Stop throwing the exceptions and instead catch them earlier.

src/sig/plugin/TwosideKeeper/AutoUpdatePlugin.java

@@ -2,6 +2,7 @@ package sig.plugin.TwosideKeeper;
 
 import java.io.File;
 import java.io.FileInputStream;
+import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.net.URL;
 import java.nio.file.CopyOption;
@@ -30,22 +31,39 @@ public class AutoUpdatePlugin implements Runnable {
 	
 	@Override
 	public void run() {
-		try {
 		FetchPlugins();
+	}
+	
+	void FetchPlugins(){
+		for (int i=0;i<plugins.size();i++) {
+			try {
+				FileUtils.copyURLToFile(new URL(plugins.get(i).url), new File(TwosideKeeper.filesave,"updates/"+plugins.get(i).name));
 			} catch (IOException e) {
 				// TODO Auto-generated catch block
 				e.printStackTrace();
 			}
-	}
-	
-	void FetchPlugins() throws IOException {
-		for (int i=0;i<plugins.size();i++) {
-			FileUtils.copyURLToFile(new URL(plugins.get(i).url), new File(TwosideKeeper.filesave,"updates/"+plugins.get(i).name));
 			
 			//After that's done, check the hash.
-			FileInputStream file = new FileInputStream(new File(TwosideKeeper.filesave,"updates/"+plugins.get(i).name));
+			FileInputStream file = null;
-			String md5 = org.apache.commons.codec.digest.DigestUtils.md5Hex(file);
+			try {
+				file = new FileInputStream(new File(TwosideKeeper.filesave,"updates/"+plugins.get(i).name));
+			} catch (FileNotFoundException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
+			String md5 = null;
+			try {
+				md5 = org.apache.commons.codec.digest.DigestUtils.md5Hex(file);
+			} catch (IOException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
+			try {
 				file.close();
+			} catch (IOException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
 			
 			if (plugins.get(i).hash==null || !md5.equalsIgnoreCase(plugins.get(i).hash)) {
 				//This plugin is different! Update the hash for it. Prepare for a restart of the server!
@@ -55,8 +73,13 @@ public class AutoUpdatePlugin implements Runnable {
 				SaveHash(plugins.get(i));
 				Bukkit.broadcastMessage("The server has detected a new version of "+ChatColor.YELLOW+plugins.get(i).name+". The server will restart in 3 minutes!");
 				//Move the file to the new location.
+				try {
 					FileUtils.copyFile(new File(TwosideKeeper.filesave,"updates/"+plugins.get(i).name),
 							new File(TwosideKeeper.filesave,"../"+plugins.get(i).name+".jar"));
+				} catch (IOException e) {
+					// TODO Auto-generated catch block
+					e.printStackTrace();
+				}
 			}
 		}
 		if (restarting) {

src/sig/plugin/TwosideKeeper/TwosideKeeper.java

@@ -370,13 +370,7 @@ public class TwosideKeeper extends JavaPlugin implements Listener {
 			//Every 5 minutes, check for a plugin update.
 			getServer().getScheduler().scheduleSyncRepeatingTask(this, new  Runnable(){
 				public void run(){
-					try {
 					pluginupdater.FetchPlugins();
-					} catch (IOException e) {
-						// TODO Auto-generated catch block 
-						e.printStackTrace();
-						
-					}
 			}}, 20*300, 20*300);
 		}