diff --git a/main-actions/src/main/scala/sbt/compiler/Eval.scala b/main-actions/src/main/scala/sbt/compiler/Eval.scala
index 3bd69b09a..a075f61a8 100644
--- a/main-actions/src/main/scala/sbt/compiler/Eval.scala
+++ b/main-actions/src/main/scala/sbt/compiler/Eval.scala
@@ -485,7 +485,11 @@ 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) else bytes(f.lastModified)) ++
+    (if (f.isDirectory) filesModifiedBytes(f listFiles classDirFilter)
+     else
+       bytes(
+         try IO.getModifiedTime(f)
+         catch { case _: java.io.FileNotFoundException => 0L })) ++
       bytes(f.getAbsolutePath)
   def fileExistsBytes(f: File): Array[Byte] =
     bytes(f.exists) ++
diff --git a/main/src/main/scala/sbt/Defaults.scala b/main/src/main/scala/sbt/Defaults.scala
index 1f2dcfd3a..b006c115d 100755
--- a/main/src/main/scala/sbt/Defaults.scala
+++ b/main/src/main/scala/sbt/Defaults.scala
@@ -2315,7 +2315,7 @@ object Classpaths {
         case Some(period) =>
           val fullUpdateOutput = cacheDirectory / "out"
           val now = System.currentTimeMillis
-          val diff = now - fullUpdateOutput.lastModified()
+          val diff = now - IO.getModifiedTime(fullUpdateOutput)
           val elapsedDuration = new FiniteDuration(diff, TimeUnit.MILLISECONDS)
           fullUpdateOutput.exists() && elapsedDuration > period
       }
diff --git a/main/src/main/scala/sbt/internal/LibraryManagement.scala b/main/src/main/scala/sbt/internal/LibraryManagement.scala
index a245344dc..fc832ffff 100644
--- a/main/src/main/scala/sbt/internal/LibraryManagement.scala
+++ b/main/src/main/scala/sbt/internal/LibraryManagement.scala
@@ -13,6 +13,7 @@ import sbt.internal.librarymanagement._
 import sbt.librarymanagement._
 import sbt.librarymanagement.syntax._
 import sbt.util.{ CacheStore, CacheStoreFactory, Logger, Tracked }
+import sbt.io.IO
 
 private[sbt] object LibraryManagement {
 
@@ -126,7 +127,7 @@ private[sbt] object LibraryManagement {
   }
 
   private[this] def fileUptodate(file: File, stamps: Map[File, Long]): Boolean =
-    stamps.get(file).forall(_ == file.lastModified)
+    stamps.get(file).forall(_ == IO.getModifiedTime(file))
 
   private[sbt] def transitiveScratch(
       lm: DependencyResolution,
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index a628f6aaf..f8e14429f 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -12,10 +12,10 @@ object Dependencies {
   val baseScalaVersion = scala212
 
   // sbt modules
-  private val ioVersion = "1.1.1"
-  private val utilVersion = "1.1.0"
-  private val lmVersion = "1.1.0"
-  private val zincVersion = "1.1.0-RC1"
+  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 sbtIO = "org.scala-sbt" %% "io" % ioVersion
 
diff --git a/project/SiteMap.scala b/project/SiteMap.scala
index ed1f5239e..2cfb5d8ea 100644
--- a/project/SiteMap.scala
+++ b/project/SiteMap.scala
@@ -68,6 +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.
     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 89556cd2e..0b87b02db 100644
--- a/project/Util.scala
+++ b/project/Util.scala
@@ -105,6 +105,8 @@ 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.
     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/plugins.sbt b/project/plugins.sbt
index 4cfe0e774..66097a8b9 100644
--- a/project/plugins.sbt
+++ b/project/plugins.sbt
@@ -1,15 +1,8 @@
 scalaVersion := "2.12.3"
 scalacOptions ++= Seq("-feature", "-language:postfixOps")
 
-addSbtPlugin("com.typesafe" % "sbt-mima-plugin" % "0.1.17")
-// addSbtPlugin("com.typesafe.sbt" % "sbt-ghpages" % "0.6.0")
-// addSbtPlugin("com.typesafe.sbt" % "sbt-git" % "0.9.2")
-// addSbtPlugin("com.typesafe.sbt" % "sbt-javaversioncheck" % "0.1.0")
-// addSbtPlugin("com.typesafe.sbt" % "sbt-site" % "1.2.0")
-
-addSbtPlugin("org.foundweekends" % "sbt-bintray" % "0.5.1")
-addSbtPlugin("org.scala-sbt" % "sbt-contraband" % "0.3.1")
-addSbtPlugin("com.jsuereth" % "sbt-pgp" % "1.1.0-M1")
+addSbtPlugin("org.scala-sbt" % "sbt-houserules" % "0.3.4")
+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/protocol/src/main/contraband-scala/sbt/internal/langserver/ClientCapabilities.scala b/protocol/src/main/contraband-scala/sbt/internal/langserver/ClientCapabilities.scala
index 7bbfe152a..8e046ede9 100644
--- a/protocol/src/main/contraband-scala/sbt/internal/langserver/ClientCapabilities.scala
+++ b/protocol/src/main/contraband-scala/sbt/internal/langserver/ClientCapabilities.scala
@@ -9,7 +9,7 @@ final class ClientCapabilities private () extends Serializable {
 
 
 override def equals(o: Any): Boolean = o match {
-  case x: ClientCapabilities => true
+  case _: ClientCapabilities => true
   case _ => false
 }
 override def hashCode: Int = {
diff --git a/protocol/src/main/contraband-scala/sbt/protocol/CommandMessage.scala b/protocol/src/main/contraband-scala/sbt/protocol/CommandMessage.scala
index 9292dbd16..79b15d024 100644
--- a/protocol/src/main/contraband-scala/sbt/protocol/CommandMessage.scala
+++ b/protocol/src/main/contraband-scala/sbt/protocol/CommandMessage.scala
@@ -11,7 +11,7 @@ abstract class CommandMessage() extends Serializable {
 
 
 override def equals(o: Any): Boolean = o match {
-  case x: CommandMessage => true
+  case _: CommandMessage => true
   case _ => false
 }
 override def hashCode: Int = {
diff --git a/protocol/src/main/contraband-scala/sbt/protocol/EventMessage.scala b/protocol/src/main/contraband-scala/sbt/protocol/EventMessage.scala
index 6e934413e..9e4435096 100644
--- a/protocol/src/main/contraband-scala/sbt/protocol/EventMessage.scala
+++ b/protocol/src/main/contraband-scala/sbt/protocol/EventMessage.scala
@@ -11,7 +11,7 @@ abstract class EventMessage() extends Serializable {
 
 
 override def equals(o: Any): Boolean = o match {
-  case x: EventMessage => true
+  case _: EventMessage => true
   case _ => false
 }
 override def hashCode: Int = {
diff --git a/protocol/src/main/contraband-scala/sbt/protocol/SettingQueryResponse.scala b/protocol/src/main/contraband-scala/sbt/protocol/SettingQueryResponse.scala
index a63a99897..f8fe40388 100644
--- a/protocol/src/main/contraband-scala/sbt/protocol/SettingQueryResponse.scala
+++ b/protocol/src/main/contraband-scala/sbt/protocol/SettingQueryResponse.scala
@@ -10,7 +10,7 @@ abstract class SettingQueryResponse() extends sbt.protocol.EventMessage() with S
 
 
 override def equals(o: Any): Boolean = o match {
-  case x: SettingQueryResponse => true
+  case _: SettingQueryResponse => true
   case _ => false
 }
 override def hashCode: Int = {
diff --git a/sbt/src/sbt-test/run/error/test b/sbt/src/sbt-test/run/error/test
index a603016e6..d3599f40d 100644
--- a/sbt/src/sbt-test/run/error/test
+++ b/sbt/src/sbt-test/run/error/test
@@ -13,7 +13,6 @@ $ copy-file changes/ThreadRunError.scala src/main/scala/Run.scala
 $ copy-file changes/RunExplicitSuccess.scala src/main/scala/Run.scala
 > run
 
-# https://github.com/sbt/sbt/issues/3543
-# # explicitly calling System.exit(1) should fail the 'run' task
-# $ copy-file changes/RunExplicitFailure.scala src/main/scala/Run.scala
-# -> run
+# explicitly calling System.exit(1) should fail the 'run' task
+$ copy-file changes/RunExplicitFailure.scala src/main/scala/Run.scala
+-> run
\ No newline at end of file
diff --git a/testing/src/main/contraband-scala/sbt/protocol/testing/TestInitEvent.scala b/testing/src/main/contraband-scala/sbt/protocol/testing/TestInitEvent.scala
index 978524687..b6178c40f 100644
--- a/testing/src/main/contraband-scala/sbt/protocol/testing/TestInitEvent.scala
+++ b/testing/src/main/contraband-scala/sbt/protocol/testing/TestInitEvent.scala
@@ -10,7 +10,7 @@ final class TestInitEvent private () extends sbt.protocol.testing.TestMessage()
 
 
 override def equals(o: Any): Boolean = o match {
-  case x: TestInitEvent => true
+  case _: TestInitEvent => true
   case _ => false
 }
 override def hashCode: Int = {
diff --git a/testing/src/main/contraband-scala/sbt/protocol/testing/TestMessage.scala b/testing/src/main/contraband-scala/sbt/protocol/testing/TestMessage.scala
index 406807c6f..3ef0f0a76 100644
--- a/testing/src/main/contraband-scala/sbt/protocol/testing/TestMessage.scala
+++ b/testing/src/main/contraband-scala/sbt/protocol/testing/TestMessage.scala
@@ -11,7 +11,7 @@ abstract class TestMessage() extends Serializable {
 
 
 override def equals(o: Any): Boolean = o match {
-  case x: TestMessage => true
+  case _: TestMessage => true
   case _ => false
 }
 override def hashCode: Int = {