Cleanup code and Eclipse compile errors in new gitrepo API

Commit d3348e introduced few errors in Eclipse.

This commit cleans up the new API:
 - fixes API error in RepoCommand after moving IncludedFileReader type
 - fixes unused imports in RepoCommand & RepoCommandTest
 - fix javadoc errors in ManifestParser & RepoProject
 - makes three (implicitly final) fields in ManifestParser final.

Change-Id: I4185f451d97039d155391f62815bb9d3afe39fa6
Signed-off-by: Andrey Loskutov <loskutov@gmx.de>

org.eclipse.jgit.test/tst/org/eclipse/jgit/gitrepo/RepoCommandTest.java

@@ -49,8 +49,6 @@ import static org.junit.Assert.assertTrue;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileReader;
-import java.util.HashSet;
-import java.util.Set;
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.junit.JGitTestUtil;

org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/ManifestParser.java

@@ -83,11 +83,12 @@ public class ManifestParser extends DefaultHandler {
 	private final Map<String, String> remotes;
 	private final Set<String> plusGroups;
 	private final Set<String> minusGroups;
-	private List<RepoProject> projects;
-	private List<RepoProject> filteredProjects;
+	private final List<RepoProject> projects;
+	private final List<RepoProject> filteredProjects;
+	private final IncludedFileReader includedReader;
+
 	private String defaultRemote;
 	private String defaultRevision;
-	private IncludedFileReader includedReader;
 	private int xmlInRead;
 	private RepoProject currentProject;
 
@@ -154,6 +155,7 @@ public class ManifestParser extends DefaultHandler {
 	 * Read the xml file.
 	 *
 	 * @param inputStream
+	 * @throws IOException
 	 */
 	public void read(InputStream inputStream) throws IOException {
 		xmlInRead++;
@@ -295,6 +297,8 @@ public class ManifestParser extends DefaultHandler {
 
 	/**
 	 * Getter for projects.
+	 *
+	 * @return projects list reference, never null
 	 */
 	public List<RepoProject> getProjects() {
 		return projects;
@@ -302,6 +306,8 @@ public class ManifestParser extends DefaultHandler {
 
 	/**
 	 * Getter for filterdProjects.
+	 *
+	 * @return filtered projects list reference, never null
 	 */
 	public List<RepoProject> getFilteredProjects() {
 		return filteredProjects;

org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/RepoCommand.java

@@ -46,7 +46,6 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
-import java.net.URI;
 import java.text.MessageFormat;
 import java.util.ArrayList;
 import java.util.List;
@@ -340,7 +339,7 @@ public class RepoCommand extends GitCommand<RevCommit> {
 	 *
 	 * @param reader
 	 * @return this command
-	 * @since 3.5
+	 * @since 4.0
 	 */
 	public RepoCommand setIncludedFileReader(IncludedFileReader reader) {
 		this.includedReader = reader;

org.eclipse.jgit/src/org/eclipse/jgit/gitrepo/RepoProject.java

@@ -96,6 +96,8 @@ public class RepoProject implements Comparable<RepoProject> {
 
 		/**
 		 * Do the copy file action.
+		 *
+		 * @throws IOException
 		 */
 		public void copy() throws IOException {
 			File srcFile = new File(repo.getWorkTree(),
@@ -186,7 +188,11 @@ public class RepoProject implements Comparable<RepoProject> {
 	}
 
 	/**
-	 * Check if this sub repo is the ancestor of another sub repo.
+	 * Check if this sub repo is the ancestor of given sub repo.
+	 *
+	 * @param that
+	 *            non null
+	 * @return true if this sub repo is the ancestor of given sub repo.
 	 */
 	public boolean isAncestorOf(RepoProject that) {
 		return that.getPathWithSlash().startsWith(this.getPathWithSlash());