diff --git a/build.gradle-template b/build.gradle-template
index 8af1b54..14cb9dd 100644
--- a/build.gradle-template
+++ b/build.gradle-template
@@ -57,6 +57,15 @@ dependencies {
 
 /*==== You probably don't have to edit below this line =======*/
 
+// The run task added by the application plugin
+// is also of type JavaExec.
+tasks.withType(JavaExec) {
+    // Assign all Java system properties from
+    // the command line to the JavaExec task.
+    systemProperties System.properties
+}
+
+
 protobuf {
     // Configure the protoc executable
     protoc {
diff --git a/meerkat-common/build.gradle b/meerkat-common/build.gradle
index b744fcd..236bd82 100644
--- a/meerkat-common/build.gradle
+++ b/meerkat-common/build.gradle
@@ -57,6 +57,16 @@ dependencies {
 
 /*==== You probably don't have to edit below this line =======*/
 
+
+// The run task added by the application plugin
+// is also of type JavaExec.
+tasks.withType(JavaExec) {
+    // Assign all Java system properties from
+    // the command line to the JavaExec task.
+    systemProperties System.properties
+}
+
+
 protobuf {
     // Configure the protoc executable
     protoc {
@@ -91,33 +101,6 @@ idea {
  *        "Fat" Build targets
  *===================================*/
 
-task fatjar(type: Jar) {
-    description = "Generate a single jar containing everything. Use -Pfatmain=... to override main class"
-
-    destinationDir = buildDir
-
-    def fatMain = hasProperty('fatmain') ? fatmain : mainClassName
-    def testJar = hasProperty('test')
-
-    appendix = "${fatMain}-fat"
-
-    if (testJar) {
-        from sourceSets.test.output
-        from configurations.testRuntime.collect { it.isDirectory() ? it : zipTree(it) }
-    }
-
-    from sourceSets.main.output // that's it
-    from { configurations.runtime.collect { it.isDirectory() ? it : zipTree(it) } }
-
-    exclude 'META-INF/MANIFEST.MF'
-    exclude 'META-INF/*.SF'
-    exclude 'META-INF/*.DSA'
-    exclude 'META-INF/*.RSA'
-
-
-    manifest { attributes 'Main-Class': fatMain }
-}
-
 
 task mavenCapsule(type: MavenCapsule){
     description = "Generate a capsule jar that automatically downloads and caches dependencies when run."