From eecaad8b8e2c447429c31a01d49260ddd6b4ee03 Mon Sep 17 00:00:00 2001
From: Paul Martin <paul@paulsputer.com>
Date: Sat, 16 Apr 2016 17:35:32 -0400
Subject: [PATCH] Proof of concept #1026

---
 src/main/java/com/gitblit/utils/JGitUtils.java | 1267 +++++++++++++++++++++++++++++++++++++++++++++------------
 1 files changed, 996 insertions(+), 271 deletions(-)

diff --git a/src/main/java/com/gitblit/utils/JGitUtils.java b/src/main/java/com/gitblit/utils/JGitUtils.java
index 345375a..adcbb4d 100644
--- a/src/main/java/com/gitblit/utils/JGitUtils.java
+++ b/src/main/java/com/gitblit/utils/JGitUtils.java
@@ -15,14 +15,13 @@
  */
 package com.gitblit.utils;
 
-import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.IOException;
-import java.io.InputStream;
 import java.text.DecimalFormat;
 import java.text.MessageFormat;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.Date;
 import java.util.HashMap;
@@ -30,21 +29,29 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
+import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
+import org.apache.commons.io.filefilter.TrueFileFilter;
 import org.eclipse.jgit.api.CloneCommand;
 import org.eclipse.jgit.api.FetchCommand;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.TagCommand;
+import org.eclipse.jgit.api.errors.ConcurrentRefUpdateException;
 import org.eclipse.jgit.api.errors.GitAPIException;
+import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.diff.DiffEntry;
 import org.eclipse.jgit.diff.DiffEntry.ChangeType;
 import org.eclipse.jgit.diff.DiffFormatter;
 import org.eclipse.jgit.diff.RawTextComparator;
+import org.eclipse.jgit.dircache.DirCache;
+import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.errors.ConfigInvalidException;
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
+import org.eclipse.jgit.errors.LargeObjectException;
 import org.eclipse.jgit.errors.MissingObjectException;
 import org.eclipse.jgit.errors.StopWalkException;
+import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.BlobBasedConfig;
 import org.eclipse.jgit.lib.CommitBuilder;
 import org.eclipse.jgit.lib.Constants;
@@ -60,6 +67,9 @@
 import org.eclipse.jgit.lib.RepositoryCache.FileKey;
 import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.lib.TreeFormatter;
+import org.eclipse.jgit.merge.MergeStrategy;
+import org.eclipse.jgit.merge.RecursiveMerger;
+import org.eclipse.jgit.merge.ThreeWayMerger;
 import org.eclipse.jgit.revwalk.RevBlob;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevObject;
@@ -72,6 +82,7 @@
 import org.eclipse.jgit.transport.CredentialsProvider;
 import org.eclipse.jgit.transport.FetchResult;
 import org.eclipse.jgit.transport.RefSpec;
+import org.eclipse.jgit.treewalk.CanonicalTreeParser;
 import org.eclipse.jgit.treewalk.TreeWalk;
 import org.eclipse.jgit.treewalk.filter.AndTreeFilter;
 import org.eclipse.jgit.treewalk.filter.OrTreeFilter;
@@ -80,23 +91,26 @@
 import org.eclipse.jgit.treewalk.filter.PathSuffixFilter;
 import org.eclipse.jgit.treewalk.filter.TreeFilter;
 import org.eclipse.jgit.util.FS;
-import org.eclipse.jgit.util.io.DisabledOutputStream;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import com.gitblit.GitBlit;
+import com.gitblit.GitBlitException;
+import com.gitblit.manager.GitblitManager;
+import com.gitblit.models.FilestoreModel;
 import com.gitblit.models.GitNote;
 import com.gitblit.models.PathModel;
 import com.gitblit.models.PathModel.PathChangeModel;
 import com.gitblit.models.RefModel;
 import com.gitblit.models.SubmoduleModel;
-import com.sun.jna.Library;
-import com.sun.jna.Native;
+import com.gitblit.servlet.FilestoreServlet;
+import com.google.common.base.Strings;
 
 /**
  * Collection of static methods for retrieving information from a repository.
- * 
+ *
  * @author James Moger
- * 
+ *
  */
 public class JGitUtils {
 
@@ -104,7 +118,7 @@
 
 	/**
 	 * Log an error message and exception.
-	 * 
+	 *
 	 * @param t
 	 * @param repository
 	 *            if repository is not null it MUST be the {0} parameter in the
@@ -128,7 +142,7 @@
 	/**
 	 * Returns the displayable name of the person in the form "Real Name <email
 	 * address>".  If the email address is empty, just "Real Name" is returned.
-	 * 
+	 *
 	 * @param person
 	 * @return "Real Name <email address>" or "Real Name"
 	 */
@@ -157,7 +171,7 @@
 	 * Clone or Fetch a repository. If the local repository does not exist,
 	 * clone is called. If the repository does exist, fetch is called. By
 	 * default the clone/fetch retrieves the remote heads, tags, and notes.
-	 * 
+	 *
 	 * @param repositoriesFolder
 	 * @param name
 	 * @param fromUrl
@@ -173,7 +187,7 @@
 	 * Clone or Fetch a repository. If the local repository does not exist,
 	 * clone is called. If the repository does exist, fetch is called. By
 	 * default the clone/fetch retrieves the remote heads, tags, and notes.
-	 * 
+	 *
 	 * @param repositoriesFolder
 	 * @param name
 	 * @param fromUrl
@@ -214,7 +228,7 @@
 				clone.setCredentialsProvider(credentialsProvider);
 			}
 			Repository repository = clone.call().getRepository();
-			
+
 			// Now we have to fetch because CloneCommand doesn't fetch
 			// refs/notes nor does it allow manual RefSpec.
 			result.createdRepository = true;
@@ -227,7 +241,7 @@
 	/**
 	 * Fetch updates from the remote repository. If refSpecs is unspecifed,
 	 * remote heads, tags, and notes are retrieved.
-	 * 
+	 *
 	 * @param credentialsProvider
 	 * @param repository
 	 * @param refSpecs
@@ -256,122 +270,197 @@
 
 	/**
 	 * Creates a bare repository.
-	 * 
+	 *
 	 * @param repositoriesFolder
 	 * @param name
 	 * @return Repository
 	 */
 	public static Repository createRepository(File repositoriesFolder, String name) {
+		return createRepository(repositoriesFolder, name, "FALSE");
+	}
+
+	/**
+	 * Creates a bare, shared repository.
+	 *
+	 * @param repositoriesFolder
+	 * @param name
+	 * @param shared
+	 *          the setting for the --shared option of "git init".
+	 * @return Repository
+	 */
+	public static Repository createRepository(File repositoriesFolder, String name, String shared) {
 		try {
-			Git git = Git.init().setDirectory(new File(repositoriesFolder, name)).setBare(true).call();
-			return git.getRepository();
-		} catch (GitAPIException e) {
+			Repository repo = null;
+			try {
+				Git git = Git.init().setDirectory(new File(repositoriesFolder, name)).setBare(true).call();
+				repo = git.getRepository();
+			} catch (GitAPIException e) {
+				throw new RuntimeException(e);
+			}
+
+			GitConfigSharedRepository sharedRepository = new GitConfigSharedRepository(shared);
+			if (sharedRepository.isShared()) {
+				StoredConfig config = repo.getConfig();
+				config.setString("core", null, "sharedRepository", sharedRepository.getValue());
+				config.setBoolean("receive", null, "denyNonFastforwards", true);
+				config.save();
+
+				if (! JnaUtils.isWindows()) {
+					Iterator<File> iter = org.apache.commons.io.FileUtils.iterateFilesAndDirs(repo.getDirectory(),
+							TrueFileFilter.INSTANCE, TrueFileFilter.INSTANCE);
+					// Adjust permissions on file/directory
+					while (iter.hasNext()) {
+						adjustSharedPerm(iter.next(), sharedRepository);
+					}
+				}
+			}
+
+			return repo;
+		} catch (IOException e) {
 			throw new RuntimeException(e);
 		}
 	}
 
-    /**
-     * Creates a bare, shared repository.
-     * 
-     * @param repositoriesFolder
-     * @param name
-     * @param shared
-     *          the setting for the --shared option of "git init".
-     * @return Repository
-     */
-    public static Repository createRepository(File repositoriesFolder, String name, String shared) {
-        try {
-            Repository repo = createRepository(repositoriesFolder, name);
+	private enum GitConfigSharedRepositoryValue
+	{
+		UMASK("0", 0), FALSE("0", 0), OFF("0", 0), NO("0", 0),
+		GROUP("1", 0660), TRUE("1", 0660), ON("1", 0660), YES("1", 0660),
+		ALL("2", 0664), WORLD("2", 0664), EVERYBODY("2", 0664),
+		Oxxx(null, -1);
 
-            GitConfigSharedRepository sharedRepository = new GitConfigSharedRepository(shared);
-            if (sharedRepository.isShared()) {
-                StoredConfig config = repo.getConfig();
-                config.setString("core", null, "sharedRepository", sharedRepository.getValue());
-                config.setBoolean("receive", null, "denyNonFastforwards", true);
-                config.save();
+		private String configValue;
+		private int permValue;
+		private GitConfigSharedRepositoryValue(String config, int perm) { configValue = config; permValue = perm; };
 
-                if (! System.getProperty("os.name").toLowerCase().startsWith("windows")) {
-                    final CLibrary libc = (CLibrary) Native.loadLibrary("c", CLibrary.class);
+		public String getConfigValue() { return configValue; };
+		public int getPerm() { return permValue; };
 
-                    //libc.chmod("/path/to/file", 0755);
-                }
-            }
+	}
 
-            return repo;
-        } catch (IOException e) {
-            throw new RuntimeException(e);
-        }
-    }
-    interface CLibrary extends Library {
-        public int chmod(String path, int mode);
-    }
-    private enum GitConfigSharedRepositoryValue {
-        UMASK("0", 0), FALSE("0", 0), OFF("0", 0), NO("0", 0),
-        GROUP("1", 0660), TRUE("1", 0660), ON("1", 0660), YES("1", 0660),
-        ALL("2", 0664), WORLD("2", 0664), EVERYBODY("2", 0664),
-        Oxxx(null, -1);
+	private static class GitConfigSharedRepository
+	{
+		private int intValue;
+		private GitConfigSharedRepositoryValue enumValue;
 
-        private String configValue;
-        private int permValue;
-        private GitConfigSharedRepositoryValue(String config, int perm) { configValue = config; permValue = perm; };
+		GitConfigSharedRepository(String s) {
+			if ( s == null || s.trim().isEmpty() ) {
+				enumValue = GitConfigSharedRepositoryValue.GROUP;
+			}
+			else {
+				try {
+					// Try one of the string values
+					enumValue = GitConfigSharedRepositoryValue.valueOf(s.trim().toUpperCase());
+				} catch (IllegalArgumentException  iae) {
+					try {
+						// Try if this is an octal number
+						int i = Integer.parseInt(s, 8);
+						if ( (i & 0600) != 0600 ) {
+							String msg = String.format("Problem with core.sharedRepository filemode value (0%03o).\nThe owner of files must always have read and write permissions.", i);
+							throw new IllegalArgumentException(msg);
+						}
+						intValue = i & 0666;
+						enumValue = GitConfigSharedRepositoryValue.Oxxx;
+					} catch (NumberFormatException nfe) {
+						throw new IllegalArgumentException("Bad configuration value for 'shared': '" + s + "'");
+					}
+				}
+			}
+		}
 
-        public String getConfigValue() { return configValue; };
-        public int getPerm() { return permValue; };
+		String getValue() {
+			if ( enumValue == GitConfigSharedRepositoryValue.Oxxx ) {
+				if (intValue == 0) return "0";
+				return String.format("0%o", intValue);
+			}
+			return enumValue.getConfigValue();
+		}
 
-    }
-    private static class GitConfigSharedRepository
-    {
-        private int intValue;
-        GitConfigSharedRepositoryValue enumValue;
+		int getPerm() {
+			if ( enumValue == GitConfigSharedRepositoryValue.Oxxx ) return intValue;
+			return enumValue.getPerm();
+		}
 
-        GitConfigSharedRepository(String s)
-        {
-            if ( s == null || s.trim().isEmpty() ) {
-                enumValue = GitConfigSharedRepositoryValue.GROUP;
-            }
-            else {
-                try {
-                    // Try one of the string values
-                    enumValue = GitConfigSharedRepositoryValue.valueOf(s.trim().toUpperCase());
-                } catch (IllegalArgumentException  iae) {
-                    try {
-                        // Try if this is an octal number
-                        int i = Integer.parseInt(s, 8);
-                        if ( (i & 0600) != 0600 ) {
-                            String msg = String.format("Problem with core.sharedRepository filemode value (0%03o).\nThe owner of files must always have read and write permissions.", i);
-                            throw new IllegalArgumentException(msg);
-                        }
-                        intValue = i & 0666;
-                        enumValue = GitConfigSharedRepositoryValue.Oxxx;
-                    } catch (NumberFormatException nfe) {
-                        throw new IllegalArgumentException("Bad configuration value for 'shared': '" + s + "'");
-                    }
-                }
-            }
-        }
-        
-        String getValue()
-        {
-            if ( enumValue == GitConfigSharedRepositoryValue.Oxxx ) return Integer.toOctalString(intValue);
-            return enumValue.getConfigValue();
-        }
+		boolean isCustom() {
+			return enumValue == GitConfigSharedRepositoryValue.Oxxx;
+		}
 
-        int getPerm()
-        {
-            if ( enumValue == GitConfigSharedRepositoryValue.Oxxx ) return intValue;
-            return enumValue.getPerm();
-        }
+		boolean isShared() {
+			return (enumValue.getPerm() > 0) || enumValue == GitConfigSharedRepositoryValue.Oxxx;
+		}
+	}
 
-        boolean isShared()
-        {
-            return (enumValue.getPerm() > 0) || enumValue == GitConfigSharedRepositoryValue.Oxxx;
-        }
-    }
+
+	/**
+	 * Adjust file permissions of a file/directory for shared repositories
+	 *
+	 * @param path
+	 * 			File that should get its permissions changed.
+	 * @param configShared
+	 * 			Configuration string value for the shared mode.
+	 * @return Upon successful completion, a value of 0 is returned. Otherwise, a value of -1 is returned.
+	 */
+	public static int adjustSharedPerm(File path, String configShared) {
+		return adjustSharedPerm(path, new GitConfigSharedRepository(configShared));
+	}
+
+
+	/**
+	 * Adjust file permissions of a file/directory for shared repositories
+	 *
+	 * @param path
+	 * 			File that should get its permissions changed.
+	 * @param configShared
+	 * 			Configuration setting for the shared mode.
+	 * @return Upon successful completion, a value of 0 is returned. Otherwise, a value of -1 is returned.
+	 */
+	public static int adjustSharedPerm(File path, GitConfigSharedRepository configShared) {
+		if (! configShared.isShared()) return 0;
+		if (! path.exists()) return -1;
+
+		int perm = configShared.getPerm();
+		JnaUtils.Filestat stat = JnaUtils.getFilestat(path);
+		if (stat == null) return -1;
+		int mode = stat.mode;
+		if (mode < 0) return -1;
+
+		// Now, here is the kicker: Under Linux, chmod'ing a sgid file whose guid is different from the process'
+		// effective guid will reset the sgid flag of the file. Since there is no way to get the sgid flag back in
+		// that case, we decide to rather not touch is and getting the right permissions will have to be achieved
+		// in a different way, e.g. by using an appropriate umask for the Gitblit process.
+		if (System.getProperty("os.name").toLowerCase().startsWith("linux")) {
+			if ( ((mode & (JnaUtils.S_ISGID | JnaUtils.S_ISUID)) != 0)
+				&& stat.gid != JnaUtils.getegid() ) {
+				LOGGER.debug("Not adjusting permissions to prevent clearing suid/sgid bits for '" + path + "'" );
+				return 0;
+			}
+		}
+
+		// If the owner has no write access, delete it from group and other, too.
+		if ((mode & JnaUtils.S_IWUSR) == 0) perm &= ~0222;
+		// If the owner has execute access, set it for all blocks that have read access.
+		if ((mode & JnaUtils.S_IXUSR) == JnaUtils.S_IXUSR) perm |= (perm & 0444) >> 2;
+
+		if (configShared.isCustom()) {
+			// Use the custom value for access permissions.
+			mode = (mode & ~0777) | perm;
+		}
+		else {
+			// Just add necessary bits to existing permissions.
+			mode |= perm;
+		}
+
+		if (path.isDirectory()) {
+			mode |= (mode & 0444) >> 2;
+			mode |= JnaUtils.S_ISGID;
+		}
+
+		return JnaUtils.setFilemode(path, mode);
+	}
 
 
 	/**
 	 * Returns a list of repository names in the specified folder.
-	 * 
+	 *
 	 * @param repositoriesFolder
 	 * @param onlyBare
 	 *            if true, only bare repositories repositories are listed. If
@@ -405,7 +494,7 @@
 
 	/**
 	 * Recursive function to find git repositories.
-	 * 
+	 *
 	 * @param basePath
 	 *            basePath is stripped from the repository name as repositories
 	 *            are relative to this path
@@ -428,7 +517,7 @@
 		if (depth == 0) {
 			return list;
 		}
-		
+
 		int nextDepth = (depth == -1) ? -1 : depth - 1;
 		for (File file : searchFolder.listFiles()) {
 			if (file.isDirectory()) {
@@ -473,7 +562,7 @@
 	/**
 	 * Returns the first commit on a branch. If the repository does not exist or
 	 * is empty, null is returned.
-	 * 
+	 *
 	 * @param repository
 	 * @param branch
 	 *            if unspecified, HEAD is assumed.
@@ -509,7 +598,7 @@
 	 * Returns the date of the first commit on a branch. If the repository does
 	 * not exist, Date(0) is returned. If the repository does exist bit is
 	 * empty, the last modified date of the repository folder is returned.
-	 * 
+	 *
 	 * @param repository
 	 * @param branch
 	 *            if unspecified, HEAD is assumed.
@@ -530,7 +619,7 @@
 	/**
 	 * Determine if a repository has any commits. This is determined by checking
 	 * the for loose and packed objects.
-	 * 
+	 *
 	 * @param repository
 	 * @return true if the repository has commits
 	 */
@@ -541,18 +630,18 @@
 		}
 		return false;
 	}
-	
+
 	/**
 	 * Encapsulates the result of cloning or pulling from a repository.
 	 */
 	public static class LastChange {
 		public Date when;
 		public String who;
-		
+
 		LastChange() {
-			when = new Date(0);			
+			when = new Date(0);
 		}
-		
+
 		LastChange(long lastModified) {
 			this.when = new Date(lastModified);
 		}
@@ -562,7 +651,7 @@
 	 * Returns the date and author of the most recent commit on a branch. If the
 	 * repository does not exist Date(0) is returned. If it does exist but is
 	 * empty, the last modified date of the repository folder is returned.
-	 * 
+	 *
 	 * @param repository
 	 * @return a LastChange object
 	 */
@@ -579,7 +668,7 @@
 		List<RefModel> branchModels = getLocalBranches(repository, true, -1);
 		if (branchModels.size() > 0) {
 			// find most recent branch update
-			LastChange lastChange = new LastChange();			
+			LastChange lastChange = new LastChange();
 			for (RefModel branchModel : branchModels) {
 				if (branchModel.getDate().after(lastChange.when)) {
 					lastChange.when = branchModel.getDate();
@@ -588,14 +677,14 @@
 			}
 			return lastChange;
 		}
-		
+
 		// default to the repository folder modification date
 		return new LastChange(repository.getDirectory().lastModified());
 	}
 
 	/**
 	 * Retrieves a Java Date from a Git commit.
-	 * 
+	 *
 	 * @param commit
 	 * @return date of the commit or Date(0) if the commit is null
 	 */
@@ -608,7 +697,7 @@
 
 	/**
 	 * Retrieves a Java Date from a Git commit.
-	 * 
+	 *
 	 * @param commit
 	 * @return date of the commit or Date(0) if the commit is null
 	 */
@@ -616,13 +705,16 @@
 		if (commit == null) {
 			return new Date(0);
 		}
-		return commit.getAuthorIdent().getWhen();
+		if (commit.getAuthorIdent() != null) {
+			return commit.getAuthorIdent().getWhen();
+		}
+		return getCommitDate(commit);
 	}
 
 	/**
 	 * Returns the specified commit from the repository. If the repository does
 	 * not exist or is empty, null is returned.
-	 * 
+	 *
 	 * @param repository
 	 * @param objectId
 	 *            if unspecified, HEAD is assumed.
@@ -633,27 +725,34 @@
 			return null;
 		}
 		RevCommit commit = null;
+		RevWalk walk = null;
 		try {
 			// resolve object id
 			ObjectId branchObject;
-			if (StringUtils.isEmpty(objectId)) {
+			if (StringUtils.isEmpty(objectId) || "HEAD".equalsIgnoreCase(objectId)) {
 				branchObject = getDefaultBranch(repository);
 			} else {
 				branchObject = repository.resolve(objectId);
 			}
-			RevWalk walk = new RevWalk(repository);
+			if (branchObject == null) {
+				return null;
+			}
+			walk = new RevWalk(repository);
 			RevCommit rev = walk.parseCommit(branchObject);
 			commit = rev;
-			walk.dispose();
 		} catch (Throwable t) {
 			error(t, repository, "{0} failed to get commit {1}", objectId);
+		} finally {
+			if (walk != null) {
+				walk.dispose();
+			}
 		}
 		return commit;
 	}
 
 	/**
 	 * Retrieves the raw byte content of a file in the specified tree.
-	 * 
+	 *
 	 * @param repository
 	 * @param tree
 	 *            if null, the RevTree from HEAD is assumed.
@@ -668,6 +767,8 @@
 		try {
 			if (tree == null) {
 				ObjectId object = getDefaultBranch(repository);
+				if (object == null)
+					return null;
 				RevCommit commit = rw.parseCommit(object);
 				tree = commit.getTree();
 			}
@@ -680,18 +781,8 @@
 				ObjectId entid = tw.getObjectId(0);
 				FileMode entmode = tw.getFileMode(0);
 				if (entmode != FileMode.GITLINK) {
-					RevObject ro = rw.lookupAny(entid, entmode.getObjectType());
-					rw.parseBody(ro);
-					ByteArrayOutputStream os = new ByteArrayOutputStream();
-					ObjectLoader ldr = repository.open(ro.getId(), Constants.OBJ_BLOB);
-					byte[] tmp = new byte[4096];
-					InputStream in = ldr.openStream();
-					int n;
-					while ((n = in.read(tmp)) > 0) {
-						os.write(tmp, 0, n);
-					}
-					in.close();
-					content = os.toByteArray();
+					ObjectLoader ldr = repository.open(entid, Constants.OBJ_BLOB);
+					content = ldr.getCachedBytes();
 				}
 			}
 		} catch (Throwable t) {
@@ -700,14 +791,14 @@
 			}
 		} finally {
 			rw.dispose();
-			tw.release();
+			tw.close();
 		}
 		return content;
 	}
 
 	/**
 	 * Returns the UTF-8 string content of a file in the specified tree.
-	 * 
+	 *
 	 * @param repository
 	 * @param tree
 	 *            if null, the RevTree from HEAD is assumed.
@@ -725,7 +816,7 @@
 
 	/**
 	 * Gets the raw byte content of the specified blob object.
-	 * 
+	 *
 	 * @param repository
 	 * @param objectId
 	 * @return byte [] blob content
@@ -735,17 +826,8 @@
 		byte[] content = null;
 		try {
 			RevBlob blob = rw.lookupBlob(ObjectId.fromString(objectId));
-			rw.parseBody(blob);
-			ByteArrayOutputStream os = new ByteArrayOutputStream();
 			ObjectLoader ldr = repository.open(blob.getId(), Constants.OBJ_BLOB);
-			byte[] tmp = new byte[4096];
-			InputStream in = ldr.openStream();
-			int n;
-			while ((n = in.read(tmp)) > 0) {
-				os.write(tmp, 0, n);
-			}
-			in.close();
-			content = os.toByteArray();
+			content = ldr.getCachedBytes();
 		} catch (Throwable t) {
 			error(t, repository, "{0} can't find blob {1}", objectId);
 		} finally {
@@ -756,7 +838,7 @@
 
 	/**
 	 * Gets the UTF-8 string content of the blob specified by objectId.
-	 * 
+	 *
 	 * @param repository
 	 * @param objectId
 	 * @param charsets optional
@@ -774,7 +856,7 @@
 	 * Returns the list of files in the specified folder at the specified
 	 * commit. If the repository does not exist or is empty, an empty list is
 	 * returned.
-	 * 
+	 *
 	 * @param repository
 	 * @param path
 	 *            if unspecified, root folder is assumed.
@@ -820,7 +902,64 @@
 		} catch (IOException e) {
 			error(e, repository, "{0} failed to get files for commit {1}", commit.getName());
 		} finally {
-			tw.release();
+			tw.close();
+		}
+		Collections.sort(list);
+		return list;
+	}
+
+	/**
+	 * Returns the list of files in the specified folder at the specified
+	 * commit. If the repository does not exist or is empty, an empty list is
+	 * returned.
+	 *
+	 * This is modified version that implements path compression feature.
+	 *
+	 * @param repository
+	 * @param path
+	 *            if unspecified, root folder is assumed.
+	 * @param commit
+	 *            if null, HEAD is assumed.
+	 * @return list of files in specified path
+	 */
+	public static List<PathModel> getFilesInPath2(Repository repository, String path, RevCommit commit) {
+
+		List<PathModel> list = new ArrayList<PathModel>();
+		if (!hasCommits(repository)) {
+			return list;
+		}
+		if (commit == null) {
+			commit = getCommit(repository, null);
+		}
+		final TreeWalk tw = new TreeWalk(repository);
+		try {
+
+			tw.addTree(commit.getTree());
+			final boolean isPathEmpty = Strings.isNullOrEmpty(path);
+
+			if (!isPathEmpty) {
+				PathFilter f = PathFilter.create(path);
+				tw.setFilter(f);
+			}
+
+			tw.setRecursive(true);
+			List<String> paths = new ArrayList<>();
+
+			while (tw.next()) {
+					String child = isPathEmpty ? tw.getPathString()
+							: tw.getPathString().replaceFirst(String.format("%s/", path), "");
+					paths.add(child);
+			}
+
+			for(String p: PathUtils.compressPaths(paths)) {
+				String pathString = isPathEmpty ? p : String.format("%s/%s", path, p);
+				list.add(getPathModel(repository, pathString, path, commit));
+			}
+
+		} catch (IOException e) {
+			error(e, repository, "{0} failed to get files for commit {1}", commit.getName());
+		} finally {
+			tw.close();
 		}
 		Collections.sort(list);
 		return list;
@@ -829,13 +968,28 @@
 	/**
 	 * Returns the list of files changed in a specified commit. If the
 	 * repository does not exist or is empty, an empty list is returned.
-	 * 
+	 *
 	 * @param repository
 	 * @param commit
 	 *            if null, HEAD is assumed.
 	 * @return list of files changed in a commit
 	 */
 	public static List<PathChangeModel> getFilesInCommit(Repository repository, RevCommit commit) {
+		return getFilesInCommit(repository, commit, true);
+	}
+
+	/**
+	 * Returns the list of files changed in a specified commit. If the
+	 * repository does not exist or is empty, an empty list is returned.
+	 *
+	 * @param repository
+	 * @param commit
+	 *            if null, HEAD is assumed.
+	 * @param calculateDiffStat
+	 *            if true, each PathChangeModel will have insertions/deletions
+	 * @return list of files changed in a commit
+	 */
+	public static List<PathChangeModel> getFilesInCommit(Repository repository, RevCommit commit, boolean calculateDiffStat) {
 		List<PathChangeModel> list = new ArrayList<PathChangeModel>();
 		if (!hasCommits(repository)) {
 			return list;
@@ -853,33 +1007,49 @@
 				tw.setRecursive(true);
 				tw.addTree(commit.getTree());
 				while (tw.next()) {
-					list.add(new PathChangeModel(tw.getPathString(), tw.getPathString(), 0, tw
-							.getRawMode(0), tw.getObjectId(0).getName(), commit.getId().getName(),
+					long size = 0;
+					FilestoreModel filestoreItem = null;
+					ObjectId objectId = tw.getObjectId(0);
+					
+					try {
+						if (!tw.isSubtree() && (tw.getFileMode(0) != FileMode.GITLINK)) {
+
+							size = tw.getObjectReader().getObjectSize(objectId, Constants.OBJ_BLOB);
+
+							if (isPossibleFilestoreItem(size)) {
+								filestoreItem = getFilestoreItem(tw.getObjectReader().open(objectId));
+							}
+						}
+					} catch (Throwable t) {
+						error(t, null, "failed to retrieve blob size for " + tw.getPathString());
+					}
+					
+					list.add(new PathChangeModel(tw.getPathString(), tw.getPathString(),filestoreItem, size, tw
+							.getRawMode(0), objectId.getName(), commit.getId().getName(),
 							ChangeType.ADD));
 				}
-				tw.release();
+				tw.close();
 			} else {
 				RevCommit parent = rw.parseCommit(commit.getParent(0).getId());
-				DiffFormatter df = new DiffFormatter(DisabledOutputStream.INSTANCE);
+				DiffStatFormatter df = new DiffStatFormatter(commit.getName(), repository);
 				df.setRepository(repository);
 				df.setDiffComparator(RawTextComparator.DEFAULT);
 				df.setDetectRenames(true);
 				List<DiffEntry> diffs = df.scan(parent.getTree(), commit.getTree());
 				for (DiffEntry diff : diffs) {
-					String objectId = diff.getNewId().name();
-					if (diff.getChangeType().equals(ChangeType.DELETE)) {
-						list.add(new PathChangeModel(diff.getOldPath(), diff.getOldPath(), 0, diff
-								.getNewMode().getBits(), objectId, commit.getId().getName(), diff
-								.getChangeType()));
-					} else if (diff.getChangeType().equals(ChangeType.RENAME)) {
-						list.add(new PathChangeModel(diff.getOldPath(), diff.getNewPath(), 0, diff
-								.getNewMode().getBits(), objectId, commit.getId().getName(), diff
-								.getChangeType()));
-					} else {
-						list.add(new PathChangeModel(diff.getNewPath(), diff.getNewPath(), 0, diff
-								.getNewMode().getBits(), objectId, commit.getId().getName(), diff
-								.getChangeType()));
+					// create the path change model
+					PathChangeModel pcm = PathChangeModel.from(diff, commit.getName(), repository);
+						
+						if (calculateDiffStat) {
+						// update file diffstats
+						df.format(diff);
+						PathChangeModel pathStat = df.getDiffStat().getPath(pcm.path);
+						if (pathStat != null) {
+							pcm.insertions = pathStat.insertions;
+							pcm.deletions = pathStat.deletions;
+						}
 					}
+					list.add(pcm);
 				}
 			}
 		} catch (Throwable t) {
@@ -893,7 +1063,37 @@
 	/**
 	 * Returns the list of files changed in a specified commit. If the
 	 * repository does not exist or is empty, an empty list is returned.
-	 * 
+	 *
+	 * @param repository
+	 * @param startCommit
+	 *            earliest commit
+	 * @param endCommit
+	 *            most recent commit. if null, HEAD is assumed.
+	 * @return list of files changed in a commit range
+	 */
+	public static List<PathChangeModel> getFilesInRange(Repository repository, String startCommit, String endCommit) {
+		List<PathChangeModel> list = new ArrayList<PathChangeModel>();
+		if (!hasCommits(repository)) {
+			return list;
+		}
+		try {
+			ObjectId startRange = repository.resolve(startCommit);
+			ObjectId endRange = repository.resolve(endCommit);
+			RevWalk rw = new RevWalk(repository);
+			RevCommit start = rw.parseCommit(startRange);
+			RevCommit end = rw.parseCommit(endRange);
+			list.addAll(getFilesInRange(repository, start, end));
+			rw.close();
+		} catch (Throwable t) {
+			error(t, repository, "{0} failed to determine files in range {1}..{2}!", startCommit, endCommit);
+		}
+		return list;
+	}
+
+	/**
+	 * Returns the list of files changed in a specified commit. If the
+	 * repository does not exist or is empty, an empty list is returned.
+	 *
 	 * @param repository
 	 * @param startCommit
 	 *            earliest commit
@@ -914,21 +1114,9 @@
 
 			List<DiffEntry> diffEntries = df.scan(startCommit.getTree(), endCommit.getTree());
 			for (DiffEntry diff : diffEntries) {
-				
-				if (diff.getChangeType().equals(ChangeType.DELETE)) {
-					list.add(new PathChangeModel(diff.getOldPath(), diff.getOldPath(), 0, diff
-							.getNewMode().getBits(), diff.getOldId().name(), null, diff
-							.getChangeType()));
-				} else if (diff.getChangeType().equals(ChangeType.RENAME)) {
-					list.add(new PathChangeModel(diff.getOldPath(), diff.getNewPath(), 0, diff
-							.getNewMode().getBits(), diff.getNewId().name(), null, diff
-							.getChangeType()));
-				} else {
-					list.add(new PathChangeModel(diff.getNewPath(), diff.getNewPath(), 0, diff
-							.getNewMode().getBits(), diff.getNewId().name(), null, diff
-							.getChangeType()));
-				}
-			}			
+				PathChangeModel pcm = PathChangeModel.from(diff,  endCommit.getName(), repository);
+				list.add(pcm);
+			}
 			Collections.sort(list);
 		} catch (Throwable t) {
 			error(t, repository, "{0} failed to determine files in range {1}..{2}!", startCommit, endCommit);
@@ -939,7 +1127,7 @@
 	 * Returns the list of files in the repository on the default branch that
 	 * match one of the specified extensions. This is a CASE-SENSITIVE search.
 	 * If the repository does not exist or is empty, an empty list is returned.
-	 * 
+	 *
 	 * @param repository
 	 * @param extensions
 	 * @return list of files in repository with a matching extension
@@ -952,7 +1140,7 @@
 	 * Returns the list of files in the repository in the specified commit that
 	 * match one of the specified extensions. This is a CASE-SENSITIVE search.
 	 * If the repository does not exist or is empty, an empty list is returned.
-	 * 
+	 *
 	 * @param repository
 	 * @param extensions
 	 * @param objectId
@@ -972,10 +1160,10 @@
 				List<TreeFilter> suffixFilters = new ArrayList<TreeFilter>();
 				for (String extension : extensions) {
 					if (extension.charAt(0) == '.') {
-						suffixFilters.add(PathSuffixFilter.create("\\" + extension));
+						suffixFilters.add(PathSuffixFilter.create(extension));
 					} else {
 						// escape the . since this is a regexp filter
-						suffixFilters.add(PathSuffixFilter.create("\\." + extension));
+						suffixFilters.add(PathSuffixFilter.create("." + extension));
 					}
 				}
 				TreeFilter filter;
@@ -993,7 +1181,7 @@
 		} catch (IOException e) {
 			error(e, repository, "{0} failed to get documents for commit {1}", commit.getName());
 		} finally {
-			tw.release();
+			tw.close();
 		}
 		Collections.sort(list);
 		return list;
@@ -1001,7 +1189,7 @@
 
 	/**
 	 * Returns a path model of the current file in the treewalk.
-	 * 
+	 *
 	 * @param tw
 	 * @param basePath
 	 * @param commit
@@ -1010,26 +1198,104 @@
 	private static PathModel getPathModel(TreeWalk tw, String basePath, RevCommit commit) {
 		String name;
 		long size = 0;
+		
 		if (StringUtils.isEmpty(basePath)) {
 			name = tw.getPathString();
 		} else {
 			name = tw.getPathString().substring(basePath.length() + 1);
 		}
 		ObjectId objectId = tw.getObjectId(0);
+		FilestoreModel filestoreItem = null;
+		
 		try {
 			if (!tw.isSubtree() && (tw.getFileMode(0) != FileMode.GITLINK)) {
+
 				size = tw.getObjectReader().getObjectSize(objectId, Constants.OBJ_BLOB);
+
+				if (isPossibleFilestoreItem(size)) {
+					filestoreItem = getFilestoreItem(tw.getObjectReader().open(objectId));
+				}
 			}
 		} catch (Throwable t) {
 			error(t, null, "failed to retrieve blob size for " + tw.getPathString());
 		}
-		return new PathModel(name, tw.getPathString(), size, tw.getFileMode(0).getBits(),
+		return new PathModel(name, tw.getPathString(), filestoreItem, size, tw.getFileMode(0).getBits(),
 				objectId.getName(), commit.getName());
+	}
+	
+	public static boolean isPossibleFilestoreItem(long size) {
+		return (   (size >= com.gitblit.Constants.LEN_FILESTORE_META_MIN) 
+				&& (size <= com.gitblit.Constants.LEN_FILESTORE_META_MAX));
+	}
+	
+	/**
+	 * 
+	 * @return Representative FilestoreModel if valid, otherwise null
+	 */
+	public static FilestoreModel getFilestoreItem(ObjectLoader obj){
+		try {
+			final byte[] blob = obj.getCachedBytes(com.gitblit.Constants.LEN_FILESTORE_META_MAX);
+			final String meta = new String(blob, "UTF-8");
+		
+			return FilestoreModel.fromMetaString(meta);
+
+		} catch (LargeObjectException e) {
+			//Intentionally failing silent
+		} catch (Exception e) {
+			error(e, null, "failed to retrieve filestoreItem " + obj.toString());
+		}
+		
+		return null;
 	}
 
 	/**
+	 * Returns a path model by path string
+	 *
+	 * @param repo
+	 * @param path
+	 * @param filter
+	 * @param commit
+	 * @return a path model of the specified object
+	 */
+	private static PathModel getPathModel(Repository repo, String path, String filter, RevCommit commit)
+			throws IOException {
+
+		long size = 0;
+		FilestoreModel filestoreItem = null;
+		TreeWalk tw = TreeWalk.forPath(repo, path, commit.getTree());
+		String pathString = path;
+
+		if (!tw.isSubtree() && (tw.getFileMode(0) != FileMode.GITLINK)) {
+
+			pathString = PathUtils.getLastPathComponent(pathString);
+			
+			size = tw.getObjectReader().getObjectSize(tw.getObjectId(0), Constants.OBJ_BLOB);
+			
+			if (isPossibleFilestoreItem(size)) {
+				filestoreItem = getFilestoreItem(tw.getObjectReader().open(tw.getObjectId(0)));
+			}
+		} else if (tw.isSubtree()) {
+
+			// do not display dirs that are behind in the path
+			if (!Strings.isNullOrEmpty(filter)) {
+				pathString = path.replaceFirst(filter + "/", "");
+			}
+
+			// remove the last slash from path in displayed link
+			if (pathString != null && pathString.charAt(pathString.length()-1) == '/') {
+				pathString = pathString.substring(0, pathString.length()-1);
+			}
+		}
+
+		return new PathModel(pathString, tw.getPathString(), filestoreItem, size, tw.getFileMode(0).getBits(),
+				tw.getObjectId(0).getName(), commit.getName());
+
+	}
+
+
+	/**
 	 * Returns a permissions representation of the mode bits.
-	 * 
+	 *
 	 * @param mode
 	 * @return string representation of the mode bits
 	 */
@@ -1051,7 +1317,7 @@
 	/**
 	 * Returns a list of commits since the minimum date starting from the
 	 * specified object id.
-	 * 
+	 *
 	 * @param repository
 	 * @param objectId
 	 *            if unspecified, HEAD is assumed.
@@ -1089,7 +1355,7 @@
 
 	/**
 	 * Returns a list of commits starting from HEAD and working backwards.
-	 * 
+	 *
 	 * @param repository
 	 * @param maxCount
 	 *            if < 0, all commits for the repository are returned.
@@ -1104,7 +1370,7 @@
 	 * offset and maxCount for paging. This is similar to LIMIT n OFFSET p in
 	 * SQL. If the repository does not exist or is empty, an empty list is
 	 * returned.
-	 * 
+	 *
 	 * @param repository
 	 * @param objectId
 	 *            if unspecified, HEAD is assumed.
@@ -1123,7 +1389,7 @@
 	 * repository. Caller may specify ending revision with objectId. Caller may
 	 * specify offset and maxCount to achieve pagination of results. If the
 	 * repository does not exist or is empty, an empty list is returned.
-	 * 
+	 *
 	 * @param repository
 	 * @param objectId
 	 *            if unspecified, HEAD is assumed.
@@ -1168,7 +1434,7 @@
 			RevWalk rw = new RevWalk(repository);
 			rw.markStart(rw.parseCommit(endRange));
 			if (startRange != null) {
-				rw.markUninteresting(rw.parseCommit(startRange));	
+				rw.markUninteresting(rw.parseCommit(startRange));
 			}
 			if (!StringUtils.isEmpty(path)) {
 				TreeFilter filter = AndTreeFilter.create(
@@ -1207,7 +1473,7 @@
 	 * Returns a list of commits for the repository within the range specified
 	 * by startRangeId and endRangeId. If the repository does not exist or is
 	 * empty, an empty list is returned.
-	 * 
+	 *
 	 * @param repository
 	 * @param startRangeId
 	 *            the first commit (not included in results)
@@ -1252,7 +1518,7 @@
 	 * Search results require a specified SearchType of AUTHOR, COMMITTER, or
 	 * COMMIT. Results may be paginated using offset and maxCount. If the
 	 * repository does not exist or is empty, an empty list is returned.
-	 * 
+	 *
 	 * @param repository
 	 * @param objectId
 	 *            if unspecified, HEAD is assumed.
@@ -1266,14 +1532,17 @@
 	 */
 	public static List<RevCommit> searchRevlogs(Repository repository, String objectId,
 			String value, final com.gitblit.Constants.SearchType type, int offset, int maxCount) {
-		final String lcValue = value.toLowerCase();
 		List<RevCommit> list = new ArrayList<RevCommit>();
+		if (StringUtils.isEmpty(value)) {
+			return list;
+		}
 		if (maxCount == 0) {
 			return list;
 		}
 		if (!hasCommits(repository)) {
 			return list;
 		}
+		final String lcValue = value.toLowerCase();
 		try {
 			// resolve branch
 			ObjectId branchObject;
@@ -1349,7 +1618,7 @@
 	 * Returns the default branch to use for a repository. Normally returns
 	 * whatever branch HEAD points to, but if HEAD points to nothing it returns
 	 * the most recently updated branch.
-	 * 
+	 *
 	 * @param repository
 	 * @return the objectid of a branch
 	 * @throws Exception
@@ -1390,29 +1659,12 @@
 		String target = null;
 		try {
 			target = repository.getFullBranch();
-			if (!target.startsWith(Constants.R_HEADS)) {
-				// refers to an actual commit, probably a tag
-				// find latest tag that matches the commit, if any
-				List<RefModel> tagModels = getTags(repository, true, -1);
-				if (tagModels.size() > 0) {
-					RefModel tag = null;
-					Date lastDate = new Date(0);
-					for (RefModel tagModel : tagModels) {
-						if (tagModel.getReferencedObjectId().getName().equals(target) &&
-								tagModel.getDate().after(lastDate)) {
-							tag = tagModel;
-							lastDate = tag.getDate();
-						}
-					}
-					target = tag.getName();
-				}
-			}
 		} catch (Throwable t) {
 			error(t, repository, "{0} failed to get symbolic HEAD target");
 		}
 		return target;
 	}
-	
+
 	/**
 	 * Sets the symbolic ref HEAD to the specified target ref. The
 	 * HEAD will be detached if the target ref is not a branch.
@@ -1439,7 +1691,7 @@
 			case FORCED:
 			case NO_CHANGE:
 			case FAST_FORWARD:
-				return true;				
+				return true;
 			default:
 				LOGGER.error(MessageFormat.format("{0} HEAD update to {1} returned result {2}",
 						repository.getDirectory().getAbsolutePath(), targetRef, result));
@@ -1449,7 +1701,7 @@
 		}
 		return false;
 	}
-	
+
 	/**
 	 * Sets the local branch ref to point to the specified commit id.
 	 *
@@ -1460,7 +1712,7 @@
 	 */
 	public static boolean setBranchRef(Repository repository, String branch, String commitId) {
 		String branchName = branch;
-		if (!branchName.startsWith(Constants.R_HEADS)) {
+		if (!branchName.startsWith(Constants.R_REFS)) {
 			branchName = Constants.R_HEADS + branch;
 		}
 
@@ -1474,7 +1726,7 @@
 			case FORCED:
 			case NO_CHANGE:
 			case FAST_FORWARD:
-				return true;				
+				return true;
 			default:
 				LOGGER.error(MessageFormat.format("{0} {1} update to {2} returned result {3}",
 						repository.getDirectory().getAbsolutePath(), branchName, commitId, result));
@@ -1484,22 +1736,18 @@
 		}
 		return false;
 	}
-	
+
 	/**
 	 * Deletes the specified branch ref.
-	 *  
+	 *
 	 * @param repository
 	 * @param branch
 	 * @return true if successful
 	 */
 	public static boolean deleteBranchRef(Repository repository, String branch) {
-		String branchName = branch;
-		if (!branchName.startsWith(Constants.R_HEADS)) {
-			branchName = Constants.R_HEADS + branch;
-		}
 
 		try {
-			RefUpdate refUpdate = repository.updateRef(branchName, false);
+			RefUpdate refUpdate = repository.updateRef(branch, false);
 			refUpdate.setForceUpdate(true);
 			RefUpdate.Result result = refUpdate.delete();
 			switch (result) {
@@ -1507,17 +1755,17 @@
 			case FORCED:
 			case NO_CHANGE:
 			case FAST_FORWARD:
-				return true;				
+				return true;
 			default:
 				LOGGER.error(MessageFormat.format("{0} failed to delete to {1} returned result {2}",
-						repository.getDirectory().getAbsolutePath(), branchName, result));
+						repository.getDirectory().getAbsolutePath(), branch, result));
 			}
 		} catch (Throwable t) {
-			error(t, repository, "{0} failed to delete {1}", branchName);
+			error(t, repository, "{0} failed to delete {1}", branch);
 		}
 		return false;
 	}
-	
+
 	/**
 	 * Get the full branch and tag ref names for any potential HEAD targets.
 	 *
@@ -1538,17 +1786,17 @@
 
 	/**
 	 * Returns all refs grouped by their associated object id.
-	 * 
+	 *
 	 * @param repository
 	 * @return all refs grouped by their referenced object id
 	 */
 	public static Map<ObjectId, List<RefModel>> getAllRefs(Repository repository) {
 		return getAllRefs(repository, true);
 	}
-	
+
 	/**
 	 * Returns all refs grouped by their associated object id.
-	 * 
+	 *
 	 * @param repository
 	 * @param includeRemoteRefs
 	 * @return all refs grouped by their referenced object id
@@ -1572,7 +1820,7 @@
 	/**
 	 * Returns the list of tags in the repository. If repository does not exist
 	 * or is empty, an empty list is returned.
-	 * 
+	 *
 	 * @param repository
 	 * @param fullName
 	 *            if true, /refs/tags/yadayadayada is returned. If false,
@@ -1586,9 +1834,27 @@
 	}
 
 	/**
+	 * Returns the list of tags in the repository. If repository does not exist
+	 * or is empty, an empty list is returned.
+	 *
+	 * @param repository
+	 * @param fullName
+	 *            if true, /refs/tags/yadayadayada is returned. If false,
+	 *            yadayadayada is returned.
+	 * @param maxCount
+	 *            if < 0, all tags are returned
+	 * @param offset
+	 *            if maxCount provided sets the starting point of the records to return
+	 * @return list of tags
+	 */
+	public static List<RefModel> getTags(Repository repository, boolean fullName, int maxCount, int offset) {
+		return getRefs(repository, Constants.R_TAGS, fullName, maxCount, offset);
+	}
+
+	/**
 	 * Returns the list of local branches in the repository. If repository does
 	 * not exist or is empty, an empty list is returned.
-	 * 
+	 *
 	 * @param repository
 	 * @param fullName
 	 *            if true, /refs/heads/yadayadayada is returned. If false,
@@ -1605,7 +1871,7 @@
 	/**
 	 * Returns the list of remote branches in the repository. If repository does
 	 * not exist or is empty, an empty list is returned.
-	 * 
+	 *
 	 * @param repository
 	 * @param fullName
 	 *            if true, /refs/remotes/yadayadayada is returned. If false,
@@ -1622,7 +1888,7 @@
 	/**
 	 * Returns the list of note branches. If repository does not exist or is
 	 * empty, an empty list is returned.
-	 * 
+	 *
 	 * @param repository
 	 * @param fullName
 	 *            if true, /refs/notes/yadayadayada is returned. If false,
@@ -1635,11 +1901,11 @@
 			int maxCount) {
 		return getRefs(repository, Constants.R_NOTES, fullName, maxCount);
 	}
-	
+
 	/**
-	 * Returns the list of refs in the specified base ref. If repository does 
+	 * Returns the list of refs in the specified base ref. If repository does
 	 * not exist or is empty, an empty list is returned.
-	 * 
+	 *
 	 * @param repository
 	 * @param fullName
 	 *            if true, /refs/yadayadayada is returned. If false,
@@ -1653,7 +1919,7 @@
 	/**
 	 * Returns a list of references in the repository matching "refs". If the
 	 * repository is null or empty, an empty list is returned.
-	 * 
+	 *
 	 * @param repository
 	 * @param refs
 	 *            if unspecified, all refs are returned
@@ -1666,6 +1932,27 @@
 	 */
 	private static List<RefModel> getRefs(Repository repository, String refs, boolean fullName,
 			int maxCount) {
+		return getRefs(repository, refs, fullName, maxCount, 0);
+	}
+
+	/**
+	 * Returns a list of references in the repository matching "refs". If the
+	 * repository is null or empty, an empty list is returned.
+	 *
+	 * @param repository
+	 * @param refs
+	 *            if unspecified, all refs are returned
+	 * @param fullName
+	 *            if true, /refs/something/yadayadayada is returned. If false,
+	 *            yadayadayada is returned.
+	 * @param maxCount
+	 *            if < 0, all references are returned
+	 * @param offset
+	 *            if maxCount provided sets the starting point of the records to return
+	 * @return list of references
+	 */
+	private static List<RefModel> getRefs(Repository repository, String refs, boolean fullName,
+			int maxCount, int offset) {
 		List<RefModel> list = new ArrayList<RefModel>();
 		if (maxCount == 0) {
 			return list;
@@ -1689,7 +1976,14 @@
 			Collections.sort(list);
 			Collections.reverse(list);
 			if (maxCount > 0 && list.size() > maxCount) {
-				list = new ArrayList<RefModel>(list.subList(0, maxCount));
+				if (offset < 0) {
+					offset = 0;
+				}
+				int endIndex = offset + maxCount;
+				if (endIndex > list.size()) {
+					endIndex = list.size();
+				}
+				list = new ArrayList<RefModel>(list.subList(offset, endIndex));
 			}
 		} catch (IOException e) {
 			error(e, repository, "{0} failed to retrieve {1}", refs);
@@ -1700,7 +1994,7 @@
 	/**
 	 * Returns a RefModel for the gh-pages branch in the repository. If the
 	 * branch can not be found, null is returned.
-	 * 
+	 *
 	 * @param repository
 	 * @return a refmodel for the gh-pages branch or null
 	 */
@@ -1711,7 +2005,7 @@
 	/**
 	 * Returns a RefModel for a specific branch name in the repository. If the
 	 * branch can not be found, null is returned.
-	 * 
+	 *
 	 * @param repository
 	 * @return a refmodel for the branch or null
 	 */
@@ -1740,10 +2034,10 @@
 		}
 		return branch;
 	}
-		
+
 	/**
 	 * Returns the list of submodules for this repository.
-	 * 
+	 *
 	 * @param repository
 	 * @param commit
 	 * @return list of submodules
@@ -1752,10 +2046,10 @@
 		RevCommit commit = getCommit(repository, commitId);
 		return getSubmodules(repository, commit.getTree());
 	}
-	
+
 	/**
 	 * Returns the list of submodules for this repository.
-	 * 
+	 *
 	 * @param repository
 	 * @param commit
 	 * @return list of submodules
@@ -1778,11 +2072,11 @@
 		}
 		return list;
 	}
-	
+
 	/**
 	 * Returns the submodule definition for the specified path at the specified
 	 * commit.  If no module is defined for the path, null is returned.
-	 * 
+	 *
 	 * @param repository
 	 * @param commit
 	 * @param path
@@ -1796,7 +2090,7 @@
 		}
 		return null;
 	}
-	
+
 	public static String getSubmoduleCommitId(Repository repository, String path, RevCommit commit) {
 		String commitId = null;
 		RevWalk rw = new RevWalk(repository);
@@ -1818,7 +2112,7 @@
 			error(t, repository, "{0} can't find {1} in commit {2}", path, commit.name());
 		} finally {
 			rw.dispose();
-			tw.release();
+			tw.close();
 		}
 		return commitId;
 	}
@@ -1827,7 +2121,7 @@
 	 * Returns the list of notes entered about the commit from the refs/notes
 	 * namespace. If the repository does not exist or is empty, an empty list is
 	 * returned.
-	 * 
+	 *
 	 * @param repository
 	 * @param commit
 	 * @return list of notes
@@ -1851,7 +2145,7 @@
 				list.add(gitNote);
 				continue;
 			}
-			
+
 			// folder structure
 			StringBuilder sb = new StringBuilder(commit.getName());
 			sb.insert(2, '/');
@@ -1871,7 +2165,7 @@
 	/**
 	 * this method creates an incremental revision number as a tag according to
 	 * the amount of already existing tags, which start with a defined prefix.
-	 * 
+	 *
 	 * @param repository
 	 * @param objectId
 	 * @param tagger
@@ -1905,7 +2199,7 @@
 
 	/**
 	 * creates a tag in a repository
-	 * 
+	 *
 	 * @param repository
 	 * @param objectId, the ref the tag points towards
 	 * @param tagger, the person tagging the object
@@ -1914,7 +2208,7 @@
 	 * @return boolean, true if operation was successful, otherwise false
 	 */
 	public static boolean createTag(Repository repository, String objectId, PersonIdent tagger, String tag, String message) {
-		try {			
+		try {
 			Git gitClient = Git.open(repository.getDirectory());
 			TagCommand tagCommand = gitClient.tag();
 			tagCommand.setTagger(tagger);
@@ -1924,17 +2218,17 @@
 				tagCommand.setObjectId(revObj);
 			}
 			tagCommand.setName(tag);
-			Ref call = tagCommand.call();			
+			Ref call = tagCommand.call();
 			return call != null ? true : false;
 		} catch (Exception e) {
 			error(e, repository, "Failed to create tag {1} in repository {0}", objectId, tag);
 		}
 		return false;
 	}
-	
+
 	/**
 	 * Create an orphaned branch in a repository.
-	 * 
+	 *
 	 * @param repository
 	 * @param branchName
 	 * @param author
@@ -1992,20 +2286,20 @@
 						success = false;
 					}
 				} finally {
-					revWalk.release();
+					revWalk.close();
 				}
 			} finally {
-				odi.release();
+				odi.close();
 			}
 		} catch (Throwable t) {
 			error(t, repository, "Failed to create orphan branch {1} in repository {0}", branchName);
 		}
 		return success;
 	}
-	
+
 	/**
 	 * Reads the sparkleshare id, if present, from the repository.
-	 * 
+	 *
 	 * @param repository
 	 * @return an id or null
 	 */
@@ -2016,4 +2310,435 @@
 		}
 		return StringUtils.decodeString(content);
 	}
+
+	/**
+	 * Automatic repair of (some) invalid refspecs.  These are the result of a
+	 * bug in JGit cloning where a double forward-slash was injected.  :(
+	 *
+	 * @param repository
+	 * @return true, if the refspecs were repaired
+	 */
+	public static boolean repairFetchSpecs(Repository repository) {
+		StoredConfig rc = repository.getConfig();
+
+		// auto-repair broken fetch ref specs
+		for (String name : rc.getSubsections("remote")) {
+			int invalidSpecs = 0;
+			int repairedSpecs = 0;
+			List<String> specs = new ArrayList<String>();
+			for (String spec : rc.getStringList("remote", name, "fetch")) {
+				try {
+					RefSpec rs = new RefSpec(spec);
+					// valid spec
+					specs.add(spec);
+				} catch (IllegalArgumentException e) {
+					// invalid spec
+					invalidSpecs++;
+					if (spec.contains("//")) {
+						// auto-repair this known spec bug
+						spec = spec.replace("//", "/");
+						specs.add(spec);
+						repairedSpecs++;
+					}
+				}
+			}
+
+			if (invalidSpecs == repairedSpecs && repairedSpecs > 0) {
+				// the fetch specs were automatically repaired
+				rc.setStringList("remote", name, "fetch", specs);
+				try {
+					rc.save();
+					rc.load();
+					LOGGER.debug("repaired {} invalid fetch refspecs for {}", repairedSpecs, repository.getDirectory());
+					return true;
+				} catch (Exception e) {
+					LOGGER.error(null, e);
+				}
+			} else if (invalidSpecs > 0) {
+				LOGGER.error("mirror executor found {} invalid fetch refspecs for {}", invalidSpecs, repository.getDirectory());
+			}
+		}
+		return false;
+	}
+
+	/**
+	 * Returns true if the commit identified by commitId is an ancestor or the
+	 * the commit identified by tipId.
+	 *
+	 * @param repository
+	 * @param commitId
+	 * @param tipId
+	 * @return true if there is the commit is an ancestor of the tip
+	 */
+	public static boolean isMergedInto(Repository repository, String commitId, String tipId) {
+		try {
+			return isMergedInto(repository, repository.resolve(commitId), repository.resolve(tipId));
+		} catch (Exception e) {
+			LOGGER.error("Failed to determine isMergedInto", e);
+		}
+		return false;
+	}
+
+	/**
+	 * Returns true if the commit identified by commitId is an ancestor or the
+	 * the commit identified by tipId.
+	 *
+	 * @param repository
+	 * @param commitId
+	 * @param tipId
+	 * @return true if there is the commit is an ancestor of the tip
+	 */
+	public static boolean isMergedInto(Repository repository, ObjectId commitId, ObjectId tipCommitId) {
+		// traverse the revlog looking for a commit chain between the endpoints
+		RevWalk rw = new RevWalk(repository);
+		try {
+			// must re-lookup RevCommits to workaround undocumented RevWalk bug
+			RevCommit tip = rw.lookupCommit(tipCommitId);
+			RevCommit commit = rw.lookupCommit(commitId);
+			return rw.isMergedInto(commit, tip);
+		} catch (Exception e) {
+			LOGGER.error("Failed to determine isMergedInto", e);
+		} finally {
+			rw.dispose();
+		}
+		return false;
+	}
+
+	/**
+	 * Returns the merge base of two commits or null if there is no common
+	 * ancestry.
+	 *
+	 * @param repository
+	 * @param commitIdA
+	 * @param commitIdB
+	 * @return the commit id of the merge base or null if there is no common base
+	 */
+	public static String getMergeBase(Repository repository, ObjectId commitIdA, ObjectId commitIdB) {
+		RevWalk rw = new RevWalk(repository);
+		try {
+			RevCommit a = rw.lookupCommit(commitIdA);
+			RevCommit b = rw.lookupCommit(commitIdB);
+
+			rw.setRevFilter(RevFilter.MERGE_BASE);
+			rw.markStart(a);
+			rw.markStart(b);
+			RevCommit mergeBase = rw.next();
+			if (mergeBase == null) {
+				return null;
+			}
+			return mergeBase.getName();
+		} catch (Exception e) {
+			LOGGER.error("Failed to determine merge base", e);
+		} finally {
+			rw.dispose();
+		}
+		return null;
+	}
+
+	public static enum MergeStatus {
+		MISSING_INTEGRATION_BRANCH, MISSING_SRC_BRANCH, NOT_MERGEABLE, FAILED, ALREADY_MERGED, MERGEABLE, MERGED;
+	}
+
+	/**
+	 * Determines if we can cleanly merge one branch into another.  Returns true
+	 * if we can merge without conflict, otherwise returns false.
+	 *
+	 * @param repository
+	 * @param src
+	 * @param toBranch
+	 * @return true if we can merge without conflict
+	 */
+	public static MergeStatus canMerge(Repository repository, String src, String toBranch) {
+		RevWalk revWalk = null;
+		try {
+			revWalk = new RevWalk(repository);
+			ObjectId branchId = repository.resolve(toBranch);
+			if (branchId == null) {
+				return MergeStatus.MISSING_INTEGRATION_BRANCH;
+			}
+			ObjectId srcId = repository.resolve(src);
+			if (srcId == null) {
+				return MergeStatus.MISSING_SRC_BRANCH;
+			}
+			RevCommit branchTip = revWalk.lookupCommit(branchId);
+			RevCommit srcTip = revWalk.lookupCommit(srcId);
+			if (revWalk.isMergedInto(srcTip, branchTip)) {
+				// already merged
+				return MergeStatus.ALREADY_MERGED;
+			} else if (revWalk.isMergedInto(branchTip, srcTip)) {
+				// fast-forward
+				return MergeStatus.MERGEABLE;
+			}
+			RecursiveMerger merger = (RecursiveMerger) MergeStrategy.RECURSIVE.newMerger(repository, true);
+			boolean canMerge = merger.merge(branchTip, srcTip);
+			if (canMerge) {
+				return MergeStatus.MERGEABLE;
+			}
+		} catch (NullPointerException e) {
+			LOGGER.error("Failed to determine canMerge", e);
+		} catch (IOException e) {
+			LOGGER.error("Failed to determine canMerge", e);
+		} finally {
+			if (revWalk != null) {
+				revWalk.close();
+			}
+		}
+		return MergeStatus.NOT_MERGEABLE;
+	}
+
+
+	public static class MergeResult {
+		public final MergeStatus status;
+		public final String sha;
+
+		MergeResult(MergeStatus status, String sha) {
+			this.status = status;
+			this.sha = sha;
+		}
+	}
+
+	/**
+	 * Tries to merge a commit into a branch.  If there are conflicts, the merge
+	 * will fail.
+	 *
+	 * @param repository
+	 * @param src
+	 * @param toBranch
+	 * @param committer
+	 * @param message
+	 * @return the merge result
+	 */
+	public static MergeResult merge(Repository repository, String src, String toBranch,
+			PersonIdent committer, String message) {
+
+		if (!toBranch.startsWith(Constants.R_REFS)) {
+			// branch ref doesn't start with ref, assume this is a branch head
+			toBranch = Constants.R_HEADS + toBranch;
+		}
+
+		RevWalk revWalk = null;
+		try {
+			revWalk = new RevWalk(repository);
+			RevCommit branchTip = revWalk.lookupCommit(repository.resolve(toBranch));
+			RevCommit srcTip = revWalk.lookupCommit(repository.resolve(src));
+			if (revWalk.isMergedInto(srcTip, branchTip)) {
+				// already merged
+				return new MergeResult(MergeStatus.ALREADY_MERGED, null);
+			}
+			RecursiveMerger merger = (RecursiveMerger) MergeStrategy.RECURSIVE.newMerger(repository, true);
+			boolean merged = merger.merge(branchTip, srcTip);
+			if (merged) {
+				// create a merge commit and a reference to track the merge commit
+				ObjectId treeId = merger.getResultTreeId();
+				ObjectInserter odi = repository.newObjectInserter();
+				try {
+					// Create a commit object
+					CommitBuilder commitBuilder = new CommitBuilder();
+					commitBuilder.setCommitter(committer);
+					commitBuilder.setAuthor(committer);
+					commitBuilder.setEncoding(Constants.CHARSET);
+					if (StringUtils.isEmpty(message)) {
+						message = MessageFormat.format("merge {0} into {1}", srcTip.getName(), branchTip.getName());
+					}
+					commitBuilder.setMessage(message);
+					commitBuilder.setParentIds(branchTip.getId(), srcTip.getId());
+					commitBuilder.setTreeId(treeId);
+
+					// Insert the merge commit into the repository
+					ObjectId mergeCommitId = odi.insert(commitBuilder);
+					odi.flush();
+
+					// set the merge ref to the merge commit
+					RevCommit mergeCommit = revWalk.parseCommit(mergeCommitId);
+					RefUpdate mergeRefUpdate = repository.updateRef(toBranch);
+					mergeRefUpdate.setNewObjectId(mergeCommitId);
+					mergeRefUpdate.setRefLogMessage("commit: " + mergeCommit.getShortMessage(), false);
+					RefUpdate.Result rc = mergeRefUpdate.update();
+					switch (rc) {
+					case FAST_FORWARD:
+						// successful, clean merge
+						break;
+					default:
+						throw new GitBlitException(MessageFormat.format("Unexpected result \"{0}\" when merging commit {1} into {2} in {3}",
+								rc.name(), srcTip.getName(), branchTip.getName(), repository.getDirectory()));
+					}
+
+					// return the merge commit id
+					return new MergeResult(MergeStatus.MERGED, mergeCommitId.getName());
+				} finally {
+					odi.close();
+				}
+			}
+		} catch (IOException e) {
+			LOGGER.error("Failed to merge", e);
+		} finally {
+			if (revWalk != null) {
+				revWalk.close();
+			}
+		}
+		return new MergeResult(MergeStatus.FAILED, null);
+	}
+	
+	
+	/**
+	 * Returns the LFS URL for the given oid 
+	 * Currently assumes that the Gitblit Filestore is used 
+	 *
+	 * @param baseURL
+	 * @param repository name
+	 * @param oid of lfs item
+	 * @return the lfs item URL
+	 */
+	public static String getLfsRepositoryUrl(String baseURL, String repositoryName, String oid) {
+		
+		if (baseURL.length() > 0 && baseURL.charAt(baseURL.length() - 1) == '/') {
+			baseURL = baseURL.substring(0, baseURL.length() - 1);
+		}
+		
+		return baseURL + com.gitblit.Constants.R_PATH 
+					   + repositoryName + "/" 
+					   + com.gitblit.Constants.R_LFS 
+					   + "objects/" + oid;
+		
+	}
+	
+	/**
+	 * Returns all tree entries that do not match the ignore paths.
+	 *
+	 * @param db
+	 * @param ignorePaths
+	 * @param dcBuilder
+	 * @throws IOException
+	 */
+	public static List<DirCacheEntry> getTreeEntries(Repository db, String branch, Collection<String> ignorePaths) throws IOException {
+		List<DirCacheEntry> list = new ArrayList<DirCacheEntry>();
+		TreeWalk tw = null;
+		try {
+			ObjectId treeId = db.resolve(branch + "^{tree}");
+			if (treeId == null) {
+				// branch does not exist yet
+				return list;
+			}
+			tw = new TreeWalk(db);
+			int hIdx = tw.addTree(treeId);
+			tw.setRecursive(true);
+
+			while (tw.next()) {
+				String path = tw.getPathString();
+				CanonicalTreeParser hTree = null;
+				if (hIdx != -1) {
+					hTree = tw.getTree(hIdx, CanonicalTreeParser.class);
+				}
+				if (!ignorePaths.contains(path)) {
+					// add all other tree entries
+					if (hTree != null) {
+						final DirCacheEntry entry = new DirCacheEntry(path);
+						entry.setObjectId(hTree.getEntryObjectId());
+						entry.setFileMode(hTree.getEntryFileMode());
+						list.add(entry);
+					}
+				}
+			}
+		} finally {
+			if (tw != null) {
+				tw.close();
+			}
+		}
+		return list;
+	}
+	
+	public static boolean commitIndex(Repository db, String branch, DirCache index,
+									  ObjectId parentId, boolean forceCommit,
+									  String author, String authorEmail, String message) throws IOException, ConcurrentRefUpdateException {
+		boolean success = false;
+
+		ObjectId headId = db.resolve(branch + "^{commit}");
+		ObjectId baseId = parentId;
+		if (baseId == null || headId == null) { return false; }
+		
+		ObjectInserter odi = db.newObjectInserter();
+		try {
+			// Create the in-memory index of the new/updated ticket
+			ObjectId indexTreeId = index.writeTree(odi);
+
+			// Create a commit object
+			PersonIdent ident = new PersonIdent(author, authorEmail);
+			
+			if (forceCommit == false) {
+				ThreeWayMerger merger = MergeStrategy.RECURSIVE.newMerger(db, true);
+				merger.setObjectInserter(odi);
+				merger.setBase(baseId);
+				boolean mergeSuccess = merger.merge(indexTreeId, headId);
+				
+				if (mergeSuccess) {
+					indexTreeId = merger.getResultTreeId();
+				 } else {
+					//Manual merge required
+					return false; 
+				 }
+			}
+			
+			CommitBuilder commit = new CommitBuilder();
+			commit.setAuthor(ident);
+			commit.setCommitter(ident);
+			commit.setEncoding(com.gitblit.Constants.ENCODING);
+			commit.setMessage(message);
+			commit.setParentId(headId);
+			commit.setTreeId(indexTreeId);
+
+			// Insert the commit into the repository
+			ObjectId commitId = odi.insert(commit);
+			odi.flush();
+
+			RevWalk revWalk = new RevWalk(db);
+			try {
+				RevCommit revCommit = revWalk.parseCommit(commitId);
+				RefUpdate ru = db.updateRef(branch);
+				ru.setForceUpdate(forceCommit);
+				ru.setNewObjectId(commitId);
+				ru.setExpectedOldObjectId(headId);
+				ru.setRefLogMessage("commit: " + revCommit.getShortMessage(), false);
+				Result rc = ru.update();
+
+				switch (rc) {
+				case NEW:
+				case FORCED:
+				case FAST_FORWARD:
+					success = true;
+					break;
+				case REJECTED:
+				case LOCK_FAILURE:
+					throw new ConcurrentRefUpdateException(JGitText.get().couldNotLockHEAD,
+							ru.getRef(), rc);
+				default:
+					throw new JGitInternalException(MessageFormat.format(
+							JGitText.get().updatingRefFailed, branch, commitId.toString(),
+							rc));
+				}
+			} finally {
+				revWalk.close();
+			}
+		} finally {
+			odi.close();
+		}
+		return success;
+	}
+	
+	/**
+	 * Returns true if the commit identified by commitId is at the tip of it's branch.
+	 *
+	 * @param repository
+	 * @param commitId
+	 * @return true if the given commit is the tip
+	 */
+	public static boolean isTip(Repository repository, String commitId) {
+		try {
+			RefModel tip = getBranch(repository, commitId);
+			return (tip != null);	
+		} catch (Exception e) {
+			LOGGER.error("Failed to determine isTip", e);
+		}
+		return false;
+	}
+
 }

--
Gitblit v1.9.1