Some more Gradle cleanup

-Add more comments for documentation purposes
-Remove unnecessary comments and code
-Move WebContent to \src\main\webapp to remove more build code

Core/WPISuite/build.gradle

@@ -1,37 +1,30 @@
+//Import the Tomcat plugin
 buildscript {
     repositories {
         jcenter()
-    //  maven {
-    //      url "https://source.db4o.com/maven"
-    //  }
     }
     dependencies {
-        classpath 'org.gradle.api.plugins:gradle-tomcat-plugin:1.2.3'
+        classpath 'org.gradle.api.plugins:gradle-tomcat-plugin:1.2.4'
     }
 }
 
+//Apply plugins
 apply plugin: 'war'
 apply plugin: 'tomcat'
 
-webAppDirName = 'WebContent'
+//Which version of Tomcat should be used
+def tomcatVersion = '7.0.54'
 
 dependencies {
-	def tomcatVersion = '7.0.54'
-
-	providedCompile "javax.servlet:javax.servlet-api:3.0.1"
-
-    tomcat "org.apache.tomcat.embed:tomcat-embed-core:${tomcatVersion}",
-           "org.apache.tomcat.embed:tomcat-embed-logging-juli:${tomcatVersion}"
+
+    //Depend on tomcat
+    tomcat "org.apache.tomcat.embed:tomcat-embed-core:${tomcatVersion}"
+    tomcat "org.apache.tomcat.embed:tomcat-embed-logging-juli:${tomcatVersion}"
     tomcat("org.apache.tomcat.embed:tomcat-embed-jasper:${tomcatVersion}") {
         exclude group: 'org.eclipse.jdt.core.compiler', module: 'ecj'
     }
 
-//	tomcat {
-//		httpPort = 8090
-//		httpsPort = 8091
-//		enableSSL = true
-//	}
-
+    //Core project dependency	
     compile project(':WPISuite-Interfaces')
 
     //Modules

Janeway/build.gradle

@@ -11,6 +11,7 @@ apply plugin: 'application'
 mainClassName = "edu.wpi.cs.wpisuitetng.janeway.Janeway"
 //applicationDefaultJvmArgs = ["-Dgreeting.language=en"]
 
+//Janeway depends on it's modules, look at the modules first
 modulesList.each {
     evaluationDependsOn(":${it}")
 }
@@ -27,31 +28,42 @@ dependencies{
     compile project(':WPISuite-Interfaces')
     compile project(':Network')
 
-	//Modules
+    //We depend on each modules
     modulesList.each {
-	    runtime project(":${it}")
-        }
+        runtime project(":${it}")
+    }
 }
 
+//Workaround so that Eclipse knows how to run the Gradle tasks 'modules' in order to prepare modules. 'modules' is dependency for running Janeway
+//TODO Pretty sure there is a better way of doing this
 eclipse{
-	project{
-		if (Os.isFamily(Os.FAMILY_WINDOWS)) {
-			buildCommand 'org.eclipse.ui.externaltools.ExternalToolBuilder', LaunchConfigHandle: '<project>/.externalToolBuilders/Gradle - Prepare Modules - Windows.launch'
-		} else {
-			buildCommand 'org.eclipse.ui.externaltools.ExternalToolBuilder', LaunchConfigHandle: '<project>/.externalToolBuilders/Gradle - Prepare Modules - Unix.launch'
-		}
-	}
+    project{
+        if (Os.isFamily(Os.FAMILY_WINDOWS)) {
+            buildCommand 'org.eclipse.ui.externaltools.ExternalToolBuilder', LaunchConfigHandle: '<project>/.externalToolBuilders/Gradle - Prepare Modules - Windows.launch'
+        } else {
+            buildCommand 'org.eclipse.ui.externaltools.ExternalToolBuilder', LaunchConfigHandle: '<project>/.externalToolBuilders/Gradle - Prepare Modules - Unix.launch'
+        }
+    }
 }
 
+//Add the dependencies to the .jar manifest
 jar {
     manifest{
         attributes('Class-Path': configurations.runtime.files.collect {
-            if(!modulesList.contains(it.name.minus(".jar")) || 'Janeway'.equals(it.name.minus("jar")))
+            //Don't include the modules in the manifest, we're including them in the modules folder
+            if(!modulesList.contains(it.name.minus(".jar"))) 
             {"${libsDir}/${it.name}"}}.join(' ') )
         attributes('Main-Class': "${mainClassName}")
     }
 }
 
+//Remove the default distribution tasks, since Janeway requires more complicated configuration
+tasks.removeAll([distZip, distTar, installApp, startScripts])
+
+/**
+ * Custom Gradle tasks to prepare the Janeway modules, and create a distribution. Equivalent to Ant targets
+ */
+
 task modules(type: Copy) {
 	description = "Copy over each module .jar file for Janeway into the modules folder"
 	group = "Application"
@@ -66,16 +78,6 @@ task modules(type: Copy) {
     }
 }
 
-//TODO Start using when Distribution plugin is further developed
-//Until then a custom task is more ideal
-
-//distZip.enabled = false
-//distTar.enabled = false
-//installApp.enabled = false
-//startScripts.enabled = false
-
-tasks.removeAll([distZip, distTar, installApp, startScripts])
-
 task distribution(type: Zip){
 	description = "Create a .zip distribution for Janeway"
 	group = "Application"
@@ -87,9 +89,6 @@ task distribution(type: Zip){
         into "${project.name}"
     }
 
-    //Scripts to launch
-    //from(startScripts)
-
     //Libraries
     from(configurations.runtime){
         into "${project.name}/${libsDir}"