Merge "Prepare 4.3.1-SNAPSHOT versions"

11 files changed, 150 insertions, 58 deletions

diff --git a/org.eclipse.jgit/META-INF/MANIFEST.MF b/org.eclipse.jgit/META-INF/MANIFEST.MF
index 3e155a7d3e..1832ed3a37 100644
--- a/org.eclipse.jgit/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit/META-INF/MANIFEST.MF
@@ -2,12 +2,12 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %plugin_name
 Bundle-SymbolicName: org.eclipse.jgit
-Bundle-Version: 4.3.0.qualifier
+Bundle-Version: 4.3.1.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
 Bundle-ActivationPolicy: lazy
-Export-Package: org.eclipse.jgit.annotations;version="4.3.0",
- org.eclipse.jgit.api;version="4.3.0";
+Export-Package: org.eclipse.jgit.annotations;version="4.3.1",
+ org.eclipse.jgit.api;version="4.3.1";
   uses:="org.eclipse.jgit.revwalk,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.diff,
@@ -21,47 +21,47 @@ Export-Package: org.eclipse.jgit.annotations;version="4.3.0",
    org.eclipse.jgit.submodule,
    org.eclipse.jgit.transport,
    org.eclipse.jgit.merge",
- org.eclipse.jgit.api.errors;version="4.3.0";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.errors",
- org.eclipse.jgit.attributes;version="4.3.0",
- org.eclipse.jgit.blame;version="4.3.0";
+ org.eclipse.jgit.api.errors;version="4.3.1";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.errors",
+ org.eclipse.jgit.attributes;version="4.3.1",
+ org.eclipse.jgit.blame;version="4.3.1";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.revwalk,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.diff",
- org.eclipse.jgit.diff;version="4.3.0";
+ org.eclipse.jgit.diff;version="4.3.1";
   uses:="org.eclipse.jgit.patch,
    org.eclipse.jgit.lib,
    org.eclipse.jgit.treewalk,
    org.eclipse.jgit.revwalk,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.util",
- org.eclipse.jgit.dircache;version="4.3.0";
+ org.eclipse.jgit.dircache;version="4.3.1";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.treewalk,
    org.eclipse.jgit.util,
    org.eclipse.jgit.events,
    org.eclipse.jgit.attributes",
- org.eclipse.jgit.errors;version="4.3.0";
+ org.eclipse.jgit.errors;version="4.3.1";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.internal.storage.pack,
    org.eclipse.jgit.transport,
    org.eclipse.jgit.dircache",
- org.eclipse.jgit.events;version="4.3.0";uses:="org.eclipse.jgit.lib",
- org.eclipse.jgit.fnmatch;version="4.3.0",
- org.eclipse.jgit.gitrepo;version="4.3.0";
+ org.eclipse.jgit.events;version="4.3.1";uses:="org.eclipse.jgit.lib",
+ org.eclipse.jgit.fnmatch;version="4.3.1",
+ org.eclipse.jgit.gitrepo;version="4.3.1";
   uses:="org.eclipse.jgit.api,
    org.eclipse.jgit.lib,
    org.eclipse.jgit.revwalk,
    org.xml.sax.helpers,
    org.xml.sax",
- org.eclipse.jgit.gitrepo.internal;version="4.3.0";x-internal:=true,
- org.eclipse.jgit.hooks;version="4.3.0";uses:="org.eclipse.jgit.lib",
- org.eclipse.jgit.ignore;version="4.3.0",
- org.eclipse.jgit.ignore.internal;version="4.3.0";x-friends:="org.eclipse.jgit.test",
- org.eclipse.jgit.internal;version="4.3.0";x-friends:="org.eclipse.jgit.test,org.eclipse.jgit.http.test",
- org.eclipse.jgit.internal.ketch;version="4.3.0";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
- org.eclipse.jgit.internal.storage.dfs;version="4.3.0";x-friends:="org.eclipse.jgit.test,org.eclipse.jgit.http.server",
- org.eclipse.jgit.internal.storage.file;version="4.3.0";
+ org.eclipse.jgit.gitrepo.internal;version="4.3.1";x-internal:=true,
+ org.eclipse.jgit.hooks;version="4.3.1";uses:="org.eclipse.jgit.lib",
+ org.eclipse.jgit.ignore;version="4.3.1",
+ org.eclipse.jgit.ignore.internal;version="4.3.1";x-friends:="org.eclipse.jgit.test",
+ org.eclipse.jgit.internal;version="4.3.1";x-friends:="org.eclipse.jgit.test,org.eclipse.jgit.http.test",
+ org.eclipse.jgit.internal.ketch;version="4.3.1";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
+ org.eclipse.jgit.internal.storage.dfs;version="4.3.1";x-friends:="org.eclipse.jgit.test,org.eclipse.jgit.http.server",
+ org.eclipse.jgit.internal.storage.file;version="4.3.1";
   x-friends:="org.eclipse.jgit.test,
    org.eclipse.jgit.junit,
    org.eclipse.jgit.junit.http,
@@ -69,9 +69,9 @@ Export-Package: org.eclipse.jgit.annotations;version="4.3.0",
    org.eclipse.jgit.lfs.server,
    org.eclipse.jgit.pgm,
    org.eclipse.jgit.pgm.test",
- org.eclipse.jgit.internal.storage.pack;version="4.3.0";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
- org.eclipse.jgit.internal.storage.reftree;version="4.3.0";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
- org.eclipse.jgit.lib;version="4.3.0";
+ org.eclipse.jgit.internal.storage.pack;version="4.3.1";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
+ org.eclipse.jgit.internal.storage.reftree;version="4.3.1";x-friends:="org.eclipse.jgit.junit,org.eclipse.jgit.test,org.eclipse.jgit.pgm",
+ org.eclipse.jgit.lib;version="4.3.1";
   uses:="org.eclipse.jgit.revwalk,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.util,
@@ -81,32 +81,32 @@ Export-Package: org.eclipse.jgit.annotations;version="4.3.0",
    org.eclipse.jgit.treewalk,
    org.eclipse.jgit.transport,
    org.eclipse.jgit.submodule",
- org.eclipse.jgit.merge;version="4.3.0";
+ org.eclipse.jgit.merge;version="4.3.1";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.treewalk,
    org.eclipse.jgit.revwalk,
    org.eclipse.jgit.diff,
    org.eclipse.jgit.dircache,
    org.eclipse.jgit.api",
- org.eclipse.jgit.nls;version="4.3.0",
- org.eclipse.jgit.notes;version="4.3.0";
+ org.eclipse.jgit.nls;version="4.3.1",
+ org.eclipse.jgit.notes;version="4.3.1";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.treewalk,
    org.eclipse.jgit.revwalk,
    org.eclipse.jgit.merge",
- org.eclipse.jgit.patch;version="4.3.0";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.diff",
- org.eclipse.jgit.revplot;version="4.3.0";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.revwalk",
- org.eclipse.jgit.revwalk;version="4.3.0";
+ org.eclipse.jgit.patch;version="4.3.1";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.diff",
+ org.eclipse.jgit.revplot;version="4.3.1";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.revwalk",
+ org.eclipse.jgit.revwalk;version="4.3.1";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.treewalk,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.diff,
    org.eclipse.jgit.revwalk.filter",
- org.eclipse.jgit.revwalk.filter;version="4.3.0";uses:="org.eclipse.jgit.revwalk,org.eclipse.jgit.lib,org.eclipse.jgit.util",
- org.eclipse.jgit.storage.file;version="4.3.0";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.util",
- org.eclipse.jgit.storage.pack;version="4.3.0";uses:="org.eclipse.jgit.lib",
- org.eclipse.jgit.submodule;version="4.3.0";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.treewalk.filter,org.eclipse.jgit.treewalk",
- org.eclipse.jgit.transport;version="4.3.0";
+ org.eclipse.jgit.revwalk.filter;version="4.3.1";uses:="org.eclipse.jgit.revwalk,org.eclipse.jgit.lib,org.eclipse.jgit.util",
+ org.eclipse.jgit.storage.file;version="4.3.1";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.util",
+ org.eclipse.jgit.storage.pack;version="4.3.1";uses:="org.eclipse.jgit.lib",
+ org.eclipse.jgit.submodule;version="4.3.1";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.treewalk.filter,org.eclipse.jgit.treewalk",
+ org.eclipse.jgit.transport;version="4.3.1";
   uses:="org.eclipse.jgit.transport.resolver,
    org.eclipse.jgit.revwalk,
    org.eclipse.jgit.internal.storage.pack,
@@ -118,22 +118,22 @@ Export-Package: org.eclipse.jgit.annotations;version="4.3.0",
    org.eclipse.jgit.transport.http,
    org.eclipse.jgit.errors,
    org.eclipse.jgit.storage.pack",
- org.eclipse.jgit.transport.http;version="4.3.0";uses:="javax.net.ssl",
- org.eclipse.jgit.transport.resolver;version="4.3.0";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.transport",
- org.eclipse.jgit.treewalk;version="4.3.0";
+ org.eclipse.jgit.transport.http;version="4.3.1";uses:="javax.net.ssl",
+ org.eclipse.jgit.transport.resolver;version="4.3.1";uses:="org.eclipse.jgit.lib,org.eclipse.jgit.transport",
+ org.eclipse.jgit.treewalk;version="4.3.1";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.revwalk,
    org.eclipse.jgit.attributes,
    org.eclipse.jgit.treewalk.filter,
    org.eclipse.jgit.util,
    org.eclipse.jgit.dircache",
- org.eclipse.jgit.treewalk.filter;version="4.3.0";uses:="org.eclipse.jgit.treewalk",
- org.eclipse.jgit.util;version="4.3.0";
+ org.eclipse.jgit.treewalk.filter;version="4.3.1";uses:="org.eclipse.jgit.treewalk",
+ org.eclipse.jgit.util;version="4.3.1";
   uses:="org.eclipse.jgit.lib,
    org.eclipse.jgit.transport.http,
    org.eclipse.jgit.storage.file,
    org.ietf.jgss",
- org.eclipse.jgit.util.io;version="4.3.0"
+ org.eclipse.jgit.util.io;version="4.3.1"
 Bundle-RequiredExecutionEnvironment: JavaSE-1.7
 Require-Bundle: com.jcraft.jsch;bundle-version="[0.1.37,0.2.0)"
 Import-Package: com.googlecode.javaewah;version="[0.7.9,0.8.0)",
diff --git a/org.eclipse.jgit/META-INF/SOURCE-MANIFEST.MF b/org.eclipse.jgit/META-INF/SOURCE-MANIFEST.MF
index 6cdf122152..b95d013113 100644
--- a/org.eclipse.jgit/META-INF/SOURCE-MANIFEST.MF
+++ b/org.eclipse.jgit/META-INF/SOURCE-MANIFEST.MF
@@ -3,5 +3,5 @@ Bundle-ManifestVersion: 2
 Bundle-Name: org.eclipse.jgit - Sources
 Bundle-SymbolicName: org.eclipse.jgit.source
 Bundle-Vendor: Eclipse.org - JGit
-Bundle-Version: 4.3.0.qualifier
-Eclipse-SourceBundle: org.eclipse.jgit;version="4.3.0.qualifier";roots="."
+Bundle-Version: 4.3.1.qualifier
+Eclipse-SourceBundle: org.eclipse.jgit;version="4.3.1.qualifier";roots="."
diff --git a/org.eclipse.jgit/pom.xml b/org.eclipse.jgit/pom.xml
index a65ec96073..eac3738ab6 100644
--- a/org.eclipse.jgit/pom.xml
+++ b/org.eclipse.jgit/pom.xml
@@ -53,7 +53,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>org.eclipse.jgit-parent</artifactId>
-    <version>4.3.0-SNAPSHOT</version>
+    <version>4.3.1-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit</artifactId>
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java
index 3b94f16f1a..1f37833a41 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java
@@ -45,6 +45,7 @@ package org.eclipse.jgit.api;
 
 import static org.eclipse.jgit.lib.Constants.OBJ_BLOB;
 import static org.eclipse.jgit.lib.FileMode.GITLINK;
+import static org.eclipse.jgit.lib.FileMode.TYPE_GITLINK;
 import static org.eclipse.jgit.lib.FileMode.TYPE_TREE;
 
 import java.io.IOException;
@@ -201,7 +202,10 @@ public class AddCommand extends GitCommand<DirCache> {
 					continue;
 				}
 
-				if (f.getEntryRawMode() == TYPE_TREE) {
+				if ((f.getEntryRawMode() == TYPE_TREE
+						&& f.getIndexFileMode(c) != FileMode.GITLINK) ||
+						(f.getEntryRawMode() == TYPE_GITLINK
+								&& f.getIndexFileMode(c) == FileMode.TREE)) {
 					// Index entry exists and is symlink, gitlink or file,
 					// otherwise the tree would have been entered above.
 					// Replace the index entry by diving into tree of files.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java
index c37c317c51..6c80289452 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java
@@ -430,6 +430,8 @@ public class CheckoutCommand extends GitCommand<Ref> {
 				continue;
 
 			final EolStreamType eolStreamType = treeWalk.getEolStreamType();
+			final String filterCommand = treeWalk
+					.getFilterCommand(Constants.ATTR_FILTER_TYPE_SMUDGE);
 			editor.add(new PathEdit(path) {
 				public void apply(DirCacheEntry ent) {
 					int stage = ent.getStage();
@@ -437,15 +439,15 @@ public class CheckoutCommand extends GitCommand<Ref> {
 						if (checkoutStage != null) {
 							if (stage == checkoutStage.number)
 								checkoutPath(ent, r, new CheckoutMetadata(
-										eolStreamType, null));
+										eolStreamType, filterCommand));
 						} else {
 							UnmergedPathException e = new UnmergedPathException(
 									ent);
 							throw new JGitInternalException(e.getMessage(), e);
 						}
 					} else {
-						checkoutPath(ent, r,
-								new CheckoutMetadata(eolStreamType, null));
+						checkoutPath(ent, r, new CheckoutMetadata(eolStreamType,
+								filterCommand));
 					}
 				}
 			});
@@ -464,12 +466,14 @@ public class CheckoutCommand extends GitCommand<Ref> {
 			final ObjectId blobId = treeWalk.getObjectId(0);
 			final FileMode mode = treeWalk.getFileMode(0);
 			final EolStreamType eolStreamType = treeWalk.getEolStreamType();
+			final String filterCommand = treeWalk
+					.getFilterCommand(Constants.ATTR_FILTER_TYPE_SMUDGE);
 			editor.add(new PathEdit(treeWalk.getPathString()) {
 				public void apply(DirCacheEntry ent) {
 					ent.setObjectId(blobId);
 					ent.setFileMode(mode);
 					checkoutPath(ent, r,
-							new CheckoutMetadata(eolStreamType, null));
+							new CheckoutMetadata(eolStreamType, filterCommand));
 				}
 			});
 		}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java
index 3233eba008..9e3e0b78fd 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java
@@ -235,6 +235,12 @@ public class ConfigConstants {
 	 */
 	public static final String CONFIG_KEY_HIDEDOTFILES = "hidedotfiles";
 
+	/**
+	 * The "dirnogitlinks" key
+	 * @since 4.3
+	 */
+	public static final String CONFIG_KEY_DIRNOGITLINKS = "dirNoGitLinks";
+
 	/** The "precomposeunicode" key */
 	public static final String CONFIG_KEY_PRECOMPOSEUNICODE = "precomposeunicode";
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/AbstractTreeIterator.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/AbstractTreeIterator.java
index dc835e4f36..07fc829db4 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/AbstractTreeIterator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/AbstractTreeIterator.java
@@ -729,4 +729,13 @@ public abstract class AbstractTreeIterator {
 	public String toString() {
 		return getClass().getSimpleName() + "[" + getEntryPathString() + "]"; //$NON-NLS-1$
 	}
+
+	/**
+	 * @return whether or not this Iterator is iterating through the Work Tree
+	 *
+	 * @since 4.3
+	 */
+	public boolean isWorkTree() {
+		return false;
+	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/FileTreeIterator.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/FileTreeIterator.java
index eb4f1a87d0..db81e1af9b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/FileTreeIterator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/FileTreeIterator.java
@@ -94,7 +94,10 @@ public class FileTreeIterator extends WorkingTreeIterator {
 	 *            the repository whose working tree will be scanned.
 	 */
 	public FileTreeIterator(Repository repo) {
-		this(repo, DefaultFileModeStrategy.INSTANCE);
+		this(repo,
+				repo.getConfig().get(WorkingTreeOptions.KEY).isDirNoGitLinks() ?
+						NoGitlinksStrategy.INSTANCE :
+						DefaultFileModeStrategy.INSTANCE);
 	}
 
 	/**
@@ -291,6 +294,35 @@ public class FileTreeIterator extends WorkingTreeIterator {
 		}
 	}
 
+	/**
+	 * A FileModeStrategy that implements native git's DIR_NO_GITLINKS
+	 * behavior. This is the same as the default FileModeStrategy, except
+	 * all directories will be treated as directories regardless of whether
+	 * or not they contain a .git directory or file.
+	 *
+	 * @since 4.3
+	 */
+	static public class NoGitlinksStrategy implements FileModeStrategy {
+
+		/**
+		 * a singleton instance of the default FileModeStrategy
+		 */
+		public final static NoGitlinksStrategy INSTANCE = new NoGitlinksStrategy();
+
+		@Override
+		public FileMode getMode(File f, FS.Attributes attributes) {
+			if (attributes.isSymbolicLink()) {
+				return FileMode.SYMLINK;
+			} else if (attributes.isDirectory()) {
+				return FileMode.TREE;
+			} else if (attributes.isExecutable()) {
+				return FileMode.EXECUTABLE_FILE;
+			} else {
+				return FileMode.REGULAR_FILE;
+			}
+		}
+	}
+
 
 	/**
 	 * Wrapper for a standard Java IO file
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/TreeWalk.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/TreeWalk.java
index aecbac11ea..501d676735 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/TreeWalk.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/TreeWalk.java
@@ -1187,7 +1187,12 @@ public class TreeWalk implements AutoCloseable, AttributesProvider {
 		for (int i = 0; i < trees.length; i++) {
 			final AbstractTreeIterator t = trees[i];
 			final AbstractTreeIterator n;
-			if (t.matches == ch && !t.eof() && FileMode.TREE.equals(t.mode))
+			// If we find a GITLINK when attempting to enter a subtree, then the
+			// GITLINK must exist as a TREE in the index, meaning the working tree
+			// entry should be treated as a TREE
+			if (t.matches == ch && !t.eof() &&
+					(FileMode.TREE.equals(t.mode)
+							|| (FileMode.GITLINK.equals(t.mode) && t.isWorkTree())))
 				n = t.createSubtreeIterator(reader, idBuffer);
 			else
 				n = t.createEmptyTreeIterator();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java
index ca8f9aa373..39176c621e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java
@@ -264,7 +264,7 @@ public abstract class WorkingTreeIterator extends AbstractTreeIterator {
 			// the cached index information for the path.
 			//
 			DirCacheIterator i = state.walk.getTree(state.dirCacheTree,
-					DirCacheIterator.class);
+							DirCacheIterator.class);
 			if (i != null) {
 				DirCacheEntry ent = i.getDirCacheEntry();
 				if (ent != null && compareMetadata(ent) == MetadataDiff.EQUAL) {
@@ -289,6 +289,11 @@ public abstract class WorkingTreeIterator extends AbstractTreeIterator {
 		return zeroid;
 	}
 
+	@Override
+	public boolean isWorkTree() {
+		return true;
+	}
+
 	/**
 	 * Get submodule id for given entry.
 	 *
@@ -916,17 +921,31 @@ public abstract class WorkingTreeIterator extends AbstractTreeIterator {
 	 */
 	public FileMode getIndexFileMode(final DirCacheIterator indexIter) {
 		final FileMode wtMode = getEntryFileMode();
-		if (indexIter == null)
-			return wtMode;
-		if (getOptions().isFileMode())
+		if (indexIter == null) {
 			return wtMode;
+		}
 		final FileMode iMode = indexIter.getEntryFileMode();
-		if (FileMode.REGULAR_FILE == wtMode
-				&& FileMode.EXECUTABLE_FILE == iMode)
+		if (getOptions().isFileMode() && iMode != FileMode.GITLINK && iMode != FileMode.TREE) {
+			return wtMode;
+		}
+		if (!getOptions().isFileMode()) {
+			if (FileMode.REGULAR_FILE == wtMode
+					&& FileMode.EXECUTABLE_FILE == iMode) {
+				return iMode;
+			}
+			if (FileMode.EXECUTABLE_FILE == wtMode
+					&& FileMode.REGULAR_FILE == iMode) {
+				return iMode;
+			}
+		}
+		if (FileMode.GITLINK == iMode
+				&& FileMode.TREE == wtMode) {
 			return iMode;
-		if (FileMode.EXECUTABLE_FILE == wtMode
-				&& FileMode.REGULAR_FILE == iMode)
+		}
+		if (FileMode.TREE == iMode
+				&& FileMode.GITLINK == wtMode) {
 			return iMode;
+		}
 		return wtMode;
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeOptions.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeOptions.java
index a8990b1e95..dea07c1973 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeOptions.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeOptions.java
@@ -73,6 +73,8 @@ public class WorkingTreeOptions {
 
 	private final HideDotFiles hideDotFiles;
 
+	private final boolean dirNoGitLinks;
+
 	private WorkingTreeOptions(final Config rc) {
 		fileMode = rc.getBoolean(ConfigConstants.CONFIG_CORE_SECTION,
 				ConfigConstants.CONFIG_KEY_FILEMODE, true);
@@ -87,6 +89,9 @@ public class WorkingTreeOptions {
 		hideDotFiles = rc.getEnum(ConfigConstants.CONFIG_CORE_SECTION, null,
 				ConfigConstants.CONFIG_KEY_HIDEDOTFILES,
 				HideDotFiles.DOTGITONLY);
+		dirNoGitLinks = rc.getBoolean(ConfigConstants.CONFIG_CORE_SECTION, null,
+				ConfigConstants.CONFIG_KEY_DIRNOGITLINKS,
+				false);
 	}
 
 	/** @return true if the execute bit on working files should be trusted. */
@@ -131,4 +136,12 @@ public class WorkingTreeOptions {
 	public HideDotFiles getHideDotFiles() {
 		return hideDotFiles;
 	}
+
+	/**
+	 * @return whether or not we treat nested repos as directories.
+	 * 		   If true, folders containing .git entries will not be
+	 * 		   treated as gitlinks.
+	 * @since 4.3
+	 */
+	public boolean isDirNoGitLinks() { return dirNoGitLinks; }
 }