Make ApplyCommand create missing parent directories for new files

Otherwise applying will fail with a FileNotFoundException, because
File.createNewFile() fails with missing parents.

Contains change & according test.

Change-Id: I970522b549b8bb260ca6720da11f12c57ee8a492
Signed-off-by: Chris Aniszczyk <zx@twitter.com>

org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/A1_sub.patch

@@ -0,0 +1,9 @@
+diff --git a/sub/A1 b/sub/A1
+new file mode 100644
+index 0000000..de98044
+--- /dev/null
++++ b/sub/A1
+@@ -0,0 +1,3 @@
++a
++b
++c

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ApplyCommandTest.java

@@ -111,6 +111,14 @@ public class ApplyCommandTest extends RepositoryTestCase {
 				b.getString(0, b.size(), false));
 	}
 
+	@Test
+	public void testAddA1Sub() throws Exception {
+		ApplyResult result = init("A1_sub", false, false);
+		assertEquals(1, result.getUpdatedFiles().size());
+		assertEquals(new File(db.getWorkTree(), "sub/A1"), result
+				.getUpdatedFiles().get(0));
+	}
+
 	@Test
 	public void testDeleteD() throws Exception {
 		ApplyResult result = init("D", true, false);

org.eclipse.jgit/src/org/eclipse/jgit/api/ApplyCommand.java

@@ -167,6 +167,8 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
 		File f = new File(getRepository().getWorkTree(), path);
 		if (create)
 			try {
+				File parent = f.getParentFile();
+				FileUtils.mkdirs(parent, true);
 				FileUtils.createNewFile(f);
 			} catch (IOException e) {
 				throw new PatchApplyException(MessageFormat.format(