Allow setting FileMode to executable when applying patches in ApplyCommand

git-apply allows modifying file modes in patched files using either
"new mode" or "new file mode" headers. This patch adds support for
setting files as executables and vice-versa.

Change-Id: I24848966b46f686f540a8efa8150b42e0d9c3ad1
Signed-off-by: Nadav Cohen <nadavcoh@gmail.com>

org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M1.patch

+diff --git a/M1 b/M1
+new file mode 100755
+index 0000000..de98044
+--- /dev/null
++++ b/M1
+@@ -0,0 +1,3 @@
++a
++b
++c

org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M1_PostImage

+a
+b
+c

org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M2.patch

+diff --git a/M2 b/M2
+old mode 100644
+new mode 100755
+index 0000000..de98044
+--- a/M2
++++ b/M2
+@@ -1,3 +1,1 @@
+ a
+-b
+-c

org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M2_PostImage

+a

org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M2_PreImage

+a
+b
+c

org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M3.patch

+diff --git a/M3 b/M3
+old mode 100755
+new mode 100644
+index 0000000..de98044
+--- a/M3
++++ b/M3
+@@ -1,1 +1,3 @@
+ a
++b
++c

org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M3_PostImage

+a
+b
+c

org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/M3_PreImage

+a

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

 
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
 import java.io.ByteArrayOutputStream;
 				b.getString(0, b.size(), false));
 	}
 
+	@Test
+	public void testAddM1() throws Exception {
+		ApplyResult result = init("M1", false, true);
+		assertEquals(1, result.getUpdatedFiles().size());
+		assertTrue(result.getUpdatedFiles().get(0).canExecute());
+		checkFile(new File(db.getWorkTree(), "M1"),
+				b.getString(0, b.size(), false));
+	}
+
+	@Test
+	public void testModifyM2() throws Exception {
+		ApplyResult result = init("M2", true, true);
+		assertEquals(1, result.getUpdatedFiles().size());
+		assertTrue(result.getUpdatedFiles().get(0).canExecute());
+		checkFile(new File(db.getWorkTree(), "M2"),
+				b.getString(0, b.size(), false));
+	}
+
+	@Test
+	public void testModifyM3() throws Exception {
+		ApplyResult result = init("M3", true, true);
+		assertEquals(1, result.getUpdatedFiles().size());
+		assertFalse(result.getUpdatedFiles().get(0).canExecute());
+		checkFile(new File(db.getWorkTree(), "M3"),
+				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

 import org.eclipse.jgit.diff.DiffEntry.ChangeType;
 import org.eclipse.jgit.diff.RawText;
 import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.patch.FileHeader;
 import org.eclipse.jgit.patch.HunkHeader;
 		FileWriter fw = new FileWriter(f);
 		fw.write(sb.toString());
 		fw.close();
+
+		getRepository().getFS().setExecute(f, fh.getNewMode() == FileMode.EXECUTABLE_FILE);
 	}
 
 	private static boolean isChanged(List<String> ol, List<String> nl) {