Fix issues with LFS on GitHub (SSH)

 * URIish seems to have a tiny feature (bug?). The path of the URI
   starts with a '/' only if the URI has a port set (it seems).
 * GitHub does not return SSH authorization on a single line as Gerrit
   does - need to account for that.
 * Increase the SSH git-lfs-authenticate timeout, as GitHub sometimes
   responds slower than expected.
 * Guard against NPE in case the download action does not contain any
   additional headers.

Change-Id: Icd1ead3d015479fd4b8bbd42ed42129b0abfb95c
Signed-off-by: Markus Duft <markus.duft@ssi-schaefer.com>

org.eclipse.jgit.lfs/META-INF/MANIFEST.MF

  org.eclipse.jgit.treewalk;version="[5.0.0,5.1.0)",
  org.eclipse.jgit.treewalk.filter;version="[5.0.0,5.1.0)",
  org.eclipse.jgit.util;version="[5.0.0,5.1.0)",
- org.eclipse.jgit.util.io;version="[5.0.0,5.1.0)"
+ org.eclipse.jgit.util.io;version="[5.0.0,5.1.0)",
+ org.slf4j;version="[1.7.0,2.0.0)"

org.eclipse.jgit.lfs/resources/org/eclipse/jgit/lfs/internal/LfsText.properties

+cannotDiscoverLfs=Cannot discover LFS URI
 corruptLongObject=The content hash ''{0}'' of the long object ''{1}'' doesn''t match its id, the corrupt object will be deleted.
 incorrectLONG_OBJECT_ID_LENGTH=Incorrect LONG_OBJECT_ID_LENGTH.
 inconsistentMediafileLength=Mediafile {0} has unexpected length; expected {1} but found {2}.

org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/internal/LfsConnectionFactory.java

 import org.eclipse.jgit.transport.http.HttpConnection;
 import org.eclipse.jgit.util.HttpSupport;
 import org.eclipse.jgit.util.SshSupport;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * Provides means to get a valid LFS connection for a given repository.
  */
 public class LfsConnectionFactory {
 
-	private static final int SSH_AUTH_TIMEOUT_SECONDS = 5;
+	private static final Logger log = LoggerFactory
+			.getLogger(LfsConnectionFactory.class);
+
+	private static final int SSH_AUTH_TIMEOUT_SECONDS = 30;
 	private static final String SCHEME_HTTPS = "https"; //$NON-NLS-1$
 	private static final String SCHEME_SSH = "ssh"; //$NON-NLS-1$
 	private static final Map<String, AuthCache> sshAuthCache = new TreeMap<>();
 			Map<String, String> additionalHeaders, String remoteUrl) {
 		try {
 			URIish u = new URIish(remoteUrl);
-			if (SCHEME_SSH.equals(u.getScheme())) {
+			if (u.getScheme() == null || SCHEME_SSH.equals(u.getScheme())) {
 				Protocol.ExpiringAction action = getSshAuthentication(
 						db, purpose, remoteUrl, u);
 				additionalHeaders.putAll(action.header);
 				return remoteUrl + Protocol.INFO_LFS_ENDPOINT;
 			}
 		} catch (Exception e) {
+			log.error(LfsText.get().cannotDiscoverLfs, e);
 			return null; // could not discover
 		}
 	}
 				.create(contentUrl, HttpSupport
 						.proxyFor(ProxySelector.getDefault(), contentUrl));
 		contentServerConn.setRequestMethod(method);
-		action.header
-				.forEach((k, v) -> contentServerConn.setRequestProperty(k, v));
+		if (action.header != null) {
+			action.header.forEach(
+					(k, v) -> contentServerConn.setRequestProperty(k, v));
+		}
 		if (contentUrl.getProtocol().equals(SCHEME_HTTPS)
 				&& !repo.getConfig().getBoolean(HttpConfig.HTTP,
 						HttpConfig.SSL_VERIFY_KEY, true)) {
 	}
 
 	private static String extractProjectName(URIish u) {
-		String path = u.getPath().substring(1);
+		String path = u.getPath();
+
+		// begins with a slash if the url contains a port (gerrit vs. github).
+		if (path.startsWith("/")) { //$NON-NLS-1$
+			path = path.substring(1);
+		}
+
 		if (path.endsWith(org.eclipse.jgit.lib.Constants.DOT_GIT)) {
 			return path.substring(0, path.length() - 4);
 		} else {

org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/internal/LfsText.java

 	}
 
 	// @formatter:off
+	/***/ public String cannotDiscoverLfs;
 	/***/ public String corruptLongObject;
 	/***/ public String inconsistentMediafileLength;
 	/***/ public String inconsistentContentLength;

org.eclipse.jgit/src/org/eclipse/jgit/util/SshSupport.java

  */
 package org.eclipse.jgit.util;
 
-import java.io.BufferedReader;
 import java.io.IOException;
-import java.io.InputStreamReader;
 
 import org.eclipse.jgit.annotations.Nullable;
-import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.transport.CredentialsProvider;
 import org.eclipse.jgit.transport.RemoteSession;
 import org.eclipse.jgit.transport.SshSessionFactory;
 	 * @param command
 	 *            the remote command to execute.
 	 * @param timeout
-	 *            a timeout in seconds.
-	 * @return The first line of output read from stdout. Stderr is discarded.
+	 *            a timeout in seconds. The timeout may be exceeded in corner
+	 *            cases.
+	 * @return The entire output read from stdout. Stderr is discarded.
 	 * @throws IOException
 	 */
 	public static String runSshCommand(URIish sshUri,
 		RemoteSession session = null;
 		Process process = null;
 		StreamCopyThread errorThread = null;
-		try (MessageWriter stderr = new MessageWriter()) {
+		StreamCopyThread outThread = null;
+		try (MessageWriter stderr = new MessageWriter();
+				MessageWriter stdout = new MessageWriter()) {
 			session = SshSessionFactory.getInstance().getSession(sshUri,
 					provider, fs, 1000 * timeout);
 			process = session.exec(command, 0);
 			errorThread = new StreamCopyThread(process.getErrorStream(),
 					stderr.getRawStream());
 			errorThread.start();
-			try (BufferedReader reader = new BufferedReader(
-					new InputStreamReader(process.getInputStream(),
-							Constants.CHARSET))) {
-				return reader.readLine();
+			outThread = new StreamCopyThread(process.getInputStream(),
+					stdout.getRawStream());
+			outThread.start();
+			try {
+				// waitFor with timeout has a bug - JSch' exitValue() throws the
+				// wrong exception type :(
+				if (process.waitFor() == 0) {
+					return stdout.toString();
+				} else {
+					return null; // still running after timeout
+				}
+			} catch (InterruptedException e) {
+				return null; // error
 			}
 		} finally {
 			if (errorThread != null) {
 					errorThread = null;
 				}
 			}
+			if (outThread != null) {
+				try {
+					outThread.halt();
+				} catch (InterruptedException e) {
+					// Stop waiting and return anyway.
+				} finally {
+					outThread = null;
+				}
+			}
 			if (process != null) {
 				process.destroy();
 			}