From Project BungeeGames.

Updater.java

package fr.skyost.bungeegames.utils;

import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.net.HttpURLConnection;
import java.net.URL;
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.regex.Pattern;

import org.bukkit.Bukkit;
import org.bukkit.plugin.Plugin;
import org.jsoup.Connection;
import org.jsoup.Jsoup;
import org.jsoup.nodes.Document;
import org.jsoup.nodes.Element;

public class Updater extends Thread {
	
	private final Plugin plugin;
	private final File pathTo;
	
	private final Logger logger;
	
	public static final String PAGE_URL = "http://dev.bukkit.org/bukkit-plugins/project-hungergames/pages/project-bungee-games/";
	public static final String DOWNLOAD_URL = "http://files.skyost.eu/files/project-hungergames/Project%20BungeeGames.jar";
	
	public Updater(final Plugin plugin, final File pluginFile) {
		this.plugin = plugin;
		final File updateFolder = Bukkit.getUpdateFolderFile();
		if(!updateFolder.exists()) {
			updateFolder.mkdir();
		}
		this.pathTo = new File(updateFolder, pluginFile.getName());
		this.logger = plugin.getLogger();
	}
	
	@Override
	public void run() {
		try {
			final Connection connection = Jsoup.connect(PAGE_URL);
			connection.data("query", "java");
			connection.timeout(10000);
			connection.ignoreHttpErrors(true);
			connection.userAgent("Project BungeeGames");
			final Document page = connection.get();
			String remoteVersion = null;
			for(final Element element : page.select("p")) {
				final String elementText = element.text();
				if(elementText.contains("Current version")) {
					remoteVersion = elementText.split("Current version : v")[1];
					break;
				}
			}
			if(remoteVersion == null || remoteVersion.length() == 0) {
				return;
			}
			final String localVersion = plugin.getDescription().getVersion();
			if(compareVersions(remoteVersion, localVersion)) {
				logger.log(Level.INFO, "Downloading a new update : " + remoteVersion + "...");
				if(download(DOWNLOAD_URL, pathTo)) {
					logger.log(Level.FINE, "The new version was downloaded with success !");
					logger.log(Level.INFO, "Please make a reboot (or a reload) to be able to use the downloaded version.");
				}
				else {
					logger.log(Level.SEVERE, "Something went wrong :s");
					logger.log(Level.INFO, "But you can download the update manually at '" + DOWNLOAD_URL + "'.");
				}
			}
		}
		catch(Exception ex) {
			logger.log(Level.SEVERE, "Error while checking for updates : \"" + ex.getClass().getName() + "\". Please report it on Project HungerGames' BukkitDev page.");
		}
	}
	
	/**
	 * Downloads a file.
	 * 
	 * @param site The URL of the file you want to download.
	 * @param pathTo The path where you want the file to be downloaded.
	 * 
	 * @return <b>true</b>If the download was a success.
	 * </b>false</b>If there is an error during the download.
	 * 
	 * @throws IOException InputOutputException.
	 */
	
	private final boolean download(final String site, final File pathTo) {
		try {
			final HttpURLConnection connection = (HttpURLConnection)new URL(site).openConnection();
			connection.addRequestProperty("User-Agent", "Project BungeeGames");
			final String response = connection.getResponseCode() + " " + connection.getResponseMessage();
			if(!response.startsWith("2")) {
				logger.log(Level.INFO, "Bad response : '" + response + "' when trying to download the update.");
				return false;
			}
			final long size = connection.getContentLengthLong();
			final long koSize = size / 1000;
			long lastPercent = 0;
			long percent = 0;
			float totalDataRead = 0;
			final InputStream inputStream = connection.getInputStream();
			final FileOutputStream fileOutputStream = new FileOutputStream(pathTo);
			final BufferedOutputStream bufferedOutputStream = new BufferedOutputStream(fileOutputStream, 1024);
			final byte[] data = new byte[1024];
			int i = 0;
			while((i = inputStream.read(data, 0, 1024)) >= 0) {
				totalDataRead += i;
				bufferedOutputStream.write(data, 0, i);
				percent = ((long)(totalDataRead * 100) / size);
				if(lastPercent != percent) {
					lastPercent = percent;
					logger.log(Level.INFO, percent + "% of " + koSize + "ko...");
				}
			}
			bufferedOutputStream.close();
			fileOutputStream.close();
			inputStream.close();
			return true;
		}
		catch(Exception ex) {
			logger.log(Level.SEVERE, "Exception '" + ex + "' occured when downloading update. Please check your network connection.");
			ex.printStackTrace();
		}
		return false;
	}
	
	/**
	 * Compare two versions.
	 * 
	 * @param version1 The version you want to compare to.
	 * @param version2 The version you want to compare with.
	 * 
	 * @return <b>true</b> If <b>versionTo</b> is inferior than <b>versionWith</b>.
	 * <br><b>false</b> If <b>versionTo</b> is superior or equals to <b>versionWith</b>.
	 */
	
	public static final boolean compareVersions(final String versionTo, final String versionWith) {
		return normalisedVersion(versionTo, ".", 4).compareTo(normalisedVersion(versionWith, ".", 4)) > 0;
	}
	
	/**
	 * Get the formatted name of a version.
	 * <br>Used for the method <b>compareVersions(...)</b> of this class.
	 * 
	 * @param version The version you want to format.
	 * @param separator The separator between the numbers of this version.
	 * @param maxWidth The max width of the formatted version.
	 * 
	 * @return A string which the formatted version of your version.
	 * 
	 * @author Peter Lawrey.
	 */

	private static final String normalisedVersion(final String version, final String separator, final int maxWidth) {
		final StringBuilder stringBuilder = new StringBuilder();
		for(final String normalised : Pattern.compile(separator, Pattern.LITERAL).split(version)) {
			stringBuilder.append(String.format("%" + maxWidth + 's', normalised));
		}
		return stringBuilder.toString();
	}
	
}