diff --git a/src/main/java/net/fabricmc/loom/mixin/MixinServiceGradle.java b/src/main/java/net/fabricmc/loom/mixin/MixinServiceGradle.java
index 17ba4d4..6b700a4 100644
--- a/src/main/java/net/fabricmc/loom/mixin/MixinServiceGradle.java
+++ b/src/main/java/net/fabricmc/loom/mixin/MixinServiceGradle.java
@@ -79,6 +79,7 @@ public class MixinServiceGradle extends MixinServiceLaunchWrapper implements ICl
 	public byte[] getClassBytes(String name, String transformedName) throws IOException {
 		InputStream inputStream = getResourceAsStream(name.replace(".", "/") + ".class");
 		byte[] classBytes = ByteStreams.toByteArray(inputStream);
+		inputStream.close();
 		if(classBytes == null){
 			return super.getClassBytes(name, transformedName);
 		}
diff --git a/src/main/java/net/fabricmc/loom/task/RunClientTask.java b/src/main/java/net/fabricmc/loom/task/RunClientTask.java
index 370c87e..ef030a7 100644
--- a/src/main/java/net/fabricmc/loom/task/RunClientTask.java
+++ b/src/main/java/net/fabricmc/loom/task/RunClientTask.java
@@ -66,7 +66,6 @@ public class RunClientTask extends JavaExec {
 
 		//Removes the deobf jars
 		libs.removeIf(s -> s.contains(Constants.MINECRAFT_FINAL_JAR.get(extension).getName()));
-		libs.removeIf(s -> s.contains(getProject().getName() + "-" + getProject().getVersion() + "-deobf.jar"));
 
 		classpath(libs);
 
@@ -77,6 +76,14 @@ public class RunClientTask extends JavaExec {
 		super.exec();
 	}
 
+	@Override
+	public void setWorkingDir(File dir) {
+		if(!dir.exists()){
+			dir.mkdirs();
+		}
+		super.setWorkingDir(dir);
+	}
+
 	@Override
 	public String getMain() {
 		return "net.minecraft.launchwrapper.Launch";
diff --git a/src/main/java/net/fabricmc/loom/task/RunServerTask.java b/src/main/java/net/fabricmc/loom/task/RunServerTask.java
index 418643b..3d62eb7 100644
--- a/src/main/java/net/fabricmc/loom/task/RunServerTask.java
+++ b/src/main/java/net/fabricmc/loom/task/RunServerTask.java
@@ -77,6 +77,14 @@ public class RunServerTask extends JavaExec {
 		return "net.minecraft.launchwrapper.Launch";
 	}
 
+	@Override
+	public void setWorkingDir(File dir) {
+		if(!dir.exists()){
+			dir.mkdirs();
+		}
+		super.setWorkingDir(dir);
+	}
+
 	@Override
 	public List<String> getJvmArgs() {
 		LoomGradleExtension extension = this.getProject().getExtensions().getByType(LoomGradleExtension.class);
diff --git a/src/main/java/net/fabricmc/loom/util/ModProcessor.java b/src/main/java/net/fabricmc/loom/util/ModProcessor.java
index a6289cc..34cd0e7 100644
--- a/src/main/java/net/fabricmc/loom/util/ModProcessor.java
+++ b/src/main/java/net/fabricmc/loom/util/ModProcessor.java
@@ -125,6 +125,7 @@ public class ModProcessor {
 			remapper.read(mcDeps);
 			remapper.apply(input.toPath(), outputConsumer);
 			outputConsumer.finish();
+			remapper.finish();
 		} catch (Exception e){
 			remapper.finish();
 			throw new RuntimeException("Failed to remap JAR to " + toM, e);
@@ -141,7 +142,10 @@ public class ModProcessor {
 			if (!entry.isDirectory() && entry.getName().endsWith(".json") && !entry.getName().contains("/") && !entry.getName().contains("\\")) {
 				// JSON file in root directory
 				try {
-					JsonObject json = gson.fromJson(new InputStreamReader(stream), JsonObject.class);
+					InputStreamReader inputStreamReader = new InputStreamReader(stream);
+					JsonObject json = gson.fromJson(inputStreamReader, JsonObject.class);
+					inputStreamReader.close();
+					stream.close();
 					if (json != null && json.has("refmap")) {
 						mixinRefmapFilenames.add(json.get("refmap").getAsString());
 					}
diff --git a/src/main/java/net/fabricmc/loom/util/ModRemapper.java b/src/main/java/net/fabricmc/loom/util/ModRemapper.java
index 187e137..c2d7275 100644
--- a/src/main/java/net/fabricmc/loom/util/ModRemapper.java
+++ b/src/main/java/net/fabricmc/loom/util/ModRemapper.java
@@ -43,25 +43,13 @@ public class ModRemapper {
 		LoomGradleExtension extension = project.getExtensions().getByType(LoomGradleExtension.class);
 		// TODO: What's the proper way of doing this?
 		File libsDir = new File(project.getBuildDir(), "libs");
-		File deobfJar = new File(libsDir, project.getName() + "-" + project.getVersion() + "-deobf.jar");
 		File modJar = new File(libsDir, project.getName() + "-" + project.getVersion() + ".jar");
 
 		if (!modJar.exists()) {
-			project.getLogger().error("Could not find mod .JAR at" + deobfJar.getAbsolutePath());
 			project.getLogger().error("This is can be fixed by adding a 'settings.gradle' file specifying 'rootProject.name'");
 			return;
 		}
 
-		if (deobfJar.exists()) {
-			deobfJar.delete();
-		}
-
-		FileUtils.touch(modJar); //Done to ensure that the file can be moved
-		//Move the pre existing mod jar to the deobf jar
-		if(!modJar.renameTo(deobfJar)){
-			throw new RuntimeException("Failed to rename " + modJar);
-		}
-
 		Path mappings = Constants.MAPPINGS_TINY.get(extension).toPath();
 
 		String fromM = "named";
@@ -86,10 +74,10 @@ public class ModRemapper {
 
 		try {
 			OutputConsumerPath outputConsumer = new OutputConsumerPath(modJar.toPath());
-			outputConsumer.addNonClassFiles(deobfJar.toPath());
-			remapper.read(deobfJar.toPath());
+			outputConsumer.addNonClassFiles(modJar.toPath());
+			remapper.read(modJar.toPath());
 			remapper.read(classpath);
-			remapper.apply(deobfJar.toPath(), outputConsumer);
+			remapper.apply(modJar.toPath(), outputConsumer);
 			outputConsumer.finish();
 			remapper.finish();
 		} catch (Exception e){
@@ -97,11 +85,9 @@ public class ModRemapper {
 			throw new RuntimeException("Failed to remap JAR", e);
 		}
 
-		if(!deobfJar.exists() || !modJar.exists()){
+		if(!modJar.exists()){
 			throw new RuntimeException("Failed to reobfuscate JAR");
 		}
-
-		deobfJar.delete();
 	}
 
 }