Enable DirCacheEntry's copyMetaData to not copy stage info

When there is a conflict sometimes we did not set the stage of
the conflict entries properly for the STAGE_1 entry.

Change-Id: I1c28ff6251fdbc95f7c40fc3e401f1b41157a9f6

org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheEntryTest.java

@@ -51,6 +51,7 @@ import static org.junit.Assert.fail;
 
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.FileMode;
+import org.eclipse.jgit.lib.ObjectId;
 import org.junit.Test;
 
 public class DirCacheEntryTest {
@@ -164,4 +165,53 @@ public class DirCacheEntryTest {
 			assertEquals("Invalid mode 40000 for path a", err.getMessage());
 		}
 	}
+
+	@Test
+	public void testCopyMetaDataWithStage() {
+		copyMetaDataHelper(false);
+	}
+
+	@Test
+	public void testCopyMetaDataWithoutStage() {
+		copyMetaDataHelper(true);
+	}
+
+	private void copyMetaDataHelper(final boolean keepStage) {
+		DirCacheEntry e = new DirCacheEntry("some/path", DirCacheEntry.STAGE_2);
+		e.setAssumeValid(false);
+		e.setCreationTime(2L);
+		e.setFileMode(FileMode.EXECUTABLE_FILE);
+		e.setLastModified(3L);
+		e.setLength(100L);
+		e.setObjectId(ObjectId
+				.fromString("0123456789012345678901234567890123456789"));
+		e.setUpdateNeeded(true);
+
+		DirCacheEntry f = new DirCacheEntry("someother/path",
+				DirCacheEntry.STAGE_1);
+		f.setAssumeValid(true);
+		f.setCreationTime(10L);
+		f.setFileMode(FileMode.SYMLINK);
+		f.setLastModified(20L);
+		f.setLength(100000000L);
+		f.setObjectId(ObjectId
+				.fromString("1234567890123456789012345678901234567890"));
+		f.setUpdateNeeded(true);
+
+		e.copyMetaData(f, keepStage);
+		assertTrue(e.isAssumeValid());
+		assertEquals(10L, e.getCreationTime());
+		assertEquals(
+				ObjectId.fromString("1234567890123456789012345678901234567890"),
+				e.getObjectId());
+		assertEquals(FileMode.SYMLINK, e.getFileMode());
+		assertEquals(20L, e.getLastModified());
+		assertEquals(100000000L, e.getLength());
+		if (keepStage)
+			assertEquals(DirCacheEntry.STAGE_2, e.getStage());
+		else
+			assertEquals(DirCacheEntry.STAGE_1, e.getStage());
+		assertTrue(e.isUpdateNeeded());
+		assertEquals("some/path", e.getPathString());
+	}
 }

org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java

@@ -795,7 +795,7 @@ public class DirCacheCheckout {
 		DirCacheEntry entry;
 		if (e != null) {
 			entry = new DirCacheEntry(e.getPathString(), DirCacheEntry.STAGE_1);
-			entry.copyMetaData(e);
+			entry.copyMetaData(e, true);
 			builder.add(entry);
 		}
 

org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheEntry.java

@@ -641,10 +641,33 @@ public class DirCacheEntry {
 	 *            the entry to copy ObjectId and meta fields from.
 	 */
 	public void copyMetaData(final DirCacheEntry src) {
-		final int pLen = NB.decodeUInt16(info, infoOffset + P_FLAGS) & NAME_MASK;
+		copyMetaData(src, false);
+	}
+
+	/**
+	 * Copy the ObjectId and other meta fields from an existing entry.
+	 * <p>
+	 * This method copies everything except the path and possibly stage from one
+	 * entry to another, supporting renaming.
+	 *
+	 * @param src
+	 *            the entry to copy ObjectId and meta fields from.
+	 * @param keepStage
+	 *            if true, the stage attribute will not be copied
+	 */
+	void copyMetaData(final DirCacheEntry src, boolean keepStage) {
+		int origflags = NB.decodeUInt16(info, infoOffset + P_FLAGS);
+		int newflags = NB.decodeUInt16(src.info, src.infoOffset + P_FLAGS);
 		System.arraycopy(src.info, src.infoOffset, info, infoOffset, INFO_LEN);
-		NB.encodeInt16(info, infoOffset + P_FLAGS, pLen
-				| NB.decodeUInt16(info, infoOffset + P_FLAGS) & ~NAME_MASK);
+		final int pLen = origflags & NAME_MASK;
+		final int SHIFTED_STAGE_MASK = 0x3 << 12;
+		final int pStageShifted;
+		if (keepStage)
+			pStageShifted = origflags & SHIFTED_STAGE_MASK;
+		else
+			pStageShifted = newflags & SHIFTED_STAGE_MASK;
+		NB.encodeInt16(info, infoOffset + P_FLAGS, pStageShifted | pLen
+				| (newflags & ~NAME_MASK & ~SHIFTED_STAGE_MASK));
 	}
 
 	/**