform" % "4.1.0"
 
   private def scala211Module(name: String, moduleVersion: String) = Def setting (
     scalaBinaryVersion.value match {
diff --git a/project/Scripted.scala b/project/Scripted.scala
index 932d55a0f..788f1d60e 100644
--- a/project/Scripted.scala
+++ b/project/Scripted.scala
@@ -37,6 +37,9 @@ trait ScriptedKeys {
 }
 
 object Scripted {
+  // This is to workaround https://github.com/sbt/io/issues/110
+  sys.props.put("jna.nosys", "true")
+
   lazy val MavenResolverPluginTest = config("mavenResolverPluginTest") extend Compile
   lazy val RepoOverrideTest = config("repoOverrideTest") extend Compile
 
diff --git a/project/SiteMap.scala b/project/SiteMap.scala
index 2cfb5d8ea..95e038eab 100644
--- a/project/SiteMap.scala
+++ b/project/SiteMap.scala
@@ -68,8 +68,8 @@ object SiteMap {
   // generates a string suitable for a sitemap file representing the last modified time of the given File
   private[this] def lastModifiedString(f: File): String = {
     val formatter = new java.text.SimpleDateFormat("yyyy-MM-dd")
-    // TODO: replace lastModified() with sbt.io.Milli.getModifiedTime(), once the build
-    // has been upgraded to a version of sbt that includes sbt.io.Milli.
+    // TODO: replace lastModified() with sbt.io.IO.getModifiedTimeOrZero(), once the build
+    // has been upgraded to a version of sbt that includes that call.
     formatter.format(new java.util.Date(f.lastModified))
   }
   // writes the provided XML node to `output` and then gzips it to `gzipped` if `gzip` is true
diff --git a/project/Util.scala b/project/Util.scala
index 4cdb02029..74ecb1c9f 100644
--- a/project/Util.scala
+++ b/project/Util.scala
@@ -106,8 +106,8 @@ object Util {
     val timestamp = formatter.format(new Date)
     val content = versionLine(version) + "\ntimestamp=" + timestamp
     val f = dir / "xsbt.version.properties"
-    // TODO: replace lastModified() with sbt.io.Milli.getModifiedTime(), once the build
-    // has been upgraded to a version of sbt that includes sbt.io.Milli.
+    // TODO: replace lastModified() with sbt.io.IO.getModifiedTimeOrZero(), once the build
+    // has been upgraded to a version of sbt that includes that call.
     if (!f.exists || f.lastModified < lastCompilationTime(analysis) || !containsVersion(f, version)) {
       s.log.info("Writing version information to " + f + " :\n" + content)
       IO.write(f, content)
diff --git a/project/build.properties b/project/build.properties
index 94005e587..394cb75cf 100644
--- a/project/build.properties
+++ b/project/build.properties
@@ -1 +1 @@
-sbt.version=1.0.0
+sbt.version=1.0.4
diff --git a/project/plugins.sbt b/project/plugins.sbt
index 4503fc161..7ea70f8ea 100644
--- a/project/plugins.sbt
+++ b/project/plugins.sbt
@@ -1,8 +1,7 @@
 scalaVersion := "2.12.4"
 scalacOptions ++= Seq("-feature", "-language:postfixOps")
 
-addSbtPlugin("org.scala-sbt" % "sbt-houserules" % "0.3.4")
+addSbtPlugin("org.scala-sbt" % "sbt-houserules" % "0.3.5")
 addSbtPlugin("org.scala-sbt" % "sbt-contraband" % "0.3.2")
-addSbtPlugin("com.lucidchart" % "sbt-scalafmt" % "1.14")
 addSbtPlugin("de.heikoseeberger" % "sbt-header" % "3.0.2")
 addSbtPlugin("com.eed3si9n" % "sbt-buildinfo" % "0.7.0")
diff --git a/sbt/src/sbt-test/tests/fork-parallel/test b/sbt/src/sbt-test/tests/fork-parallel/test
index 9d76b41e6..662328f42 100644
--- a/sbt/src/sbt-test/tests/fork-parallel/test
+++ b/sbt/src/sbt-test/tests/fork-parallel/test
@@ -1,8 +1,19 @@
-# https://github.com/sbt/sbt/issues/3545
+# The tests/fork-parallel test will currently always 
+# report success when run on less than four cores,
+# rather than  failing in one of the two cases as expected.
+# TODO: Adjust this scripted test so that it works as
+# intended on less than four cores as well.
+
+# To debug, it is possible to limit the number of cores
+# reported to sbt, and run the test, by using:
+#   taskset 0x00000003 sbt 'scripted tests/fork-parallel'
+# See: https://github.com/sbt/sbt/issues/3545
+
+# This bit won't currently work when using less than four cores.
 # > test
 # -> check
 
 > clean
 > set testForkedParallel := true
 > test
-> check
\ No newline at end of file
+> check
diff --git a/src/main/conscript/scalas/launchconfig b/src/main/conscript/scalas/launchconfig
index 497187233..98febc38c 100644
--- a/src/main/conscript/scalas/launchconfig
+++ b/src/main/conscript/scalas/launchconfig
@@ -4,7 +4,7 @@
 [app]
   org: ${sbt.organization-org.scala-sbt}
   name: sbt
-  version: ${sbt.version-read(sbt.version)[1.0.0]}
+  version: ${sbt.version-read(sbt.version)[1.1.0]}
   class: sbt.ScriptMain
   components: xsbti,extra
   cross-versioned: ${sbt.cross.versioned-false}
diff --git a/src/main/conscript/screpl/launchconfig b/src/main/conscript/screpl/launchconfig
index 4701c697e..17a32efb0 100644
--- a/src/main/conscript/screpl/launchconfig
+++ b/src/main/conscript/screpl/launchconfig
@@ -4,7 +4,7 @@
 [app]
   org: ${sbt.organization-org.scala-sbt}
   name: sbt
-  version: ${sbt.version-read(sbt.version)[1.0.0]}
+  version: ${sbt.version-read(sbt.version)[1.1.0]}
   class: sbt.ConsoleMain
   components: xsbti,extra
   cross-versioned: ${sbt.cross.versioned-false}
diff --git a/src/main/conscript/xsbt/launchconfig b/src/main/conscript/xsbt/launchconfig
index e47a59083..79ddd5ef7 100644
--- a/src/main/conscript/xsbt/launchconfig
+++ b/src/main/conscript/xsbt/launchconfig
@@ -4,7 +4,7 @@
 [app]
   org: ${sbt.organization-org.scala-sbt}
   name: sbt
-  version: ${sbt.version-read(sbt.version)[1.0.0]}
+  version: ${sbt.version-read(sbt.version)[1.1.0]}
   class: sbt.xMain
   components: xsbti,extra
   cross-versioned: ${sbt.cross.versioned-false}