[EGIT PATCH 00/10] JGit cleanups

@@ -112,15 +112,15 @@ public void close() {
 	}
 
 	class HttpObjectDB extends WalkRemoteObjectDatabase {
-		private final URL objectsUrl;
+		private final URL alternateObjectsUrl;
 
 		HttpObjectDB(final URL b) {
-			objectsUrl = b;
+			alternateObjectsUrl = b;
 		}
 
 		@Override
 		URIish getURI() {
-			return new URIish(objectsUrl);
+			return new URIish(alternateObjectsUrl);
 		}
 
 		@Override

@@ -143,7 +143,7 @@ URIish getURI() {
 		@Override
 		WalkRemoteObjectDatabase openAlternate(final String location)
 				throws IOException {
-			return new HttpObjectDB(new URL(objectsUrl, location));
+			return new HttpObjectDB(new URL(alternateObjectsUrl, location));
 		}
 
 		@Override

@@ -171,7 +171,7 @@ WalkRemoteObjectDatabase openAlternate(final String location)
 
 		@Override
 		FileStream open(final String path) throws IOException {
-			final URL base = objectsUrl;
+			final URL base = alternateObjectsUrl;
 			final URL u = new URL(base, path);
 			final Proxy proxy = HttpSupport.proxyFor(proxySelector, u);
 			final HttpURLConnection c;

@@ -201,10 +201,10 @@ FileStream open(final String path) throws IOException {
 				}
 			} catch (IOException err) {
 				try {
-					throw new TransportException(new URL(objectsUrl, INFO_REFS)
+					throw new TransportException(new URL(alternateObjectsUrl, INFO_REFS)
 							+ ": cannot read available refs", err);
 				} catch (MalformedURLException mue) {
-					throw new TransportException(objectsUrl + INFO_REFS
+					throw new TransportException(alternateObjectsUrl + INFO_REFS
 							+ ": cannot read available refs", err);
 				}
 			}

@@ -298,7 +298,7 @@ private void expandSingle(final RefSpec spec, final Set<Ref> matched)
 
 	private Collection<Ref> expandAutoFollowTags() throws TransportException {
 		final Collection<Ref> additionalTags = new ArrayList<Ref>();
-		final Map<String, Ref> have = transport.local.getAllRefs();
+		final Map<String, Ref> haveRefs = transport.local.getAllRefs();
 		for (final Ref r : conn.getRefs()) {
 			if (!isTag(r))
 				continue;

@@ -307,7 +307,7 @@ private void expandSingle(final RefSpec spec, final Set<Ref> matched)
 				continue;
 			}
 
-			final Ref local = have.get(r.getName());
+			final Ref local = haveRefs.get(r.getName());
 			if (local != null) {
 				if (!r.getObjectId().equals(local.getObjectId()))
 					wantTag(r);

@@ -321,11 +321,11 @@ private void expandSingle(final RefSpec spec, final Set<Ref> matched)
 	}
 
 	private void expandFetchTags() throws TransportException {
-		final Map<String, Ref> have = transport.local.getAllRefs();
+		final Map<String, Ref> haveRefs = transport.local.getAllRefs();
 		for (final Ref r : conn.getRefs()) {
 			if (!isTag(r))
 				continue;
-			final Ref local = have.get(r.getName());
+			final Ref local = haveRefs.get(r.getName());
 			if (local == null || !r.getObjectId().equals(local.getObjectId()))
 				wantTag(r);
 		}

@@ -1,4 +1,4 @@
-#Sun Feb 03 03:16:45 CET 2008
+#Sun Mar 15 19:46:39 CET 2009
 eclipse.preferences.version=1
 org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
 org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.5

@@ -36,10 +36,11 @@ org.eclipse.jdt.core.compiler.problem.methodWithConstructorName=error
 org.eclipse.jdt.core.compiler.problem.missingDeprecatedAnnotation=ignore
 org.eclipse.jdt.core.compiler.problem.missingJavadocComments=error
 org.eclipse.jdt.core.compiler.problem.missingJavadocCommentsOverriding=disabled
-org.eclipse.jdt.core.compiler.problem.missingJavadocCommentsVisibility=public
+org.eclipse.jdt.core.compiler.problem.missingJavadocCommentsVisibility=protected
+org.eclipse.jdt.core.compiler.problem.missingJavadocTagDescription=return_tag
 org.eclipse.jdt.core.compiler.problem.missingJavadocTags=error
 org.eclipse.jdt.core.compiler.problem.missingJavadocTagsOverriding=disabled
-org.eclipse.jdt.core.compiler.problem.missingJavadocTagsVisibility=private
+org.eclipse.jdt.core.compiler.problem.missingJavadocTagsVisibility=protected
 org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotation=ignore
 org.eclipse.jdt.core.compiler.problem.missingSerialVersion=warning
 org.eclipse.jdt.core.compiler.problem.noEffectAssignment=error

@@ -207,18 +207,23 @@ public Repository getRepository() {
 		return db;
 	}
 
-	protected ObjectId resolve(final String s) throws IOException {
+	ObjectId resolve(final String s) throws IOException {
 		final ObjectId r = db.resolve(s);
 		if (r == null)
 			throw die("Not a revision: " + s);
 		return r;
 	}
 
+	/**
+	 * @param why
+	 *            textual explanation
+	 * @return a runtime exception the caller is expected to throw
+	 */
 	protected static Die die(final String why) {
 		return new Die(why);
 	}
 
-	protected String abbreviateRef(String dst, boolean abbreviateRemote) {
+	String abbreviateRef(String dst, boolean abbreviateRemote) {
 		if (dst.startsWith(R_HEADS))
 			dst = dst.substring(R_HEADS.length());
 		else if (dst.startsWith(R_TAGS))

@@ -1,4 +1,4 @@
-#Sun Feb 03 03:16:45 CET 2008
+#Sun Mar 15 01:13:43 CET 2009
 eclipse.preferences.version=1
 org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
 org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.5

@@ -36,7 +36,8 @@ org.eclipse.jdt.core.compiler.problem.methodWithConstructorName=error
 org.eclipse.jdt.core.compiler.problem.missingDeprecatedAnnotation=ignore
 org.eclipse.jdt.core.compiler.problem.missingJavadocComments=error
 org.eclipse.jdt.core.compiler.problem.missingJavadocCommentsOverriding=disabled
-org.eclipse.jdt.core.compiler.problem.missingJavadocCommentsVisibility=public
+org.eclipse.jdt.core.compiler.problem.missingJavadocCommentsVisibility=protected
+org.eclipse.jdt.core.compiler.problem.missingJavadocTagDescription=return_tag
 org.eclipse.jdt.core.compiler.problem.missingJavadocTags=error
 org.eclipse.jdt.core.compiler.problem.missingJavadocTagsOverriding=disabled
 org.eclipse.jdt.core.compiler.problem.missingJavadocTagsVisibility=private

@@ -91,7 +91,7 @@ public DirCacheBuildIterator(final DirCacheBuilder dcb) {
 		builder = dcb;
 	}
 
-	protected DirCacheBuildIterator(final DirCacheBuildIterator p,
+	DirCacheBuildIterator(final DirCacheBuildIterator p,
 			final DirCacheTree dct) {
 		super(p, dct);
 		builder = p.builder;

@@ -105,7 +105,7 @@ public DirCacheIterator(final DirCache dc) {
 			parseEntry();
 	}
 
-	protected DirCacheIterator(final DirCacheIterator p, final DirCacheTree dct) {
+	DirCacheIterator(final DirCacheIterator p, final DirCacheTree dct) {
 		super(p, p.path, p.pathLen + 1);
 		cache = p.cache;
 		tree = dct;

@@ -238,7 +238,7 @@ private static final ObjectId fromHexString(final byte[] bs, int p) {
 		}
 	}
 
-	protected ObjectId(final int new_1, final int new_2, final int new_3,
+	ObjectId(final int new_1, final int new_2, final int new_3,
 			final int new_4, final int new_5) {
 		w1 = new_1;
 		w2 = new_2;

@@ -243,7 +243,7 @@ abstract long findCRC32(AnyObjectId objId) throws MissingObjectException,
 	 * 
 	 */
 	public static class MutableEntry {
-		protected final MutableObjectId idBuffer = new MutableObjectId();
+		final MutableObjectId idBuffer = new MutableObjectId();
 
 		long offset;
 

@@ -281,12 +281,12 @@ public MutableEntry cloneEntry() {
 			return r;
 		}
 
-		protected void ensureId() {
+		void ensureId() {
 			// Override in implementations.
 		}
 	}
 
-	protected abstract class EntriesIterator implements Iterator<MutableEntry> {
+	abstract class EntriesIterator implements Iterator<MutableEntry> {
 		protected final MutableEntry entry = initEntry();
 
 		protected long returnedNumber = 0;

@@ -931,7 +931,7 @@ boolean isDeltaRepresentation() {
 		 * @return true if object is already written; false otherwise.
 		 */
 		boolean isWritten() {
-			return offset != 0;
+			return getOffset() != 0;
 		}
 
 		PackedObjectLoader getReuseLoader() {

@@ -50,11 +50,11 @@
 
 	private File currentDirectory;
 
-	protected TreeVisitorWithCurrentDirectory(final File rootDirectory) {
+	TreeVisitorWithCurrentDirectory(final File rootDirectory) {
 		currentDirectory = rootDirectory;
 	}
 
-	protected File getCurrentDirectory() {
+	File getCurrentDirectory() {
 		return currentDirectory;
 	}
 

@@ -56,15 +56,15 @@
  * Three-way merges are no performed. See {@link #setFailOnConflict(boolean)}.
  */
 public class WorkDirCheckout {
-	protected Repository repo;
+	Repository repo;
 
-	protected File root;
+	File root;
 
-	protected GitIndex index;
+	GitIndex index;
 	
 	private boolean failOnConflict = true;
 
-	protected Tree merge;
+	Tree merge;
 
 	
 	/**

@@ -151,9 +151,9 @@ private void checkoutTwoTrees() throws FileNotFoundException, IOException {
 	ArrayList<String> conflicts  = new ArrayList<String>();
 	ArrayList<String> removed = new ArrayList<String>();
 
-	protected Tree head = null;
+	Tree head = null;
 
-	protected HashMap<String, ObjectId> updated = new HashMap<String, ObjectId>();
+	HashMap<String, ObjectId> updated = new HashMap<String, ObjectId>();
 	
 	private void checkoutOutIndexNoHead() throws IOException {
 		new IndexTreeWalker(index, merge, root, new AbstractIndexTreeVisitor() {

@@ -294,7 +294,7 @@ else if (file.isDirectory()) {
 		conflicts.removeAll(removed);
 	}
 
-	protected void processEntry(TreeEntry h, TreeEntry m, Entry i,
+	void processEntry(TreeEntry h, TreeEntry m, Entry i,
 			File file) throws IOException {
 				ObjectId iId = (i == null ? null : i.getObjectId());
 				ObjectId mId = (m == null ? null : m.getId());

@@ -77,7 +77,7 @@ public Merger newMerger(final Repository db) {
 		return new OneSide(db, treeIndex);
 	}
 
-	protected static class OneSide extends Merger {
+	static class OneSide extends Merger {
 		private final int treeIndex;
 
 		protected OneSide(final Repository local, final int index) {

@@ -68,9 +68,9 @@
 
 	private static final byte[] NEW_MODE = encodeASCII("new mode ");
 
-	protected static final byte[] DELETED_FILE_MODE = encodeASCII("deleted file mode ");
+	static final byte[] DELETED_FILE_MODE = encodeASCII("deleted file mode ");
 
-	protected static final byte[] NEW_FILE_MODE = encodeASCII("new file mode ");
+	static final byte[] NEW_FILE_MODE = encodeASCII("new file mode ");
 
 	private static final byte[] COPY_FROM = encodeASCII("copy from ");
 

@@ -88,7 +88,7 @@
 
 	private static final byte[] DISSIMILARITY_INDEX = encodeASCII("dissimilarity index ");
 
-	protected static final byte[] INDEX = encodeASCII("index ");
+	static final byte[] INDEX = encodeASCII("index ");
 
 	static final byte[] OLD_NAME = encodeASCII("--- ");
 

@@ -220,7 +220,7 @@ public String getScriptText(Charset oldCharset, Charset newCharset) {
 		return getScriptText(new Charset[] { oldCharset, newCharset });
 	}
 
-	protected String getScriptText(Charset[] charsetGuess) {
+	String getScriptText(Charset[] charsetGuess) {
 		if (getHunks().isEmpty()) {
 			// If we have no hunks then we can safely assume the entire
 			// patch is a binary style patch, or a meta-data only style

@@ -562,19 +562,19 @@ int parseGitHeaders(int ptr, final int end) {
 		return ptr;
 	}
 
-	protected void parseOldName(int ptr, final int eol) {
+	void parseOldName(int ptr, final int eol) {
 		oldName = p1(parseName(oldName, ptr + OLD_NAME.length, eol));
 		if (oldName == DEV_NULL)
 			changeType = ChangeType.ADD;
 	}
 
-	protected void parseNewName(int ptr, final int eol) {
+	void parseNewName(int ptr, final int eol) {
 		newName = p1(parseName(newName, ptr + NEW_NAME.length, eol));
 		if (newName == DEV_NULL)
 			changeType = ChangeType.DELETE;
 	}
 
-	protected void parseNewFileMode(int ptr, final int eol) {
+	void parseNewFileMode(int ptr, final int eol) {
 		oldMode = FileMode.MISSING;
 		newMode = parseFileMode(ptr + NEW_FILE_MODE.length, eol);
 		changeType = ChangeType.ADD;

@@ -633,7 +633,7 @@ private static String p1(final String r) {
 		return s > 0 ? r.substring(s + 1) : r;
 	}
 
-	protected FileMode parseFileMode(int ptr, final int end) {
+	FileMode parseFileMode(int ptr, final int end) {
 		int tmp = 0;
 		while (ptr < end - 1) {
 			tmp <<= 3;

@@ -642,7 +642,7 @@ protected FileMode parseFileMode(int ptr, final int end) {
 		return FileMode.fromBits(tmp);
 	}
 
-	protected void parseIndexLine(int ptr, final int end) {
+	void parseIndexLine(int ptr, final int end) {
 		// "index $asha1..$bsha1[ $mode]" where $asha1 and $bsha1
 		// can be unique abbreviations
 		//

@@ -307,7 +307,7 @@ void extractFileLines(final StringBuilder sb, final String[] text,
 		}
 	}
 
-	protected void copyLine(final StringBuilder sb, final String[] text,
+	void copyLine(final StringBuilder sb, final String[] text,
 			final int[] offsets, final int fileIdx) {
 		final String s = text[fileIdx];
 		final int start = offsets[fileIdx];

@@ -320,7 +320,7 @@ protected void copyLine(final StringBuilder sb, final String[] text,
 		offsets[fileIdx] = end;
 	}
 
-	protected void skipLine(final String[] text, final int[] offsets,
+	void skipLine(final String[] text, final int[] offsets,
 			final int fileIdx) {
 		final String s = text[fileIdx];
 		final int end = s.indexOf('\n', offsets[fileIdx]);

@@ -171,10 +171,19 @@ private PlotLane nextFreeLane() {
 		return p;
 	}
 
+	/**
+	 * @return a new Lane appropriate for this particular PlotList.
+	 */
 	protected L createLane() {
 		return (L) new PlotLane();
 	}
 
+	/**
+	 * Return colors and other reusable information to the plotter when a lane
+	 * is no longer needed.
+	 * 
+	 * @param lane
+	 */
 	protected void recycleLane(final L lane) {
 		// Nothing.
 	}

@@ -88,6 +88,10 @@ protected RevCommit createCommit(final AnyObjectId id) {
 		return new PlotCommit(id, getTags(id));
 	}
 
+	/**
+	 * @param commitId
+	 * @return return the list of knows tags referring to this commit
+	 */
 	protected Ref[] getTags(final AnyObjectId commitId) {
 		Collection<Ref> list = reverseRefMap.get(commitId);
 		Ref[] tags;

@@ -51,7 +51,7 @@
 
 	private boolean overridable;
 
-	protected DaemonService(final String cmdName, final String cfgName) {
+	DaemonService(final String cmdName, final String cfgName) {
 		command = cmdName.startsWith("git-") ? cmdName : "git-" + cmdName;
 		config = cfgName;
 		overridable = true;

@@ -115,6 +115,6 @@ void execute(final DaemonClient client, final String commandLine)
 			execute(client, db);
 	}
 
-	protected abstract void execute(DaemonClient client, Repository db)
+	abstract void execute(DaemonClient client, Repository db)
 			throws IOException;
 }

@@ -95,7 +95,7 @@ public static OpenSshConfig get() {
 	/** Cached entries read out of the configuration file. */
 	private Map<String, Host> hosts;
 
-	protected OpenSshConfig(final File h, final File cfg) {
+	OpenSshConfig(final File h, final File cfg) {
 		home = h;
 		configFile = cfg;
 		hosts = Collections.emptyMap();

@@ -53,11 +53,11 @@
  */
 public abstract class OperationResult {
 
-	protected Map<String, Ref> advertisedRefs = Collections.emptyMap();
+	Map<String, Ref> advertisedRefs = Collections.emptyMap();
 
-	protected URIish uri;
+	URIish uri;
 
-	protected final SortedMap<String, TrackingRefUpdate> updates = new TreeMap<String, TrackingRefUpdate>();
+	final SortedMap<String, TrackingRefUpdate> updates = new TreeMap<String, TrackingRefUpdate>();
 
 	/**
 	 * Get the URI this result came from.

@@ -122,12 +122,12 @@ public TrackingRefUpdate getTrackingRefUpdate(final String localName) {
 		return updates.get(localName);
 	}
 
-	protected void setAdvertisedRefs(final URIish u, final Map<String, Ref> ar) {
+	void setAdvertisedRefs(final URIish u, final Map<String, Ref> ar) {
 		uri = u;
 		advertisedRefs = ar;
 	}
 
-	protected void add(final TrackingRefUpdate u) {
+	void add(final TrackingRefUpdate u) {
 		updates.put(u.getLocalName(), u);
 	}
 }

@@ -49,7 +49,7 @@
  * objects from the pack. This extension of ObjectId includes the offset.
  */
 public class PackedObjectInfo extends ObjectId {
-	protected long offset;
+	private long offset;
 
 	private int crc;
 

@@ -77,7 +77,7 @@ public RemoteRefUpdate getRemoteUpdate(final String refName) {
 		return remoteUpdates.get(refName);
 	}
 
-	protected void setRemoteUpdates(
+	void setRemoteUpdates(
 			final Map<String, RemoteRefUpdate> remoteUpdates) {
 		this.remoteUpdates = remoteUpdates;
 	}

@@ -315,15 +315,15 @@ public String getMessage() {
 		return message;
 	}
 
-	protected void setStatus(final Status status) {
+	void setStatus(final Status status) {
 		this.status = status;
 	}
 
-	protected void setFastForward(boolean fastForward) {
+	void setFastForward(boolean fastForward) {
 		this.fastForward = fastForward;
 	}
 
-	protected void setMessage(final String message) {
+	void setMessage(final String message) {
 		this.message = message;
 	}
 

@@ -309,6 +309,13 @@ static int lastPathChar(final Entry e) {
 		return e.getMode() == FileMode.TREE ? '/' : '\0';
 	}
 
+	/**
+	 * Constructor helper.
+	 *
+	 * @param list
+	 *            files in the subtree of the work tree this iterator operates
+	 *            on
+	 */
 	protected void init(final Entry[] list) {
 		// Filter out nulls, . and .. as these are not valid tree entries,
 		// also cache the encoded forms of the path names for efficient use

@@ -90,7 +90,7 @@ public OldImage getOldImage(final int nthParent) {
 	}
 
 	@Override
-	void parseHeader(final int end) {
+	void parseHeader() {
 		// Parse "@@@ -55,12 -163,13 +163,15 @@@ protected boolean"
 		//
 		final byte[] buf = file.buf;

@@ -161,7 +161,7 @@ public int getLinesContext() {
 		return nContext;
 	}
 
-	void parseHeader(final int end) {
+	void parseHeader() {
 		// Parse "@@ -236,9 +236,9 @@ protected boolean"
 		//
 		final byte[] buf = file.buf;

@@ -222,7 +222,7 @@ private int parseDiffGit(final byte[] buf, final int start, final int end) {
 		final FileHeader fh = new FileHeader(buf, start);
 		int ptr = fh.parseGitFileName(start + DIFF_GIT.length, end);
 		if (ptr < 0)
-			return skipFile(buf, start, end);
+			return skipFile(buf, start);
 
 		ptr = fh.parseGitHeaders(ptr, end);
 		ptr = parseHunks(fh, ptr, end);

@@ -236,7 +236,7 @@ private int parseDiffCombined(final byte[] hdr, final byte[] buf,
 		final CombinedFileHeader fh = new CombinedFileHeader(buf, start);
 		int ptr = fh.parseGitFileName(start + hdr.length, end);
 		if (ptr < 0)
-			return skipFile(buf, start, end);
+			return skipFile(buf, start);
 
 		ptr = fh.parseGitHeaders(ptr, end);
 		ptr = parseHunks(fh, ptr, end);

@@ -255,7 +255,7 @@ private int parseTraditionalPatch(final byte[] buf, final int start,
 		return ptr;
 	}
 
-	private static int skipFile(final byte[] buf, int ptr, final int end) {
+	private static int skipFile(final byte[] buf, int ptr) {
 		ptr = nextLF(buf, ptr);
 		if (match(buf, ptr, OLD_NAME) >= 0)
 			ptr = nextLF(buf, ptr);

@@ -282,7 +282,7 @@ private int parseHunks(final FileHeader fh, int c, final int end) {
 
 			if (isHunkHdr(buf, c, end) == fh.getParentCount()) {
 				final HunkHeader h = fh.newHunkHeader(c);
-				h.parseHeader(end);
+				h.parseHeader();
 				c = h.parseBody(this, end);
 				h.endOffset = c;
 				fh.addHunk(h);

@@ -104,10 +104,10 @@ public IndexTreeWalker(GitIndex index, Tree mainTree, Tree newTree, File root, I
 	 * @throws IOException
 	 */
 	public void walk() throws IOException {
-		walk(mainTree, newTree, "");
+		walk(mainTree, newTree);
 	}
 
-	private void walk(Tree tree, Tree auxTree, String curDir) throws IOException {
+	private void walk(Tree tree, Tree auxTree) throws IOException {
 		TreeIterator mi = new TreeIterator(tree, TreeIterator.Order.POSTORDER);
 		TreeIterator ai = new TreeIterator(auxTree, TreeIterator.Order.POSTORDER);
 		TreeEntry m = mi.hasNext() ? mi.next() : null;

@@ -124,7 +124,7 @@ private void walk(Tree tree, Tree auxTree, String curDir) throws IOException {
 			Entry     pi = cmpmi >= 0 && cmpai >= 0 ? i : null;
 
 			if (pi != null)
-				visitEntry(pm, pa, pi, root);
+				visitEntry(pm, pa, pi);
 			else
 				finishVisitTree(pm, pa, curIndexPos, root);
 

@@ -135,7 +135,7 @@ private void walk(Tree tree, Tree auxTree, String curDir) throws IOException {
 	}
 
 	private void visitEntry(TreeEntry t1, TreeEntry t2,
-			Entry i, File root) throws IOException {
+			Entry i) throws IOException {
 
 		assert t1 != null || t2 != null || i != null : "Needs at least one entry";
 		assert root != null : "Needs workdir";

@@ -259,7 +259,7 @@ public void visitEntry(TreeEntry treeEntry, TreeEntry auxEntry,
 				if (treeEntry instanceof Tree || auxEntry instanceof Tree) {
 					throw new IllegalArgumentException("Can't pass me a tree!");
 				}
-				processEntry(treeEntry, auxEntry, indexEntry, file);
+				processEntry(treeEntry, auxEntry, indexEntry);
 			}
 	
 			@Override

@@ -294,8 +294,7 @@ else if (file.isDirectory()) {
 		conflicts.removeAll(removed);
 	}
 
-	void processEntry(TreeEntry h, TreeEntry m, Entry i,
-			File file) throws IOException {
+	void processEntry(TreeEntry h, TreeEntry m, Entry i) throws IOException {
 				ObjectId iId = (i == null ? null : i.getObjectId());
 				ObjectId mId = (m == null ? null : m.getId());
 				ObjectId hId = (h == null ? null : h.getId());

@@ -45,7 +45,7 @@
 @Command(common = false, usage = "Server side backend for 'jgit push'")
 class ReceivePack extends TextBuiltin {
 	@Argument(index = 0, required = true, metaVar = "DIRECTORY", usage = "Repository to receive into")
-	File gitdir;
+	File newGitdir;
 
 	@Override
 	protected final boolean requiresRepository() {

@@ -56,11 +56,11 @@ protected final boolean requiresRepository() {
 	protected void run() throws Exception {
 		final org.spearce.jgit.transport.ReceivePack rp;
 
-		if (new File(gitdir, ".git").isDirectory())
-			gitdir = new File(gitdir, ".git");
-		db = new Repository(gitdir);
+		if (new File(newGitdir, ".git").isDirectory())
+			newGitdir = new File(newGitdir, ".git");
+		db = new Repository(newGitdir);
 		if (!db.getObjectsDirectory().isDirectory())
-			throw die("'" + gitdir.getPath() + "' not a git repository");
+			throw die("'" + newGitdir.getPath() + "' not a git repository");
 		rp = new org.spearce.jgit.transport.ReceivePack(db);
 		rp.receive(System.in, System.out, System.err);
 	}

@@ -45,7 +45,7 @@
 @Command(common = false, usage = "Server side backend for 'jgit fetch'")
 class UploadPack extends TextBuiltin {
 	@Argument(index = 0, required = true, metaVar = "DIRECTORY", usage = "Repository to read from")
-	File gitdir;
+	File newGitdir;
 
 	@Override
 	protected final boolean requiresRepository() {

@@ -56,11 +56,11 @@ protected final boolean requiresRepository() {
 	protected void run() throws Exception {
 		final org.spearce.jgit.transport.UploadPack rp;
 
-		if (new File(gitdir, ".git").isDirectory())
-			gitdir = new File(gitdir, ".git");
-		db = new Repository(gitdir);
+		if (new File(newGitdir, ".git").isDirectory())
+			newGitdir = new File(newGitdir, ".git");
+		db = new Repository(newGitdir);
 		if (!db.getObjectsDirectory().isDirectory())
-			throw die("'" + gitdir.getPath() + "' not a git repository");
+			throw die("'" + newGitdir.getPath() + "' not a git repository");
 		rp = new org.spearce.jgit.transport.UploadPack(db);
 		rp.upload(System.in, System.out, System.err);
 	}

@@ -401,9 +401,9 @@ public void close() {
 		}
 
 		public void push(ProgressMonitor monitor,
-				Map<String, RemoteRefUpdate> refUpdates)
+				Map<String, RemoteRefUpdate> refsToUpdate)
 				throws TransportException {
-			for (final RemoteRefUpdate rru : refUpdates.values()) {
+			for (final RemoteRefUpdate rru : refsToUpdate.values()) {
 				assertEquals(Status.NOT_ATTEMPTED, rru.getStatus());
 				rru.setStatus(connectionUpdateStatus);
 			}

@@ -49,10 +49,10 @@
 
 public class ReadTreeTest extends RepositoryTestCase {
 	
-	private Tree head;
-	private Tree merge;
-	private GitIndex index;
-	private WorkDirCheckout readTree;
+	private Tree theHead;
+	private Tree theMerge;
+	private GitIndex theIndex;
+	private WorkDirCheckout theReadTree;
 	// Each of these rules are from the read-tree manpage
 	// go there to see what they mean.
 	// Rule 0 is left out for obvious reasons :)

@@ -87,9 +87,9 @@ public void testRules1thru3_NoIndexEntry() throws IOException {
 	void setupCase(HashMap<String, String> headEntries, 
 			HashMap<String, String> mergeEntries, 
 			HashMap<String, String> indexEntries) throws IOException {
-		head = buildTree(headEntries);
-		merge = buildTree(mergeEntries);
-		index = buildIndex(indexEntries);
+		theHead = buildTree(headEntries);
+		theMerge = buildTree(mergeEntries);
+		theIndex = buildIndex(indexEntries);
 	}
 	
 	private GitIndex buildIndex(HashMap<String, String> indexEntries) throws IOException {

@@ -129,9 +129,9 @@ ObjectId genSha1(String data) {
 	}
 	
 	private WorkDirCheckout go() throws IOException {
-		readTree = new WorkDirCheckout(db, trash, head, index, merge);
-		readTree.prescanTwoTrees();
-		return readTree;
+		theReadTree = new WorkDirCheckout(db, trash, theHead, theIndex, theMerge);
+		theReadTree.prescanTwoTrees();
+		return theReadTree;
 	}
 
     // for these rules, they all have clean yes/no options

@@ -144,17 +144,17 @@ public void testRules4thru13_IndexEntryNotInHead() throws IOException {
 		idxMap = new HashMap<String, String>();
 		idxMap.put("foo", "foo");
 		setupCase(null, null, idxMap);
-		readTree = go();
+		theReadTree = go();
 		
-		assertTrue(readTree.updated.isEmpty());
-		assertTrue(readTree.removed.isEmpty());
-		assertTrue(readTree.conflicts.isEmpty());
+		assertTrue(theReadTree.updated.isEmpty());
+		assertTrue(theReadTree.removed.isEmpty());
+		assertTrue(theReadTree.conflicts.isEmpty());
 		
 		// rules 6 and 7
 		idxMap = new HashMap<String, String>();
 		idxMap.put("foo", "foo");
 		setupCase(null, idxMap, idxMap);
-		readTree = go();
+		theReadTree = go();
 
 		assertAllEmpty();
 		

@@ -166,9 +166,9 @@ public void testRules4thru13_IndexEntryNotInHead() throws IOException {
 		setupCase(null, mergeMap, idxMap);
 		go();
 		
-		assertTrue(readTree.updated.isEmpty());
-		assertTrue(readTree.removed.isEmpty());
-		assertTrue(readTree.conflicts.contains("foo"));
+		assertTrue(theReadTree.updated.isEmpty());
+		assertTrue(theReadTree.removed.isEmpty());
+		assertTrue(theReadTree.conflicts.contains("foo"));
 		
 		// rule 10
 		

@@ -177,29 +177,29 @@ public void testRules4thru13_IndexEntryNotInHead() throws IOException {
 		setupCase(headMap, null, idxMap);
 		go();
 		
-		assertTrue(readTree.removed.contains("foo"));
-		assertTrue(readTree.updated.isEmpty());
-		assertTrue(readTree.conflicts.isEmpty());
+		assertTrue(theReadTree.removed.contains("foo"));
+		assertTrue(theReadTree.updated.isEmpty());
+		assertTrue(theReadTree.conflicts.isEmpty());
 		
 		// rule 11
 		setupCase(headMap, null, idxMap);
 		new File(trash, "foo").delete();
 		writeTrashFile("foo", "bar");
-		index.getMembers()[0].forceRecheck();
+		theIndex.getMembers()[0].forceRecheck();
 		go();
 		
-		assertTrue(readTree.removed.isEmpty());
-		assertTrue(readTree.updated.isEmpty());
-		assertTrue(readTree.conflicts.contains("foo"));
+		assertTrue(theReadTree.removed.isEmpty());
+		assertTrue(theReadTree.updated.isEmpty());
+		assertTrue(theReadTree.conflicts.contains("foo"));
 		
 		// rule 12 & 13
 		headMap.put("foo", "head");
 		setupCase(headMap, null, idxMap);
 		go();
 		
-		assertTrue(readTree.removed.isEmpty());
-		assertTrue(readTree.updated.isEmpty());
-		assertTrue(readTree.conflicts.contains("foo"));
+		assertTrue(theReadTree.removed.isEmpty());
+		assertTrue(theReadTree.updated.isEmpty());
+		assertTrue(theReadTree.conflicts.contains("foo"));
 		
 		// rules 14 & 15
 		setupCase(headMap, headMap, idxMap);

@@ -209,7 +209,7 @@ public void testRules4thru13_IndexEntryNotInHead() throws IOException {
 		
 		// rules 16 & 17
 		setupCase(headMap, mergeMap, idxMap); go();
-		assertTrue(readTree.conflicts.contains("foo"));
+		assertTrue(theReadTree.conflicts.contains("foo"));
 		
 		// rules 18 & 19
 		setupCase(headMap, idxMap, idxMap); go();

@@ -217,51 +217,51 @@ public void testRules4thru13_IndexEntryNotInHead() throws IOException {
 		
 		// rule 20
 		setupCase(idxMap, mergeMap, idxMap); go();
-		assertTrue(readTree.updated.containsKey("foo"));
+		assertTrue(theReadTree.updated.containsKey("foo"));
 		
 		// rules 21
 		setupCase(idxMap, mergeMap, idxMap); 
 		new File(trash, "foo").delete();
 		writeTrashFile("foo", "bar");
-		index.getMembers()[0].forceRecheck();
+		theIndex.getMembers()[0].forceRecheck();
 		go();
-		assertTrue(readTree.conflicts.contains("foo"));
+		assertTrue(theReadTree.conflicts.contains("foo"));
 	}
 
 	private void assertAllEmpty() {
-		assertTrue(readTree.removed.isEmpty());
-		assertTrue(readTree.updated.isEmpty());
-		assertTrue(readTree.conflicts.isEmpty());
+		assertTrue(theReadTree.removed.isEmpty());
+		assertTrue(theReadTree.updated.isEmpty());
+		assertTrue(theReadTree.conflicts.isEmpty());
 	}
 	
 	public void testDirectoryFileSimple() throws IOException {
-		index = new GitIndex(db);
-		index.add(trash, writeTrashFile("DF", "DF"));
-		Tree treeDF = db.mapTree(index.writeTree());
+		theIndex = new GitIndex(db);
+		theIndex.add(trash, writeTrashFile("DF", "DF"));
+		Tree treeDF = db.mapTree(theIndex.writeTree());
 		
 		recursiveDelete(new File(trash, "DF"));
-		index = new GitIndex(db);
-		index.add(trash, writeTrashFile("DF/DF", "DF/DF"));
-		Tree treeDFDF = db.mapTree(index.writeTree());
+		theIndex = new GitIndex(db);
+		theIndex.add(trash, writeTrashFile("DF/DF", "DF/DF"));
+		Tree treeDFDF = db.mapTree(theIndex.writeTree());
 		
-		index = new GitIndex(db);
+		theIndex = new GitIndex(db);
 		recursiveDelete(new File(trash, "DF"));
 		
-		index.add(trash, writeTrashFile("DF", "DF"));
-		readTree = new WorkDirCheckout(db, trash, treeDF, index, treeDFDF);
-		readTree.prescanTwoTrees();
+		theIndex.add(trash, writeTrashFile("DF", "DF"));
+		theReadTree = new WorkDirCheckout(db, trash, treeDF, theIndex, treeDFDF);
+		theReadTree.prescanTwoTrees();
 		
-		assertTrue(readTree.removed.contains("DF"));
-		assertTrue(readTree.updated.containsKey("DF/DF"));
+		assertTrue(theReadTree.removed.contains("DF"));
+		assertTrue(theReadTree.updated.containsKey("DF/DF"));
 		
 		recursiveDelete(new File(trash, "DF"));
-		index = new GitIndex(db);
-		index.add(trash, writeTrashFile("DF/DF", "DF/DF"));
+		theIndex = new GitIndex(db);
+		theIndex.add(trash, writeTrashFile("DF/DF", "DF/DF"));
 		
-		readTree = new WorkDirCheckout(db, trash, treeDFDF, index, treeDF);
-		readTree.prescanTwoTrees();
-		assertTrue(readTree.removed.contains("DF/DF"));
-		assertTrue(readTree.updated.containsKey("DF"));
+		theReadTree = new WorkDirCheckout(db, trash, treeDFDF, theIndex, treeDF);
+		theReadTree.prescanTwoTrees();
+		assertTrue(theReadTree.removed.contains("DF/DF"));
+		assertTrue(theReadTree.updated.containsKey("DF"));
 	}
 	
 	/*