Fix ApplyCommand when result of patch is an empty file

Such hunks are identifiable by a zero value for "new start line". Prior
to the fix, JGit throws and ArrayIndexOutOfBoundsException on such
patches.

Change-Id: I4f3deb5e5f41a08af965fcc178d678c77270cddb
Signed-off-by: Jonathan Schneider <jkschneider@gmail.com>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

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

@@ -0,0 +1,7 @@
+diff --git a/W b/W
+index a3648a1..2d44096 100644
+--- a/W
++++ b/W
+@@ -1 +0,0 @@
+-a
+\ No newline at end of file

org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/W_PreImage

@@ -0,0 +1 @@
+a

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

@@ -146,6 +146,16 @@ public class ApplyCommandTest extends RepositoryTestCase {
 				b.getString(0, b.size(), false));
 	}
 
+	@Test
+	public void testModifyW() throws Exception {
+		ApplyResult result = init("W");
+		assertEquals(1, result.getUpdatedFiles().size());
+		assertEquals(new File(db.getWorkTree(), "W"),
+				result.getUpdatedFiles().get(0));
+		checkFile(new File(db.getWorkTree(), "W"),
+				b.getString(0, b.size(), false));
+	}
+
 	@Test
 	public void testModifyX() throws Exception {
 		ApplyResult result = init("X");

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

@@ -223,12 +223,16 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
 					pos++;
 					break;
 				case '-':
-					if (!newLines.get(hh.getNewStartLine() - 1 + pos).equals(
-							hunkLine.substring(1))) {
+					if (hh.getNewStartLine() == 0) {
+						newLines.clear();
+					} else {
+						if (!newLines.get(hh.getNewStartLine() - 1 + pos)
+								.equals(hunkLine.substring(1))) {
 							throw new PatchApplyException(MessageFormat.format(
 									JGitText.get().patchApplyException, hh));
 						}
 						newLines.remove(hh.getNewStartLine() - 1 + pos);
+					}
 					break;
 				case '+':
 					newLines.add(hh.getNewStartLine() - 1 + pos,
@@ -250,7 +254,9 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
 			// still there!
 			sb.append(l).append('\n');
 		}
+		if (sb.length() > 0) {
 			sb.deleteCharAt(sb.length() - 1);
+		}
 		FileWriter fw = new FileWriter(f);
 		fw.write(sb.toString());
 		fw.close();