Ignore IOException thrown from close

AddCommandTest is flaky because IOException is thrown sometimes.

Caused by: java.io.IOException: Stream closed
        at java.lang.ProcessBuilder$NullOutputStream.write(ProcessBuilder.java:433)
        at java.io.OutputStream.write(OutputStream.java:116)
        at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
        at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140)
        at java.io.FilterOutputStream.close(FilterOutputStream.java:158)
        at org.eclipse.jgit.util.FS.runProcess(FS.java:993)
        at org.eclipse.jgit.util.FS.execute(FS.java:1102)
        at org.eclipse.jgit.treewalk.WorkingTreeIterator.filterClean(WorkingTreeIterator.java:470)
        ... 22 more

OpenJDK replaces the underlying OutputStream with NullOutputStream when
the process exits. This throws IOException for all write operation. When
it exits before JGit writes the input to the pipe buffer, the input
stays in BufferedOutputStream. The close method tries to write it again,
and IOException is thrown.

Since we ignore IOException in StreamGobbler, we also ignore it when
we close the stream.

Fixes Bug 499633.

Change-Id: I30c7ac78e05b00bd0152f697848f4d17d53efd17
Signed-off-by: Masaya Suzuki <draftcode@gmail.com>

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

@@ -990,7 +990,16 @@ public abstract class FS {
 				new StreamGobbler(inRedirect, outputStream)
 						.call();
 			}
-			outputStream.close();
+			try {
+				outputStream.close();
+			} catch (IOException e) {
+				// When the process exits before consuming the input, the OutputStream
+				// is replaced with the null output stream. This null output stream
+				// throws IOException for all write calls. When StreamGobbler fails to
+				// flush the buffer because of this, this close call tries to flush it
+				// again. This causes another IOException. Since we ignore the
+				// IOException in StreamGobbler, we also ignore the exception here.
+			}
 			return process.waitFor();
 		} catch (IOException e) {
 			ioException = e;