Cleaned up various readPipe() threading issues

Fixed random errors in discoverGitSystemConfig() on Linux where the
process error stream was closed by readPipe() before or while
GobblerThread was reading from it.

Marked readPipe() as @Nullable and fixed potential NPE in
discoverGitSystemConfig() on readPipe() return value.

Fixed process error output randomly mixed with other threads log
messages.

Change-Id: Id882af2762cfb75f010f693b2e1c46eb6968ee82
Signed-off-by: Andrey Loskutov <loskutov@gmx.de>

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

@@ -67,6 +67,7 @@ import java.util.concurrent.Executors;
 import java.util.concurrent.TimeUnit;
 import java.util.concurrent.atomic.AtomicBoolean;
 
+import org.eclipse.jdt.annotation.Nullable;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Constants;
@@ -407,6 +408,7 @@ public abstract class FS {
 	 *            to be used to parse the command's output
 	 * @return the one-line output of the command
 	 */
+	@Nullable
 	protected static String readPipe(File dir, String[] command, String encoding) {
 		return readPipe(dir, command, encoding, null);
 	}
@@ -426,6 +428,7 @@ public abstract class FS {
 	 * @return the one-line output of the command
 	 * @since 4.0
 	 */
+	@Nullable
 	protected static String readPipe(File dir, String[] command, String encoding, Map<String, String> env) {
 		final boolean debug = LOG.isDebugEnabled();
 		try {
@@ -439,36 +442,30 @@ public abstract class FS {
 				pb.environment().putAll(env);
 			}
 			Process p = pb.start();
-			BufferedReader lineRead = new BufferedReader(
-					new InputStreamReader(p.getInputStream(), encoding));
 			p.getOutputStream().close();
 			GobblerThread gobbler = new GobblerThread(p, command, dir);
 			gobbler.start();
 			String r = null;
-			try {
+			try (BufferedReader lineRead = new BufferedReader(
+					new InputStreamReader(p.getInputStream(), encoding))) {
 				r = lineRead.readLine();
 				if (debug) {
 					LOG.debug("readpipe may return '" + r + "'"); //$NON-NLS-1$ //$NON-NLS-2$
-					LOG.debug("(ignoring remaing output:"); //$NON-NLS-1$
-				}
-				String l;
-				while ((l = lineRead.readLine()) != null) {
-					if (debug) {
+					LOG.debug("remaining output:\n"); //$NON-NLS-1$
+					String l;
+					while ((l = lineRead.readLine()) != null) {
 						LOG.debug(l);
 					}
 				}
-			} finally {
-				p.getErrorStream().close();
-				lineRead.close();
 			}
 
 			for (;;) {
 				try {
 					int rc = p.waitFor();
 					gobbler.join();
-					if (rc == 0 && r != null && r.length() > 0
-							&& !gobbler.fail.get())
+					if (rc == 0 && !gobbler.fail.get()) {
 						return r;
+					}
 					if (debug) {
 						LOG.debug("readpipe rc=" + rc); //$NON-NLS-1$
 					}
@@ -499,21 +496,23 @@ public abstract class FS {
 		}
 
 		public void run() {
-			InputStream is = p.getErrorStream();
-			try {
+			StringBuilder err = new StringBuilder();
+			try (InputStream is = p.getErrorStream()) {
 				int ch;
 				while ((ch = is.read()) != -1) {
-					System.err.print((char) ch);
+					err.append((char) ch);
 				}
 			} catch (IOException e) {
-				logError(e);
-				fail.set(true);
-			}
-			try {
-				is.close();
-			} catch (IOException e) {
-				logError(e);
-				fail.set(true);
+				if (p.exitValue() != 0) {
+					logError(e);
+					fail.set(true);
+				} else {
+					// ignore. git terminated faster and stream was just closed
+				}
+			} finally {
+				if (err.length() > 0) {
+					LOG.error(err.toString());
+				}
 			}
 		}
 
@@ -546,7 +545,7 @@ public abstract class FS {
 		String v = readPipe(gitExe.getParentFile(),
 				new String[] { "git", "--version" }, //$NON-NLS-1$ //$NON-NLS-2$
 				Charset.defaultCharset().name());
-		if (v.startsWith("jgit")) { //$NON-NLS-1$
+		if (v != null && v.startsWith("jgit")) { //$NON-NLS-1$
 			return null;
 		}