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 67fb342fe..40102447a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java
@@ -43,6 +43,9 @@
  */
 package org.eclipse.jgit.api;
 
+import static org.eclipse.jgit.lib.Constants.OBJ_BLOB;
+import static org.eclipse.jgit.lib.FileMode.GITLINK;
+
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.Collection;
@@ -58,8 +61,8 @@ import org.eclipse.jgit.dircache.DirCacheBuilder;
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.dircache.DirCacheIterator;
 import org.eclipse.jgit.internal.JGitText;
-import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.FileMode;
+import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectInserter;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.treewalk.FileTreeIterator;
@@ -135,15 +138,12 @@ public class AddCommand extends GitCommand<DirCache> {
 			throw new NoFilepatternException(JGitText.get().atLeastOnePatternIsRequired);
 		checkCallable();
 		DirCache dc = null;
-		boolean addAll = false;
-		if (filepatterns.contains(".")) //$NON-NLS-1$
-			addAll = true;
+		boolean addAll = filepatterns.contains("."); //$NON-NLS-1$
 
 		try (ObjectInserter inserter = repo.newObjectInserter();
 				final TreeWalk tw = new TreeWalk(repo)) {
 			tw.setOperationType(OperationType.CHECKIN_OP);
 			dc = repo.lockDirCache();
-			DirCacheIterator c;
 
 			DirCacheBuilder builder = dc.builder();
 			tw.addTree(new DirCacheBuildIterator(builder));
@@ -158,55 +158,60 @@ public class AddCommand extends GitCommand<DirCache> {
 			String lastAddedFile = null;
 
 			while (tw.next()) {
-				String path = tw.getPathString();
-
+				DirCacheIterator c = tw.getTree(0, DirCacheIterator.class);
 				WorkingTreeIterator f = tw.getTree(1, WorkingTreeIterator.class);
-				if (tw.getTree(0, DirCacheIterator.class) == null &&
-						f != null && f.isEntryIgnored()) {
+				if (c == null && f != null && f.isEntryIgnored()) {
 					// file is not in index but is ignored, do nothing
+					continue;
+				} else if (c == null && update) {
+					// Only update of existing entries was requested.
+					continue;
 				}
-				// In case of an existing merge conflict the
-				// DirCacheBuildIterator iterates over all stages of
-				// this path, we however want to add only one
-				// new DirCacheEntry per path.
-				else if (!(path.equals(lastAddedFile))) {
-					if (!(update && tw.getTree(0, DirCacheIterator.class) == null)) {
-						c = tw.getTree(0, DirCacheIterator.class);
-						if (f != null) { // the file exists
-							long sz = f.getEntryLength();
-							DirCacheEntry entry = new DirCacheEntry(path);
-							if (c == null || c.getDirCacheEntry() == null
-									|| !c.getDirCacheEntry().isAssumeValid()) {
-								FileMode mode = f.getIndexFileMode(c);
-								entry.setFileMode(mode);
-
-								if (FileMode.GITLINK != mode) {
-									entry.setLength(sz);
-									entry.setLastModified(f
-											.getEntryLastModified());
-									long contentSize = f
-											.getEntryContentLength();
-									InputStream in = f.openEntryStream();
-									try {
-										entry.setObjectId(inserter.insert(
-												Constants.OBJ_BLOB, contentSize, in));
-									} finally {
-										in.close();
-									}
-								} else
-									entry.setObjectId(f.getEntryObjectId());
-								builder.add(entry);
-								lastAddedFile = path;
-							} else {
-								builder.add(c.getDirCacheEntry());
-							}
-
-						} else if (c != null
-								&& (!update || FileMode.GITLINK == c
-										.getEntryFileMode()))
-							builder.add(c.getDirCacheEntry());
+
+				String path = tw.getPathString();
+				if (path.equals(lastAddedFile)) {
+					// In case of an existing merge conflict the
+					// DirCacheBuildIterator iterates over all stages of
+					// this path, we however want to add only one
+					// new DirCacheEntry per path.
+					continue;
+				}
+
+				if (f == null) { // working tree file does not exist
+					if (c != null
+							&& (!update || GITLINK == c.getEntryFileMode())) {
+						builder.add(c.getDirCacheEntry());
+					}
+					continue;
+				}
+
+				if (c != null && c.getDirCacheEntry() != null
+						&& c.getDirCacheEntry().isAssumeValid()) {
+					// Index entry is marked assume valid. Even though
+					// the user specified the file to be added JGit does
+					// not consider the file for addition.
+					builder.add(c.getDirCacheEntry());
+					continue;
+				}
+
+				long sz = f.getEntryLength();
+				DirCacheEntry entry = new DirCacheEntry(path);
+				FileMode mode = f.getIndexFileMode(c);
+				entry.setFileMode(mode);
+
+				if (GITLINK != mode) {
+					entry.setLength(sz);
+					entry.setLastModified(f.getEntryLastModified());
+					long len = f.getEntryContentLength();
+					try (InputStream in = f.openEntryStream()) {
+						ObjectId id = inserter.insert(OBJ_BLOB, len, in);
+						entry.setObjectId(id);
 					}
+				} else {
+					entry.setObjectId(f.getEntryObjectId());
 				}
+				builder.add(entry);
+				lastAddedFile = path;
 			}
 			inserter.flush();
 			builder.commit();