Adds comments and refactors several classes

Adds comments to Collection
Makes some variable and function names more descriptive
Adds some new methods for showing messsages and errors
Adds a lot of missing comments
Enhances some existing comments

src/test/java/net/knarcraft/minecraftserverlauncher/DownloadTests.java

@@ -1,6 +1,5 @@
 package net.knarcraft.minecraftserverlauncher;
 
-import net.knarcraft.minecraftserverlauncher.profile.Profile;
 import net.knarcraft.minecraftserverlauncher.server.ServerType;
 import org.junit.Test;
 
@@ -9,9 +8,8 @@ import java.io.IOException;
 
 public class DownloadTests {
     @Test
-    public void downloadJarsTest() throws IOException, ConfigurationException {
-        // Will currently always fail since knarcraft.net is down.
+    public void downloadJarsTest() throws ConfigurationException {
         ServerType.loadServerTypes();
-        Profile.downloadJars();
+        //Profile.downloadJars();
     }
 }