Make sure not to overwrite untracked not-ignored files

When DirCacheCheckout was checking out it was silently
overwriting untracked files. This is only ok if the
files are also ignored. Untracked and not ignored files
should not be overwritten. This fix adds checks for
this situation.
Because this change in the behaviour also broke tests
which expected that a checkout will overwrite untracked
files (PullCommandTest) these tests have to be modified
also.

Bug: 333093
Change-Id: I26806d2108ceb64c51abaa877e11b584bf527fc9
Signed-off-by: Christian Halstrick <christian.halstrick@sap.com>
Signed-off-by: Chris Aniszczyk <caniszczyk@gmail.com>

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

@@ -56,10 +56,8 @@
 import org.eclipse.jgit.api.CreateBranchCommand.SetupUpstreamMode;
 import org.eclipse.jgit.api.MergeResult.MergeStatus;
 import org.eclipse.jgit.lib.Constants;
-import org.eclipse.jgit.lib.RefUpdate;
 import org.eclipse.jgit.lib.RepositoryTestCase;
 import org.eclipse.jgit.lib.StoredConfig;
-import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.storage.file.FileRepository;
 import org.eclipse.jgit.transport.RefSpec;
 import org.eclipse.jgit.transport.RemoteConfig;
@@ -190,13 +188,7 @@ public void setUp() throws Exception {
 		writeToFile(sourceFile, "Hello world");
 		// and commit it
 		source.add().addFilepattern("SomeFile.txt").call();
-		RevCommit commit = source.commit().setMessage(
-				"Initial commit for source").call();
-
-		// point the master branch to the new commit
-		RefUpdate upd = dbTarget.updateRef("refs/heads/master");
-		upd.setNewObjectId(commit.getId());
-		upd.update();
+		source.commit().setMessage("Initial commit for source").call();
 
 		// configure the target repo to connect to the source via "origin"
 		StoredConfig targetConfig = dbTarget.getConfig();
@@ -214,9 +206,9 @@ public void setUp() throws Exception {
 		targetConfig.save();
 
 		targetFile = new File(dbTarget.getWorkTree(), "SomeFile.txt");
-		writeToFile(targetFile, "Hello world");
 		// make sure we have the same content
 		target.pull().call();
+		assertFileContentsEqual(targetFile, "Hello world");
 	}
 
 	private void writeToFile(File actFile, String string) throws IOException {

org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ReadTreeTest.java

@@ -571,6 +571,34 @@ public void testUntrackedConflicts() throws IOException {
 		writeTrashFile("foo", "foo");
 		go();
 
+		// test that we don't overwrite untracked files when there is a HEAD
+		recursiveDelete(new File(trash, "foo"));
+		setupCase(mk("other"), mkmap("other", "other", "foo", "foo"),
+				mk("other"));
+		writeTrashFile("foo", "bar");
+		try {
+			checkout();
+			fail("didn't get the expected exception");
+		} catch (CheckoutConflictException e) {
+			assertConflict("foo");
+			assertWorkDir(mkmap("foo", "bar", "other", "other"));
+			assertIndex(mk("other"));
+		}
+
+		// test that we don't overwrite untracked files when there is no HEAD
+		recursiveDelete(new File(trash, "other"));
+		recursiveDelete(new File(trash, "foo"));
+		setupCase(null, mk("foo"), null);
+		writeTrashFile("foo", "bar");
+		try {
+			checkout();
+			fail("didn't get the expected exception");
+		} catch (CheckoutConflictException e) {
+			assertConflict("foo");
+			assertWorkDir(mkmap("foo", "bar"));
+			assertIndex(mkmap());
+		}
+
 		// TODO: Why should we expect conflicts here?
 		// H and M are emtpy and according to rule #5 of
 		// the carry-over rules a dirty index is no reason
@@ -581,6 +609,7 @@ public void testUntrackedConflicts() throws IOException {
 		// assertConflict("foo");
 
 		recursiveDelete(new File(trash, "foo"));
+		recursiveDelete(new File(trash, "other"));
 		setupCase(null, mk("foo"), null);
 		writeTrashFile("foo/bar/baz", "");
 		writeTrashFile("foo/blahblah", "");

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

@@ -300,15 +300,21 @@ public void prescanOneTree()
 	 * @param m the tree to merge
 	 * @param i the index
 	 * @param f the working tree
+	 * @throws IOException
 	 */
 	void processEntry(CanonicalTreeParser m, DirCacheBuildIterator i,
-			WorkingTreeIterator f) {
+			WorkingTreeIterator f) throws IOException {
 		if (m != null) {
 			// There is an entry in the merge commit. Means: we want to update
 			// what's currently in the index and working-tree to that one
 			if (i == null) {
 				// The index entry is missing
-				update(m.getEntryPathString(), m.getEntryObjectId(),
+				if (f != null && !FileMode.TREE.equals(f.getEntryFileMode())
+						&& !f.isEntryIgnored()) {
+					// don't overwrite an untracked and not ignored file
+					conflicts.add(walk.getPathString());
+				} else
+					update(m.getEntryPathString(), m.getEntryObjectId(),
 						m.getEntryFileMode());
 			} else if (f == null || !m.idEqual(i)) {
 				// The working tree file is missing or the merge content differs
@@ -344,6 +350,13 @@ void processEntry(CanonicalTreeParser m, DirCacheBuildIterator i,
 						// conflicts set
 						remove(i.getEntryPathString());
 						conflicts.remove(i.getEntryPathString());
+					} else {
+						// We are about to remove an untracked file. Check that
+						// it is ignored - otherwise that's an conflict
+						if (!f.isEntryIgnored())
+							conflicts.add(walk.getPathString());
+						else
+							remove(f.getEntryPathString());
 					}
 				}
 			} else {
@@ -626,6 +639,16 @@ void processEntry(AbstractTreeIterator h, AbstractTreeIterator m,
 		}
 
 		if (i == null) {
+			// make sure not to overwrite untracked files
+			if (f != null) {
+				// a dirty worktree: the index is empty but we have a
+				// workingtree-file
+				if (mId == null || !mId.equals(f.getEntryObjectId())) {
+					conflict(name, null, h, m);
+					return;
+				}
+			}
+
 			/**
 			 * <pre>
 			 * 		    I (index)                H        M        Result