githubFork/gitblit.git - Solinfo Gitblit

			@@ -1,3458 +1,72 @@
			/*
			* Copyright 2011 gitblit.com.
			*
			* Licensed under the Apache License, Version 2.0 (the "License");
			* you may not use this file except in compliance with the License.
			* You may obtain a copy of the License at
			*
			* http://www.apache.org/licenses/LICENSE-2.0
			*
			* Unless required by applicable law or agreed to in writing, software
			* distributed under the License is distributed on an "AS IS" BASIS,
			* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
			* See the License for the specific language governing permissions and
			* limitations under the License.
			*/
			package com.gitblit;

			import java.io.BufferedReader;
			import java.io.File;
			import java.io.FileFilter;
			import java.io.IOException;
			import java.io.InputStream;
			import java.io.InputStreamReader;
			import java.lang.reflect.Field;
			import java.net.URI;
			import java.net.URISyntaxException;
			import java.nio.charset.Charset;
			import java.security.Principal;
			import java.text.MessageFormat;
			import java.text.SimpleDateFormat;
			import java.util.ArrayList;
			import java.util.Arrays;
			import java.util.Calendar;
			import java.util.Collection;
			import java.util.Collections;
			import java.util.Date;
			import java.util.HashMap;
			import java.util.HashSet;
			import java.util.LinkedHashMap;
			import java.util.LinkedHashSet;
			import java.util.List;
			import java.util.Map;
			import java.util.Map.Entry;
			import java.util.Set;
			import java.util.TimeZone;
			import java.util.TreeMap;
			import java.util.TreeSet;
			import java.util.concurrent.ConcurrentHashMap;
			import java.util.concurrent.Executors;
			import java.util.concurrent.ScheduledExecutorService;
			import java.util.concurrent.TimeUnit;
			import java.util.concurrent.atomic.AtomicInteger;
			import java.util.concurrent.atomic.AtomicReference;

			import javax.mail.Message;
			import javax.mail.MessagingException;
			import javax.mail.internet.MimeBodyPart;
			import javax.mail.internet.MimeMultipart;
			import javax.servlet.ServletContext;
			import javax.servlet.ServletContextEvent;
			import javax.servlet.ServletContextListener;
			import javax.servlet.http.Cookie;
			import javax.servlet.http.HttpServletRequest;

			import org.apache.wicket.RequestCycle;
			import org.apache.wicket.protocol.http.WebResponse;
			import org.apache.wicket.resource.ContextRelativeResource;
			import org.apache.wicket.util.resource.ResourceStreamNotFoundException;
			import org.eclipse.jgit.lib.Repository;
			import org.eclipse.jgit.lib.RepositoryCache;
			import org.eclipse.jgit.lib.RepositoryCache.FileKey;
			import org.eclipse.jgit.lib.StoredConfig;
			import org.eclipse.jgit.storage.file.FileBasedConfig;
			import org.eclipse.jgit.storage.file.WindowCache;
			import org.eclipse.jgit.storage.file.WindowCacheConfig;
			import org.eclipse.jgit.util.FS;
			import org.eclipse.jgit.util.FileUtils;
			import org.slf4j.Logger;
			import org.slf4j.LoggerFactory;

			import com.gitblit.Constants.AccessPermission;
			import com.gitblit.Constants.AccessRestrictionType;
			import com.gitblit.Constants.AuthenticationType;
			import com.gitblit.Constants.AuthorizationControl;
			import com.gitblit.Constants.FederationRequest;
			import com.gitblit.Constants.FederationStrategy;
			import com.gitblit.Constants.FederationToken;
			import com.gitblit.Constants.PermissionType;
			import com.gitblit.Constants.RegistrantType;
			import com.gitblit.fanout.FanoutNioService;
			import com.gitblit.fanout.FanoutService;
			import com.gitblit.fanout.FanoutSocketService;
			import com.gitblit.git.GitDaemon;
			import com.gitblit.models.FederationModel;
			import com.gitblit.models.FederationProposal;
			import com.gitblit.models.FederationSet;
			import com.gitblit.models.ForkModel;
			import com.gitblit.models.Metric;
			import com.gitblit.models.ProjectModel;
			import com.gitblit.models.RegistrantAccessPermission;
			import com.gitblit.models.RepositoryModel;
			import com.gitblit.models.SearchResult;
			import com.gitblit.models.ServerSettings;
			import com.gitblit.models.ServerStatus;
			import com.gitblit.models.SettingModel;
			import com.gitblit.models.TeamModel;
			import com.gitblit.models.UserModel;
			import com.gitblit.utils.ArrayUtils;
			import com.gitblit.utils.Base64;
			import com.gitblit.utils.ByteFormat;
			import com.gitblit.utils.ContainerUtils;
			import com.gitblit.utils.DeepCopier;
			import com.gitblit.utils.FederationUtils;
			import com.gitblit.utils.HttpUtils;
			import com.gitblit.utils.JGitUtils;
			import com.gitblit.utils.JsonUtils;
			import com.gitblit.utils.MetricUtils;
			import com.gitblit.utils.ObjectCache;
			import com.gitblit.utils.StringUtils;
			import com.gitblit.utils.TimeUtils;
			import com.gitblit.utils.X509Utils.X509Metadata;
			import com.gitblit.wicket.GitBlitWebSession;
			import com.gitblit.wicket.WicketUtils;

			/**
			* GitBlit is the servlet context listener singleton that acts as the core for
			* the web ui and the servlets. This class is either directly instantiated by
			* the GitBlitServer class (Gitblit GO) or is reflectively instantiated from the
			* definition in the web.xml file (Gitblit WAR).
			*
			* This class is the central logic processor for Gitblit. All settings, user
			* object, and repository object operations pass through this class.
			*
			* Repository Resolution. There are two pathways for finding repositories. One
			* pathway, for web ui display and repository authentication & authorization, is
			* within this class. The other pathway is through the standard GitServlet.
			*
			* @author James Moger
			*
			*/
			public class GitBlit implements ServletContextListener {

			private static GitBlit gitblit;

			private final Logger logger = LoggerFactory.getLogger(GitBlit.class);

			private final ScheduledExecutorService scheduledExecutor = Executors.newScheduledThreadPool(5);

			private final List<FederationModel> federationRegistrations = Collections
			.synchronizedList(new ArrayList<FederationModel>());

			private final Map<String, FederationModel> federationPullResults = new ConcurrentHashMap<String, FederationModel>();

			private final ObjectCache<Long> repositorySizeCache = new ObjectCache<Long>();

			private final ObjectCache<List<Metric>> repositoryMetricsCache = new ObjectCache<List<Metric>>();

			private final Map<String, RepositoryModel> repositoryListCache = new ConcurrentHashMap<String, RepositoryModel>();

			private final Map<String, ProjectModel> projectCache = new ConcurrentHashMap<String, ProjectModel>();

			private final AtomicReference<String> repositoryListSettingsChecksum = new AtomicReference<String>("");

			private final ObjectCache<String> projectMarkdownCache = new ObjectCache<String>();

			private final ObjectCache<String> projectRepositoriesMarkdownCache = new ObjectCache<String>();

			private ServletContext servletContext;

			private File baseFolder;

			private File repositoriesFolder;

			private IUserService userService;

			private IStoredSettings settings;

			private ServerSettings settingsModel;

			private ServerStatus serverStatus;

			private MailExecutor mailExecutor;

			private LuceneExecutor luceneExecutor;

			private GCExecutor gcExecutor;

			private TimeZone timezone;

			private FileBasedConfig projectConfigs;

			private FanoutService fanoutService;

			private GitDaemon gitDaemon;

			public GitBlit() {
			if (gitblit == null) {
			// set the static singleton reference
			gitblit = this;
			}
			}

			public GitBlit(final IUserService userService) {
			this.userService = userService;
			gitblit = this;
			}

			/**
			* Returns the Gitblit singleton.
			*
			* @return gitblit singleton
			*/
			public static GitBlit self() {
			if (gitblit == null) {
			new GitBlit();
			}
			return gitblit;
			}

			/**
			* Determine if this is the GO variant of Gitblit.
			*
			* @return true if this is the GO variant of Gitblit.
			*/
			public static boolean isGO() {
			return self().settings instanceof FileSettings;
			}

			/**
			* Returns the preferred timezone for the Gitblit instance.
			*
			* @return a timezone
			*/
			public static TimeZone getTimezone() {
			if (self().timezone == null) {
			String tzid = getString("web.timezone", null);
			if (StringUtils.isEmpty(tzid)) {
			self().timezone = TimeZone.getDefault();
			return self().timezone;
			}
			self().timezone = TimeZone.getTimeZone(tzid);
			}
			return self().timezone;
			}

			/**
			* Returns the user-defined blob encodings.
			*
			* @return an array of encodings, may be empty
			*/
			public static String [] getEncodings() {
			return getStrings(Keys.web.blobEncodings).toArray(new String[0]);
			}


			/**
			* Returns the boolean value for the specified key. If the key does not
			* exist or the value for the key can not be interpreted as a boolean, the
			* defaultValue is returned.
			*
			* @see IStoredSettings.getBoolean(String, boolean)
			* @param key
			* @param defaultValue
			* @return key value or defaultValue
			*/
			public static boolean getBoolean(String key, boolean defaultValue) {
			return self().settings.getBoolean(key, defaultValue);
			}

			/**
			* Returns the integer value for the specified key. If the key does not
			* exist or the value for the key can not be interpreted as an integer, the
			* defaultValue is returned.
			*
			* @see IStoredSettings.getInteger(String key, int defaultValue)
			* @param key
			* @param defaultValue
			* @return key value or defaultValue
			*/
			public static int getInteger(String key, int defaultValue) {
			return self().settings.getInteger(key, defaultValue);
			}

			/**
			* Returns the value in bytes for the specified key. If the key does not
			* exist or the value for the key can not be interpreted as an integer, the
			* defaultValue is returned.
			*
			* @see IStoredSettings.getFilesize(String key, int defaultValue)
			* @param key
			* @param defaultValue
			* @return key value or defaultValue
			*/
			public static int getFilesize(String key, int defaultValue) {
			return self().settings.getFilesize(key, defaultValue);
			}

			/**
			* Returns the value in bytes for the specified key. If the key does not
			* exist or the value for the key can not be interpreted as a long, the
			* defaultValue is returned.
			*
			* @see IStoredSettings.getFilesize(String key, long defaultValue)
			* @param key
			* @param defaultValue
			* @return key value or defaultValue
			*/
			public static long getFilesize(String key, long defaultValue) {
			return self().settings.getFilesize(key, defaultValue);
			}

			/**
			* Returns the char value for the specified key. If the key does not exist
			* or the value for the key can not be interpreted as a character, the
			* defaultValue is returned.
			*
			* @see IStoredSettings.getChar(String key, char defaultValue)
			* @param key
			* @param defaultValue
			* @return key value or defaultValue
			*/
			public static char getChar(String key, char defaultValue) {
			return self().settings.getChar(key, defaultValue);
			}

			/**
			* Returns the string value for the specified key. If the key does not exist
			* or the value for the key can not be interpreted as a string, the
			* defaultValue is returned.
			*
			* @see IStoredSettings.getString(String key, String defaultValue)
			* @param key
			* @param defaultValue
			* @return key value or defaultValue
			*/
			public static String getString(String key, String defaultValue) {
			return self().settings.getString(key, defaultValue);
			}

			/**
			* Returns a list of space-separated strings from the specified key.
			*
			* @see IStoredSettings.getStrings(String key)
			* @param name
			* @return list of strings
			*/
			public static List<String> getStrings(String key) {
			return self().settings.getStrings(key);
			}

			/**
			* Returns a map of space-separated key-value pairs from the specified key.
			*
			* @see IStoredSettings.getStrings(String key)
			* @param name
			* @return map of string, string
			*/
			public static Map<String, String> getMap(String key) {
			return self().settings.getMap(key);
			}

			/**
			* Returns the list of keys whose name starts with the specified prefix. If
			* the prefix is null or empty, all key names are returned.
			*
			* @see IStoredSettings.getAllKeys(String key)
			* @param startingWith
			* @return list of keys
			*/

			public static List<String> getAllKeys(String startingWith) {
			return self().settings.getAllKeys(startingWith);
			}

			/**
			* Is Gitblit running in debug mode?
			*
			* @return true if Gitblit is running in debug mode
			*/
			public static boolean isDebugMode() {
			return self().settings.getBoolean(Keys.web.debugMode, false);
			}

			/**
			* Returns the file object for the specified configuration key.
			*
			* @return the file
			*/
			public static File getFileOrFolder(String key, String defaultFileOrFolder) {
			String fileOrFolder = GitBlit.getString(key, defaultFileOrFolder);
			return getFileOrFolder(fileOrFolder);
			}

			/**
			* Returns the file object which may have it's base-path determined by
			* environment variables for running on a cloud hosting service. All Gitblit
			* file or folder retrievals are (at least initially) funneled through this
			* method so it is the correct point to globally override/alter filesystem
			* access based on environment or some other indicator.
			*
			* @return the file
			*/
			public static File getFileOrFolder(String fileOrFolder) {
			return com.gitblit.utils.FileUtils.resolveParameter(Constants.baseFolder$,
			self().baseFolder, fileOrFolder);
			}

			/**
			* Returns the path of the repositories folder. This method checks to see if
			* Gitblit is running on a cloud service and may return an adjusted path.
			*
			* @return the repositories folder path
			*/
			public static File getRepositoriesFolder() {
			return getFileOrFolder(Keys.git.repositoriesFolder, "${baseFolder}/git");
			}

			/**
			* Returns the path of the proposals folder. This method checks to see if
			* Gitblit is running on a cloud service and may return an adjusted path.
			*
			* @return the proposals folder path
			*/
			public static File getProposalsFolder() {
			return getFileOrFolder(Keys.federation.proposalsFolder, "${baseFolder}/proposals");
			}

			/**
			* Returns the path of the Groovy folder. This method checks to see if
			* Gitblit is running on a cloud service and may return an adjusted path.
			*
			* @return the Groovy scripts folder path
			*/
			public static File getGroovyScriptsFolder() {
			return getFileOrFolder(Keys.groovy.scriptsFolder, "${baseFolder}/groovy");
			}

			/**
			* Updates the list of server settings.
			*
			* @param settings
			* @return true if the update succeeded
			*/
			public boolean updateSettings(Map<String, String> updatedSettings) {
			return settings.saveSettings(updatedSettings);
			}

			public ServerStatus getStatus() {
			// update heap memory status
			serverStatus.heapAllocated = Runtime.getRuntime().totalMemory();
			serverStatus.heapFree = Runtime.getRuntime().freeMemory();
			return serverStatus;
			}

			/**
			* Returns the list of non-Gitblit clone urls. This allows Gitblit to
			* advertise alternative urls for Git client repository access.
			*
			* @param repositoryName
			* @param userName
			* @return list of non-gitblit clone urls
			*/
			public List<String> getOtherCloneUrls(String repositoryName, String username) {
			List<String> cloneUrls = new ArrayList<String>();
			for (String url : settings.getStrings(Keys.web.otherUrls)) {
			cloneUrls.add(MessageFormat.format(url, repositoryName, username));
			}
			return cloneUrls;
			}

			/**
			* Set the user service. The user service authenticates all users and is
			* responsible for managing user permissions.
			*
			* @param userService
			*/
			public void setUserService(IUserService userService) {
			logger.info("Setting up user service " + userService.toString());
			this.userService = userService;
			this.userService.setup(settings);
			}

			public boolean supportsAddUser() {
			return supportsCredentialChanges(new UserModel(""));
			}

			/**
			* Returns true if the user's credentials can be changed.
			*
			* @param user
			* @return true if the user service supports credential changes
			*/
			public boolean supportsCredentialChanges(UserModel user) {
			return (user != null && user.isLocalAccount()) \|\| userService.supportsCredentialChanges();
			}

			/**
			* Returns true if the user's display name can be changed.
			*
			* @param user
			* @return true if the user service supports display name changes
			*/
			public boolean supportsDisplayNameChanges(UserModel user) {
			return (user != null && user.isLocalAccount()) \|\| userService.supportsDisplayNameChanges();
			}

			/**
			* Returns true if the user's email address can be changed.
			*
			* @param user
			* @return true if the user service supports email address changes
			*/
			public boolean supportsEmailAddressChanges(UserModel user) {
			return (user != null && user.isLocalAccount()) \|\| userService.supportsEmailAddressChanges();
			}

			/**
			* Returns true if the user's team memberships can be changed.
			*
			* @param user
			* @return true if the user service supports team membership changes
			*/
			public boolean supportsTeamMembershipChanges(UserModel user) {
			return (user != null && user.isLocalAccount()) \|\| userService.supportsTeamMembershipChanges();
			}

			/**
			* Authenticate a user based on a username and password.
			*
			* @see IUserService.authenticate(String, char[])
			* @param username
			* @param password
			* @return a user object or null
			*/
			public UserModel authenticate(String username, char[] password) {
			if (StringUtils.isEmpty(username)) {
			// can not authenticate empty username
			return null;
			}
			String pw = new String(password);
			if (StringUtils.isEmpty(pw)) {
			// can not authenticate empty password
			return null;
			}

			// check to see if this is the federation user
			if (canFederate()) {
			if (username.equalsIgnoreCase(Constants.FEDERATION_USER)) {
			List<String> tokens = getFederationTokens();
			if (tokens.contains(pw)) {
			// the federation user is an administrator
			UserModel federationUser = new UserModel(Constants.FEDERATION_USER);
			federationUser.canAdmin = true;
			return federationUser;
			}
			}
			}

			// delegate authentication to the user service
			if (userService == null) {
			return null;
			}
			return userService.authenticate(username, password);
			}

			/**
			* Authenticate a user based on their cookie.
			*
			* @param cookies
			* @return a user object or null
			*/
			protected UserModel authenticate(Cookie[] cookies) {
			if (userService == null) {
			return null;
			}
			if (userService.supportsCookies()) {
			if (cookies != null && cookies.length > 0) {
			for (Cookie cookie : cookies) {
			if (cookie.getName().equals(Constants.NAME)) {
			String value = cookie.getValue();
			return userService.authenticate(value.toCharArray());
			}
			}
			}
			}
			return null;
			}

			/**
			* Authenticate a user based on HTTP request parameters.
			*
			* Authentication by X509Certificate is tried first and then by cookie.
			*
			* @param httpRequest
			* @return a user object or null
			*/
			public UserModel authenticate(HttpServletRequest httpRequest) {
			return authenticate(httpRequest, false);
			}

			/**
			* Authenticate a user based on HTTP request parameters.
			*
			* Authentication by X509Certificate, servlet container principal, cookie,
			* and BASIC header.
			*
			* @param httpRequest
			* @param requiresCertificate
			* @return a user object or null
			*/
			public UserModel authenticate(HttpServletRequest httpRequest, boolean requiresCertificate) {
			// try to authenticate by certificate
			boolean checkValidity = settings.getBoolean(Keys.git.enforceCertificateValidity, true);
			String [] oids = getStrings(Keys.git.certificateUsernameOIDs).toArray(new String[0]);
			UserModel model = HttpUtils.getUserModelFromCertificate(httpRequest, checkValidity, oids);
			if (model != null) {
			// grab real user model and preserve certificate serial number
			UserModel user = getUserModel(model.username);
			X509Metadata metadata = HttpUtils.getCertificateMetadata(httpRequest);
			if (user != null) {
			flagWicketSession(AuthenticationType.CERTIFICATE);
			logger.debug(MessageFormat.format("{0} authenticated by client certificate {1} from {2}",
			user.username, metadata.serialNumber, httpRequest.getRemoteAddr()));
			return user;
			} else {
			logger.warn(MessageFormat.format("Failed to find UserModel for {0}, attempted client certificate ({1}) authentication from {2}",
			model.username, metadata.serialNumber, httpRequest.getRemoteAddr()));
			}
			}

			if (requiresCertificate) {
			// caller requires client certificate authentication (e.g. git servlet)
			return null;
			}

			// try to authenticate by servlet container principal
			Principal principal = httpRequest.getUserPrincipal();
			if (principal != null) {
			String username = principal.getName();
			if (StringUtils.isEmpty(username)) {
			UserModel user = getUserModel(username);
			if (user != null) {
			flagWicketSession(AuthenticationType.CONTAINER);
			logger.debug(MessageFormat.format("{0} authenticated by servlet container principal from {1}",
			user.username, httpRequest.getRemoteAddr()));
			return user;
			} else {
			logger.warn(MessageFormat.format("Failed to find UserModel for {0}, attempted servlet container authentication from {1}",
			principal.getName(), httpRequest.getRemoteAddr()));
			}
			}
			}

			// try to authenticate by cookie
			if (allowCookieAuthentication()) {
			UserModel user = authenticate(httpRequest.getCookies());
			if (user != null) {
			flagWicketSession(AuthenticationType.COOKIE);
			logger.debug(MessageFormat.format("{0} authenticated by cookie from {1}",
			user.username, httpRequest.getRemoteAddr()));
			return user;
			}
			}

			// try to authenticate by BASIC
			final String authorization = httpRequest.getHeader("Authorization");
			if (authorization != null && authorization.startsWith("Basic")) {
			// Authorization: Basic base64credentials
			String base64Credentials = authorization.substring("Basic".length()).trim();
			String credentials = new String(Base64.decode(base64Credentials),
			Charset.forName("UTF-8"));
			// credentials = username:password
			final String[] values = credentials.split(":",2);

			if (values.length == 2) {
			String username = values[0];
			char[] password = values[1].toCharArray();
			UserModel user = authenticate(username, password);
			if (user != null) {
			flagWicketSession(AuthenticationType.CREDENTIALS);
			logger.debug(MessageFormat.format("{0} authenticated by BASIC request header from {1}",
			user.username, httpRequest.getRemoteAddr()));
			return user;
			} else {
			logger.warn(MessageFormat.format("Failed login attempt for {0}, invalid credentials ({1}) from {2}",
			username, credentials, httpRequest.getRemoteAddr()));
			}
			}
			}
			return null;
			}

			protected void flagWicketSession(AuthenticationType authenticationType) {
			RequestCycle requestCycle = RequestCycle.get();
			if (requestCycle != null) {
			// flag the Wicket session, if this is a Wicket request
			GitBlitWebSession session = GitBlitWebSession.get();
			session.authenticationType = authenticationType;
			}
			}

			/**
			* Open a file resource using the Servlet container.
			* @param file to open
			* @return InputStream of the opened file
			* @throws ResourceStreamNotFoundException
			*/
			public InputStream getResourceAsStream(String file) throws ResourceStreamNotFoundException {
			ContextRelativeResource res = WicketUtils.getResource(file);
			return res.getResourceStream().getInputStream();
			}

			/**
			* Sets a cookie for the specified user.
			*
			* @param response
			* @param user
			*/
			public void setCookie(WebResponse response, UserModel user) {
			if (userService == null) {
			return;
			}
			if (userService.supportsCookies()) {
			Cookie userCookie;
			if (user == null) {
			// clear cookie for logout
			userCookie = new Cookie(Constants.NAME, "");
			} else {
			// set cookie for login
			String cookie = userService.getCookie(user);
			if (StringUtils.isEmpty(cookie)) {
			// create empty cookie
			userCookie = new Cookie(Constants.NAME, "");
			} else {
			// create real cookie
			userCookie = new Cookie(Constants.NAME, cookie);
			userCookie.setMaxAge(Integer.MAX_VALUE);
			}
			}
			userCookie.setPath("/");
			response.addCookie(userCookie);
			}
			}

			/**
			* Logout a user.
			*
			* @param user
			*/
			public void logout(UserModel user) {
			if (userService == null) {
			return;
			}
			userService.logout(user);
			}

			/**
			* Returns the list of all users available to the login service.
			*
			* @see IUserService.getAllUsernames()
			* @return list of all usernames
			*/
			public List<String> getAllUsernames() {
			List<String> names = new ArrayList<String>(userService.getAllUsernames());
			return names;
			}

			/**
			* Returns the list of all users available to the login service.
			*
			* @see IUserService.getAllUsernames()
			* @return list of all usernames
			*/
			public List<UserModel> getAllUsers() {
			List<UserModel> users = userService.getAllUsers();
			return users;
			}

			/**
			* Delete the user object with the specified username
			*
			* @see IUserService.deleteUser(String)
			* @param username
			* @return true if successful
			*/
			public boolean deleteUser(String username) {
			if (StringUtils.isEmpty(username)) {
			return false;
			}
			return userService.deleteUser(username);
			}

			/**
			* Retrieve the user object for the specified username.
			*
			* @see IUserService.getUserModel(String)
			* @param username
			* @return a user object or null
			*/
			public UserModel getUserModel(String username) {
			if (StringUtils.isEmpty(username)) {
			return null;
			}
			UserModel user = userService.getUserModel(username);
			return user;
			}

			/**
			* Returns the effective list of permissions for this user, taking into account
			* team memberships, ownerships.
			*
			* @param user
			* @return the effective list of permissions for the user
			*/
			public List<RegistrantAccessPermission> getUserAccessPermissions(UserModel user) {
			if (StringUtils.isEmpty(user.username)) {
			// new user
			return new ArrayList<RegistrantAccessPermission>();
			}
			Set<RegistrantAccessPermission> set = new LinkedHashSet<RegistrantAccessPermission>();
			set.addAll(user.getRepositoryPermissions());
			// Flag missing repositories
			for (RegistrantAccessPermission permission : set) {
			if (permission.mutable && PermissionType.EXPLICIT.equals(permission.permissionType)) {
			RepositoryModel rm = GitBlit.self().getRepositoryModel(permission.registrant);
			if (rm == null) {
			permission.permissionType = PermissionType.MISSING;
			permission.mutable = false;
			continue;
			}
			}
			}

			// TODO reconsider ownership as a user property
			// manually specify personal repository ownerships
			for (RepositoryModel rm : repositoryListCache.values()) {
			if (rm.isUsersPersonalRepository(user.username) \|\| rm.isOwner(user.username)) {
			RegistrantAccessPermission rp = new RegistrantAccessPermission(rm.name, AccessPermission.REWIND,
			PermissionType.OWNER, RegistrantType.REPOSITORY, null, false);
			// user may be owner of a repository to which they've inherited
			// a team permission, replace any existing perm with owner perm
			set.remove(rp);
			set.add(rp);
			}
			}

			List<RegistrantAccessPermission> list = new ArrayList<RegistrantAccessPermission>(set);
			Collections.sort(list);
			return list;
			}

			/**
			* Returns the list of users and their access permissions for the specified
			* repository including permission source information such as the team or
			* regular expression which sets the permission.
			*
			* @param repository
			* @return a list of RegistrantAccessPermissions
			*/
			public List<RegistrantAccessPermission> getUserAccessPermissions(RepositoryModel repository) {
			List<RegistrantAccessPermission> list = new ArrayList<RegistrantAccessPermission>();
			if (AccessRestrictionType.NONE.equals(repository.accessRestriction)) {
			// no permissions needed, REWIND for everyone!
			return list;
			}
			if (AuthorizationControl.AUTHENTICATED.equals(repository.authorizationControl)) {
			// no permissions needed, REWIND for authenticated!
			return list;
			}
			// NAMED users and teams
			for (UserModel user : userService.getAllUsers()) {
			RegistrantAccessPermission ap = user.getRepositoryPermission(repository);
			if (ap.permission.exceeds(AccessPermission.NONE)) {
			list.add(ap);
			}
			}
			return list;
			}

			/**
			* Sets the access permissions to the specified repository for the specified users.
			*
			* @param repository
			* @param permissions
			* @return true if the user models have been updated
			*/
			public boolean setUserAccessPermissions(RepositoryModel repository, Collection<RegistrantAccessPermission> permissions) {
			List<UserModel> users = new ArrayList<UserModel>();
			for (RegistrantAccessPermission up : permissions) {
			if (up.mutable) {
			// only set editable defined permissions
			UserModel user = userService.getUserModel(up.registrant);
			user.setRepositoryPermission(repository.name, up.permission);
			users.add(user);
			}
			}
			return userService.updateUserModels(users);
			}

			/**
			* Returns the list of all users who have an explicit access permission
			* for the specified repository.
			*
			* @see IUserService.getUsernamesForRepositoryRole(String)
			* @param repository
			* @return list of all usernames that have an access permission for the repository
			*/
			public List<String> getRepositoryUsers(RepositoryModel repository) {
			return userService.getUsernamesForRepositoryRole(repository.name);
			}

			/**
			* Sets the list of all uses who are allowed to bypass the access
			* restriction placed on the specified repository.
			*
			* @see IUserService.setUsernamesForRepositoryRole(String, List<String>)
			* @param repository
			* @param usernames
			* @return true if successful
			*/
			@Deprecated
			public boolean setRepositoryUsers(RepositoryModel repository, List<String> repositoryUsers) {
			// rejects all changes since 1.2.0 because this would elevate
			// all discrete access permissions to RW+
			return false;
			}

			/**
			* Adds/updates a complete user object keyed by username. This method allows
			* for renaming a user.
			*
			* @see IUserService.updateUserModel(String, UserModel)
			* @param username
			* @param user
			* @param isCreate
			* @throws GitBlitException
			*/
			public void updateUserModel(String username, UserModel user, boolean isCreate)
			throws GitBlitException {
			if (!username.equalsIgnoreCase(user.username)) {
			if (userService.getUserModel(user.username) != null) {
			throw new GitBlitException(MessageFormat.format(
			"Failed to rename ''{0}'' because ''{1}'' already exists.", username,
			user.username));
			}

			// rename repositories and owner fields for all repositories
			for (RepositoryModel model : getRepositoryModels(user)) {
			if (model.isUsersPersonalRepository(username)) {
			// personal repository
			model.addOwner(user.username);
			String oldRepositoryName = model.name;
			model.name = "~" + user.username + model.name.substring(model.projectPath.length());
			model.projectPath = "~" + user.username;
			updateRepositoryModel(oldRepositoryName, model, false);
			} else if (model.isOwner(username)) {
			// common/shared repo
			model.addOwner(user.username);
			updateRepositoryModel(model.name, model, false);
			}
			}
			}
			if (!userService.updateUserModel(username, user)) {
			throw new GitBlitException(isCreate ? "Failed to add user!" : "Failed to update user!");
			}
			}

			/**
			* Returns the list of available teams that a user or repository may be
			* assigned to.
			*
			* @return the list of teams
			*/
			public List<String> getAllTeamnames() {
			List<String> teams = new ArrayList<String>(userService.getAllTeamNames());
			return teams;
			}

			/**
			* Returns the list of available teams that a user or repository may be
			* assigned to.
			*
			* @return the list of teams
			*/
			public List<TeamModel> getAllTeams() {
			List<TeamModel> teams = userService.getAllTeams();
			return teams;
			}

			/**
			* Returns the TeamModel object for the specified name.
			*
			* @param teamname
			* @return a TeamModel object or null
			*/
			public TeamModel getTeamModel(String teamname) {
			return userService.getTeamModel(teamname);
			}

			/**
			* Returns the list of teams and their access permissions for the specified
			* repository including the source of the permission such as the admin flag
			* or a regular expression.
			*
			* @param repository
			* @return a list of RegistrantAccessPermissions
			*/
			public List<RegistrantAccessPermission> getTeamAccessPermissions(RepositoryModel repository) {
			List<RegistrantAccessPermission> list = new ArrayList<RegistrantAccessPermission>();
			for (TeamModel team : userService.getAllTeams()) {
			RegistrantAccessPermission ap = team.getRepositoryPermission(repository);
			if (ap.permission.exceeds(AccessPermission.NONE)) {
			list.add(ap);
			}
			}
			Collections.sort(list);
			return list;
			}

			/**
			* Sets the access permissions to the specified repository for the specified teams.
			*
			* @param repository
			* @param permissions
			* @return true if the team models have been updated
			*/
			public boolean setTeamAccessPermissions(RepositoryModel repository, Collection<RegistrantAccessPermission> permissions) {
			List<TeamModel> teams = new ArrayList<TeamModel>();
			for (RegistrantAccessPermission tp : permissions) {
			if (tp.mutable) {
			// only set explicitly defined access permissions
			TeamModel team = userService.getTeamModel(tp.registrant);
			team.setRepositoryPermission(repository.name, tp.permission);
			teams.add(team);
			}
			}
			return userService.updateTeamModels(teams);
			}

			/**
			* Returns the list of all teams who have an explicit access permission for
			* the specified repository.
			*
			* @see IUserService.getTeamnamesForRepositoryRole(String)
			* @param repository
			* @return list of all teamnames with explicit access permissions to the repository
			*/
			public List<String> getRepositoryTeams(RepositoryModel repository) {
			return userService.getTeamnamesForRepositoryRole(repository.name);
			}

			/**
			* Sets the list of all uses who are allowed to bypass the access
			* restriction placed on the specified repository.
			*
			* @see IUserService.setTeamnamesForRepositoryRole(String, List<String>)
			* @param repository
			* @param teamnames
			* @return true if successful
			*/
			@Deprecated
			public boolean setRepositoryTeams(RepositoryModel repository, List<String> repositoryTeams) {
			// rejects all changes since 1.2.0 because this would elevate
			// all discrete access permissions to RW+
			return false;
			}

			/**
			* Updates the TeamModel object for the specified name.
			*
			* @param teamname
			* @param team
			* @param isCreate
			*/
			public void updateTeamModel(String teamname, TeamModel team, boolean isCreate)
			throws GitBlitException {
			if (!teamname.equalsIgnoreCase(team.name)) {
			if (userService.getTeamModel(team.name) != null) {
			throw new GitBlitException(MessageFormat.format(
			"Failed to rename ''{0}'' because ''{1}'' already exists.", teamname,
			team.name));
			}
			}
			if (!userService.updateTeamModel(teamname, team)) {
			throw new GitBlitException(isCreate ? "Failed to add team!" : "Failed to update team!");
			}
			}

			/**
			* Delete the team object with the specified teamname
			*
			* @see IUserService.deleteTeam(String)
			* @param teamname
			* @return true if successful
			*/
			public boolean deleteTeam(String teamname) {
			return userService.deleteTeam(teamname);
			}

			/**
			* Adds the repository to the list of cached repositories if Gitblit is
			* configured to cache the repository list.
			*
			* @param model
			*/
			private void addToCachedRepositoryList(RepositoryModel model) {
			if (settings.getBoolean(Keys.git.cacheRepositoryList, true)) {
			repositoryListCache.put(model.name.toLowerCase(), model);

			// update the fork origin repository with this repository clone
			if (!StringUtils.isEmpty(model.originRepository)) {
			if (repositoryListCache.containsKey(model.originRepository)) {
			RepositoryModel origin = repositoryListCache.get(model.originRepository);
			origin.addFork(model.name);
			}
			}
			}
			}

			/**
			* Removes the repository from the list of cached repositories.
			*
			* @param name
			* @return the model being removed
			*/
			private RepositoryModel removeFromCachedRepositoryList(String name) {
			if (StringUtils.isEmpty(name)) {
			return null;
			}
			return repositoryListCache.remove(name.toLowerCase());
			}

			/**
			* Clears all the cached metadata for the specified repository.
			*
			* @param repositoryName
			*/
			private void clearRepositoryMetadataCache(String repositoryName) {
			repositorySizeCache.remove(repositoryName);
			repositoryMetricsCache.remove(repositoryName);
			}

			/**
			* Resets the repository list cache.
			*
			*/
			public void resetRepositoryListCache() {
			logger.info("Repository cache manually reset");
			repositoryListCache.clear();
			}

			/**
			* Calculate the checksum of settings that affect the repository list cache.
			* @return a checksum
			*/
			private String getRepositoryListSettingsChecksum() {
			StringBuilder ns = new StringBuilder();
			ns.append(settings.getString(Keys.git.cacheRepositoryList, "")).append('\n');
			ns.append(settings.getString(Keys.git.onlyAccessBareRepositories, "")).append('\n');
			ns.append(settings.getString(Keys.git.searchRepositoriesSubfolders, "")).append('\n');
			ns.append(settings.getString(Keys.git.searchRecursionDepth, "")).append('\n');
			ns.append(settings.getString(Keys.git.searchExclusions, "")).append('\n');
			String checksum = StringUtils.getSHA1(ns.toString());
			return checksum;
			}

			/**
			* Compare the last repository list setting checksum to the current checksum.
			* If different then clear the cache so that it may be rebuilt.
			*
			* @return true if the cached repository list is valid since the last check
			*/
			private boolean isValidRepositoryList() {
			String newChecksum = getRepositoryListSettingsChecksum();
			boolean valid = newChecksum.equals(repositoryListSettingsChecksum.get());
			repositoryListSettingsChecksum.set(newChecksum);
			if (!valid && settings.getBoolean(Keys.git.cacheRepositoryList, true)) {
			logger.info("Repository list settings have changed. Clearing repository list cache.");
			repositoryListCache.clear();
			}
			return valid;
			}

			/**
			* Returns the list of all repositories available to Gitblit. This method
			* does not consider user access permissions.
			*
			* @return list of all repositories
			*/
			public List<String> getRepositoryList() {
			if (repositoryListCache.size() == 0 \|\| !isValidRepositoryList()) {
			// we are not caching OR we have not yet cached OR the cached list is invalid
			long startTime = System.currentTimeMillis();
			List<String> repositories = JGitUtils.getRepositoryList(repositoriesFolder,
			settings.getBoolean(Keys.git.onlyAccessBareRepositories, false),
			settings.getBoolean(Keys.git.searchRepositoriesSubfolders, true),
			settings.getInteger(Keys.git.searchRecursionDepth, -1),
			settings.getStrings(Keys.git.searchExclusions));

			if (!settings.getBoolean(Keys.git.cacheRepositoryList, true)) {
			// we are not caching
			StringUtils.sortRepositorynames(repositories);
			return repositories;
			} else {
			// we are caching this list
			String msg = "{0} repositories identified in {1} msecs";

			// optionally (re)calculate repository sizes
			if (getBoolean(Keys.web.showRepositorySizes, true)) {
			msg = "{0} repositories identified with calculated folder sizes in {1} msecs";
			for (String repository : repositories) {
			RepositoryModel model = getRepositoryModel(repository);
			if (!model.skipSizeCalculation) {
			calculateSize(model);
			}
			}
			} else {
			// update cache
			for (String repository : repositories) {
			getRepositoryModel(repository);
			}
			}

			// rebuild fork networks
			for (RepositoryModel model : repositoryListCache.values()) {
			if (!StringUtils.isEmpty(model.originRepository)) {
			if (repositoryListCache.containsKey(model.originRepository)) {
			RepositoryModel origin = repositoryListCache.get(model.originRepository);
			origin.addFork(model.name);
			}
			}
			}

			long duration = System.currentTimeMillis() - startTime;
			logger.info(MessageFormat.format(msg, repositoryListCache.size(), duration));
			}
			}

			// return sorted copy of cached list
			List<String> list = new ArrayList<String>(repositoryListCache.keySet());
			StringUtils.sortRepositorynames(list);
			return list;
			}

			/**
			* Returns the JGit repository for the specified name.
			*
			* @param repositoryName
			* @return repository or null
			*/
			public Repository getRepository(String repositoryName) {
			return getRepository(repositoryName, true);
			}

			/**
			* Returns the JGit repository for the specified name.
			*
			* @param repositoryName
			* @param logError
			* @return repository or null
			*/
			public Repository getRepository(String repositoryName, boolean logError) {
			if (isCollectingGarbage(repositoryName)) {
			logger.warn(MessageFormat.format("Rejecting request for {0}, busy collecting garbage!", repositoryName));
			return null;
			}

			File dir = FileKey.resolve(new File(repositoriesFolder, repositoryName), FS.DETECTED);
			if (dir == null)
			return null;

			Repository r = null;
			try {
			FileKey key = FileKey.exact(dir, FS.DETECTED);
			r = RepositoryCache.open(key, true);
			} catch (IOException e) {
			if (logError) {
			logger.error("GitBlit.getRepository(String) failed to find "
			+ new File(repositoriesFolder, repositoryName).getAbsolutePath());
			}
			}
			return r;
			}

			/**
			* Returns the list of repository models that are accessible to the user.
			*
			* @param user
			* @return list of repository models accessible to user
			*/
			public List<RepositoryModel> getRepositoryModels(UserModel user) {
			long methodStart = System.currentTimeMillis();
			List<String> list = getRepositoryList();
			List<RepositoryModel> repositories = new ArrayList<RepositoryModel>();
			for (String repo : list) {
			RepositoryModel model = getRepositoryModel(user, repo);
			if (model != null) {
			repositories.add(model);
			}
			}
			if (getBoolean(Keys.web.showRepositorySizes, true)) {
			int repoCount = 0;
			long startTime = System.currentTimeMillis();
			ByteFormat byteFormat = new ByteFormat();
			for (RepositoryModel model : repositories) {
			if (!model.skipSizeCalculation) {
			repoCount++;
			model.size = byteFormat.format(calculateSize(model));
			}
			}
			long duration = System.currentTimeMillis() - startTime;
			if (duration > 250) {
			// only log calcualtion time if > 250 msecs
			logger.info(MessageFormat.format("{0} repository sizes calculated in {1} msecs",
			repoCount, duration));
			}
			}
			long duration = System.currentTimeMillis() - methodStart;
			logger.info(MessageFormat.format("{0} repository models loaded for {1} in {2} msecs",
			repositories.size(), user == null ? "anonymous" : user.username, duration));
			return repositories;
			}

			/**
			* Returns a repository model if the repository exists and the user may
			* access the repository.
			*
			* @param user
			* @param repositoryName
			* @return repository model or null
			*/
			public RepositoryModel getRepositoryModel(UserModel user, String repositoryName) {
			RepositoryModel model = getRepositoryModel(repositoryName);
			if (model == null) {
			return null;
			}
			if (user == null) {
			user = UserModel.ANONYMOUS;
			}
			if (user.canView(model)) {
			return model;
			}
			return null;
			}

			/**
			* Returns the repository model for the specified repository. This method
			* does not consider user access permissions.
			*
			* @param repositoryName
			* @return repository model or null
			*/
			public RepositoryModel getRepositoryModel(String repositoryName) {
			if (!repositoryListCache.containsKey(repositoryName)) {
			RepositoryModel model = loadRepositoryModel(repositoryName);
			if (model == null) {
			return null;
			}
			addToCachedRepositoryList(model);
			return model;
			}

			// cached model
			RepositoryModel model = repositoryListCache.get(repositoryName.toLowerCase());

			if (gcExecutor.isCollectingGarbage(model.name)) {
			// Gitblit is busy collecting garbage, use our cached model
			RepositoryModel rm = DeepCopier.copy(model);
			rm.isCollectingGarbage = true;
			return rm;
			}

			// check for updates
			Repository r = getRepository(model.name);
			if (r == null) {
			// repository is missing
			removeFromCachedRepositoryList(repositoryName);
			logger.error(MessageFormat.format("Repository \"{0}\" is missing! Removing from cache.", repositoryName));
			return null;
			}

			FileBasedConfig config = (FileBasedConfig) getRepositoryConfig(r);
			if (config.isOutdated()) {
			// reload model
			logger.debug(MessageFormat.format("Config for \"{0}\" has changed. Reloading model and updating cache.", repositoryName));
			model = loadRepositoryModel(model.name);
			removeFromCachedRepositoryList(model.name);
			addToCachedRepositoryList(model);
			} else {
			// update a few repository parameters
			if (!model.hasCommits) {
			// update hasCommits, assume a repository only gains commits :)
			model.hasCommits = JGitUtils.hasCommits(r);
			}

			model.lastChange = JGitUtils.getLastChange(r);
			}
			r.close();

			// return a copy of the cached model
			return DeepCopier.copy(model);
			}


			/**
			* Returns the map of project config. This map is cached and reloaded if
			* the underlying projects.conf file changes.
			*
			* @return project config map
			*/
			private Map<String, ProjectModel> getProjectConfigs() {
			if (projectCache.isEmpty() \|\| projectConfigs.isOutdated()) {

			try {
			projectConfigs.load();
			} catch (Exception e) {
			}

			// project configs
			String rootName = GitBlit.getString(Keys.web.repositoryRootGroupName, "main");
			ProjectModel rootProject = new ProjectModel(rootName, true);

			Map<String, ProjectModel> configs = new HashMap<String, ProjectModel>();
			// cache the root project under its alias and an empty path
			configs.put("", rootProject);
			configs.put(rootProject.name.toLowerCase(), rootProject);

			for (String name : projectConfigs.getSubsections("project")) {
			ProjectModel project;
			if (name.equalsIgnoreCase(rootName)) {
			project = rootProject;
			} else {
			project = new ProjectModel(name);
			}
			project.title = projectConfigs.getString("project", name, "title");
			project.description = projectConfigs.getString("project", name, "description");

			// project markdown
			File pmkd = new File(getRepositoriesFolder(), (project.isRoot ? "" : name) + "/project.mkd");
			if (pmkd.exists()) {
			Date lm = new Date(pmkd.lastModified());
			if (!projectMarkdownCache.hasCurrent(name, lm)) {
			String mkd = com.gitblit.utils.FileUtils.readContent(pmkd, "\n");
			projectMarkdownCache.updateObject(name, lm, mkd);
			}
			project.projectMarkdown = projectMarkdownCache.getObject(name);
			}

			// project repositories markdown
			File rmkd = new File(getRepositoriesFolder(), (project.isRoot ? "" : name) + "/repositories.mkd");
			if (rmkd.exists()) {
			Date lm = new Date(rmkd.lastModified());
			if (!projectRepositoriesMarkdownCache.hasCurrent(name, lm)) {
			String mkd = com.gitblit.utils.FileUtils.readContent(rmkd, "\n");
			projectRepositoriesMarkdownCache.updateObject(name, lm, mkd);
			}
			project.repositoriesMarkdown = projectRepositoriesMarkdownCache.getObject(name);
			}

			configs.put(name.toLowerCase(), project);
			}
			projectCache.clear();
			projectCache.putAll(configs);
			}
			return projectCache;
			}

			/**
			* Returns a list of project models for the user.
			*
			* @param user
			* @param includeUsers
			* @return list of projects that are accessible to the user
			*/
			public List<ProjectModel> getProjectModels(UserModel user, boolean includeUsers) {
			Map<String, ProjectModel> configs = getProjectConfigs();

			// per-user project lists, this accounts for security and visibility
			Map<String, ProjectModel> map = new TreeMap<String, ProjectModel>();
			// root project
			map.put("", configs.get(""));

			for (RepositoryModel model : getRepositoryModels(user)) {
			String rootPath = StringUtils.getRootPath(model.name).toLowerCase();
			if (!map.containsKey(rootPath)) {
			ProjectModel project;
			if (configs.containsKey(rootPath)) {
			// clone the project model because it's repository list will
			// be tailored for the requesting user
			project = DeepCopier.copy(configs.get(rootPath));
			} else {
			project = new ProjectModel(rootPath);
			}
			map.put(rootPath, project);
			}
			map.get(rootPath).addRepository(model);
			}

			// sort projects, root project first
			List<ProjectModel> projects;
			if (includeUsers) {
			// all projects
			projects = new ArrayList<ProjectModel>(map.values());
			Collections.sort(projects);
			projects.remove(map.get(""));
			projects.add(0, map.get(""));
			} else {
			// all non-user projects
			projects = new ArrayList<ProjectModel>();
			ProjectModel root = map.remove("");
			for (ProjectModel model : map.values()) {
			if (!model.isUserProject()) {
			projects.add(model);
			}
			}
			Collections.sort(projects);
			projects.add(0, root);
			}
			return projects;
			}

			/**
			* Returns the project model for the specified user.
			*
			* @param name
			* @param user
			* @return a project model, or null if it does not exist
			*/
			public ProjectModel getProjectModel(String name, UserModel user) {
			for (ProjectModel project : getProjectModels(user, true)) {
			if (project.name.equalsIgnoreCase(name)) {
			return project;
			}
			}
			return null;
			}

			/**
			* Returns a project model for the Gitblit/system user.
			*
			* @param name a project name
			* @return a project model or null if the project does not exist
			*/
			public ProjectModel getProjectModel(String name) {
			Map<String, ProjectModel> configs = getProjectConfigs();
			ProjectModel project = configs.get(name.toLowerCase());
			if (project == null) {
			project = new ProjectModel(name);
			if (name.length() > 0 && name.charAt(0) == '~') {
			UserModel user = getUserModel(name.substring(1));
			if (user != null) {
			project.title = user.getDisplayName();
			project.description = "personal repositories";
			}
			}
			} else {
			// clone the object
			project = DeepCopier.copy(project);
			}
			if (StringUtils.isEmpty(name)) {
			// get root repositories
			for (String repository : getRepositoryList()) {
			if (repository.indexOf('/') == -1) {
			project.addRepository(repository);
			}
			}
			} else {
			// get repositories in subfolder
			String folder = name.toLowerCase() + "/";
			for (String repository : getRepositoryList()) {
			if (repository.toLowerCase().startsWith(folder)) {
			project.addRepository(repository);
			}
			}
			}
			if (project.repositories.size() == 0) {
			// no repositories == no project
			return null;
			}
			return project;
			}

			/**
			* Returns the list of project models that are referenced by the supplied
			* repository model list. This is an alternative method exists to ensure
			* Gitblit does not call getRepositoryModels(UserModel) twice in a request.
			*
			* @param repositoryModels
			* @param includeUsers
			* @return a list of project models
			*/
			public List<ProjectModel> getProjectModels(List<RepositoryModel> repositoryModels, boolean includeUsers) {
			Map<String, ProjectModel> projects = new LinkedHashMap<String, ProjectModel>();
			for (RepositoryModel repository : repositoryModels) {
			if (!includeUsers && repository.isPersonalRepository()) {
			// exclude personal repositories
			continue;
			}
			if (!projects.containsKey(repository.projectPath)) {
			ProjectModel project = getProjectModel(repository.projectPath);
			if (project == null) {
			logger.warn(MessageFormat.format("excluding project \"{0}\" from project list because it is empty!",
			repository.projectPath));
			continue;
			}
			projects.put(repository.projectPath, project);
			// clear the repo list in the project because that is the system
			// list, not the user-accessible list and start building the
			// user-accessible list
			project.repositories.clear();
			project.repositories.add(repository.name);
			project.lastChange = repository.lastChange;
			} else {
			// update the user-accessible list
			// this is used for repository count
			ProjectModel project = projects.get(repository.projectPath);
			project.repositories.add(repository.name);
			if (project.lastChange.before(repository.lastChange)) {
			project.lastChange = repository.lastChange;
			}
			}
			}
			return new ArrayList<ProjectModel>(projects.values());
			}

			/**
			* Workaround JGit. I need to access the raw config object directly in order
			* to see if the config is dirty so that I can reload a repository model.
			* If I use the stock JGit method to get the config it already reloads the
			* config. If the config changes are made within Gitblit this is fine as
			* the returned config will still be flagged as dirty. BUT... if the config
			* is manipulated outside Gitblit then it fails to recognize this as dirty.
			*
			* @param r
			* @return a config
			*/
			private StoredConfig getRepositoryConfig(Repository r) {
			try {
			Field f = r.getClass().getDeclaredField("repoConfig");
			f.setAccessible(true);
			StoredConfig config = (StoredConfig) f.get(r);
			return config;
			} catch (Exception e) {
			logger.error("Failed to retrieve \"repoConfig\" via reflection", e);
			}
			return r.getConfig();
			}

			/**
			* Create a repository model from the configuration and repository data.
			*
			* @param repositoryName
			* @return a repositoryModel or null if the repository does not exist
			*/
			private RepositoryModel loadRepositoryModel(String repositoryName) {
			Repository r = getRepository(repositoryName);
			if (r == null) {
			return null;
			}
			RepositoryModel model = new RepositoryModel();
			model.isBare = r.isBare();
			File basePath = getFileOrFolder(Keys.git.repositoriesFolder, "${baseFolder}/git");
			if (model.isBare) {
			model.name = com.gitblit.utils.FileUtils.getRelativePath(basePath, r.getDirectory());
			} else {
			model.name = com.gitblit.utils.FileUtils.getRelativePath(basePath, r.getDirectory().getParentFile());
			}
			if (StringUtils.isEmpty(model.name)) {
			// Repository is NOT located relative to the base folder because it
			// is symlinked. Use the provided repository name.
			model.name = repositoryName;
			}
			model.hasCommits = JGitUtils.hasCommits(r);
			model.lastChange = JGitUtils.getLastChange(r);
			model.projectPath = StringUtils.getFirstPathElement(repositoryName);

			StoredConfig config = r.getConfig();
			boolean hasOrigin = !StringUtils.isEmpty(config.getString("remote", "origin", "url"));

			if (config != null) {
			model.description = getConfig(config, "description", "");
			model.addOwners(ArrayUtils.fromString(getConfig(config, "owner", "")));
			model.useTickets = getConfig(config, "useTickets", false);
			model.useDocs = getConfig(config, "useDocs", false);
			model.useIncrementalPushTags = getConfig(config, "useIncrementalPushTags", false);
			model.incrementalPushTagPrefix = getConfig(config, "incrementalPushTagPrefix", null);
			model.allowForks = getConfig(config, "allowForks", true);
			model.accessRestriction = AccessRestrictionType.fromName(getConfig(config,
			"accessRestriction", settings.getString(Keys.git.defaultAccessRestriction, null)));
			model.authorizationControl = AuthorizationControl.fromName(getConfig(config,
			"authorizationControl", settings.getString(Keys.git.defaultAuthorizationControl, null)));
			model.verifyCommitter = getConfig(config, "verifyCommitter", false);
			model.showRemoteBranches = getConfig(config, "showRemoteBranches", hasOrigin);
			model.isFrozen = getConfig(config, "isFrozen", false);
			model.showReadme = getConfig(config, "showReadme", false);
			model.skipSizeCalculation = getConfig(config, "skipSizeCalculation", false);
			model.skipSummaryMetrics = getConfig(config, "skipSummaryMetrics", false);
			model.federationStrategy = FederationStrategy.fromName(getConfig(config,
			"federationStrategy", null));
			model.federationSets = new ArrayList<String>(Arrays.asList(config.getStringList(
			Constants.CONFIG_GITBLIT, null, "federationSets")));
			model.isFederated = getConfig(config, "isFederated", false);
			model.gcThreshold = getConfig(config, "gcThreshold", settings.getString(Keys.git.defaultGarbageCollectionThreshold, "500KB"));
			model.gcPeriod = getConfig(config, "gcPeriod", settings.getInteger(Keys.git.defaultGarbageCollectionPeriod, 7));
			try {
			model.lastGC = new SimpleDateFormat(Constants.ISO8601).parse(getConfig(config, "lastGC", "1970-01-01'T'00:00:00Z"));
			} catch (Exception e) {
			model.lastGC = new Date(0);
			}
			model.maxActivityCommits = getConfig(config, "maxActivityCommits", settings.getInteger(Keys.web.maxActivityCommits, 0));
			model.origin = config.getString("remote", "origin", "url");
			if (model.origin != null) {
			model.origin = model.origin.replace('\\', '/');
			}
			model.preReceiveScripts = new ArrayList<String>(Arrays.asList(config.getStringList(
			Constants.CONFIG_GITBLIT, null, "preReceiveScript")));
			model.postReceiveScripts = new ArrayList<String>(Arrays.asList(config.getStringList(
			Constants.CONFIG_GITBLIT, null, "postReceiveScript")));
			model.mailingLists = new ArrayList<String>(Arrays.asList(config.getStringList(
			Constants.CONFIG_GITBLIT, null, "mailingList")));
			model.indexedBranches = new ArrayList<String>(Arrays.asList(config.getStringList(
			Constants.CONFIG_GITBLIT, null, "indexBranch")));

			// Custom defined properties
			model.customFields = new LinkedHashMap<String, String>();
			for (String aProperty : config.getNames(Constants.CONFIG_GITBLIT, Constants.CONFIG_CUSTOM_FIELDS)) {
			model.customFields.put(aProperty, config.getString(Constants.CONFIG_GITBLIT, Constants.CONFIG_CUSTOM_FIELDS, aProperty));
			}
			}
			model.HEAD = JGitUtils.getHEADRef(r);
			model.availableRefs = JGitUtils.getAvailableHeadTargets(r);
			model.sparkleshareId = JGitUtils.getSparkleshareId(r);
			r.close();

			if (model.origin != null && model.origin.startsWith("file://")) {
			// repository was cloned locally... perhaps as a fork
			try {
			File folder = new File(new URI(model.origin));
			String originRepo = com.gitblit.utils.FileUtils.getRelativePath(getRepositoriesFolder(), folder);
			if (!StringUtils.isEmpty(originRepo)) {
			// ensure origin still exists
			File repoFolder = new File(getRepositoriesFolder(), originRepo);
			if (repoFolder.exists()) {
			model.originRepository = originRepo.toLowerCase();
			}
			}
			} catch (URISyntaxException e) {
			logger.error("Failed to determine fork for " + model, e);
			}
			}
			return model;
			}

			/**
			* Determines if this server has the requested repository.
			*
			* @param name
			* @return true if the repository exists
			*/
			public boolean hasRepository(String repositoryName) {
			return hasRepository(repositoryName, false);
			}

			/**
			* Determines if this server has the requested repository.
			*
			* @param name
			* @param caseInsensitive
			* @return true if the repository exists
			*/
			public boolean hasRepository(String repositoryName, boolean caseSensitiveCheck) {
			if (!caseSensitiveCheck && settings.getBoolean(Keys.git.cacheRepositoryList, true)) {
			// if we are caching use the cache to determine availability
			// otherwise we end up adding a phantom repository to the cache
			return repositoryListCache.containsKey(repositoryName.toLowerCase());
			}
			Repository r = getRepository(repositoryName, false);
			if (r == null) {
			return false;
			}
			r.close();
			return true;
			}

			/**
			* Determines if the specified user has a fork of the specified origin
			* repository.
			*
			* @param username
			* @param origin
			* @return true the if the user has a fork
			*/
			public boolean hasFork(String username, String origin) {
			return getFork(username, origin) != null;
			}

			/**
			* Gets the name of a user's fork of the specified origin
			* repository.
			*
			* @param username
			* @param origin
			* @return the name of the user's fork, null otherwise
			*/
			public String getFork(String username, String origin) {
			String userProject = "~" + username.toLowerCase();
			if (settings.getBoolean(Keys.git.cacheRepositoryList, true)) {
			String userPath = userProject + "/";

			// collect all origin nodes in fork network
			Set<String> roots = new HashSet<String>();
			roots.add(origin);
			RepositoryModel originModel = repositoryListCache.get(origin);
			while (originModel != null) {
			if (!ArrayUtils.isEmpty(originModel.forks)) {
			for (String fork : originModel.forks) {
			if (!fork.startsWith(userPath)) {
			roots.add(fork);
			}
			}
			}

			if (originModel.originRepository != null) {
			roots.add(originModel.originRepository);
			originModel = repositoryListCache.get(originModel.originRepository);
			} else {
			// break
			originModel = null;
			}
			}

			for (String repository : repositoryListCache.keySet()) {
			if (repository.startsWith(userPath)) {
			RepositoryModel model = repositoryListCache.get(repository);
			if (!StringUtils.isEmpty(model.originRepository)) {
			if (roots.contains(model.originRepository)) {
			// user has a fork in this graph
			return model.name;
			}
			}
			}
			}
			} else {
			// not caching
			ProjectModel project = getProjectModel(userProject);
			if (project == null) {
			return null;
			}
			for (String repository : project.repositories) {
			if (repository.startsWith(userProject)) {
			RepositoryModel model = getRepositoryModel(repository);
			if (model.originRepository.equalsIgnoreCase(origin)) {
			// user has a fork
			return model.name;
			}
			}
			}
			}
			// user does not have a fork
			return null;
			}

			/**
			* Returns the fork network for a repository by traversing up the fork graph
			* to discover the root and then down through all children of the root node.
			*
			* @param repository
			* @return a ForkModel
			*/
			public ForkModel getForkNetwork(String repository) {
			if (settings.getBoolean(Keys.git.cacheRepositoryList, true)) {
			// find the root, cached
			RepositoryModel model = repositoryListCache.get(repository.toLowerCase());
			while (model.originRepository != null) {
			model = repositoryListCache.get(model.originRepository);
			}
			ForkModel root = getForkModelFromCache(model.name);
			return root;
			} else {
			// find the root, non-cached
			RepositoryModel model = getRepositoryModel(repository.toLowerCase());
			while (model.originRepository != null) {
			model = getRepositoryModel(model.originRepository);
			}
			ForkModel root = getForkModel(model.name);
			return root;
			}
			}

			private ForkModel getForkModelFromCache(String repository) {
			RepositoryModel model = repositoryListCache.get(repository.toLowerCase());
			if (model == null) {
			return null;
			}
			ForkModel fork = new ForkModel(model);
			if (!ArrayUtils.isEmpty(model.forks)) {
			for (String aFork : model.forks) {
			ForkModel fm = getForkModelFromCache(aFork);
			if (fm != null) {
			fork.forks.add(fm);
			}
			}
			}
			return fork;
			}

			private ForkModel getForkModel(String repository) {
			RepositoryModel model = getRepositoryModel(repository.toLowerCase());
			if (model == null) {
			return null;
			}
			ForkModel fork = new ForkModel(model);
			if (!ArrayUtils.isEmpty(model.forks)) {
			for (String aFork : model.forks) {
			ForkModel fm = getForkModel(aFork);
			if (fm != null) {
			fork.forks.add(fm);
			}
			}
			}
			return fork;
			}

			/**
			* Returns the size in bytes of the repository. Gitblit caches the
			* repository sizes to reduce the performance penalty of recursive
			* calculation. The cache is updated if the repository has been changed
			* since the last calculation.
			*
			* @param model
			* @return size in bytes
			*/
			public long calculateSize(RepositoryModel model) {
			if (repositorySizeCache.hasCurrent(model.name, model.lastChange)) {
			return repositorySizeCache.getObject(model.name);
			}
			File gitDir = FileKey.resolve(new File(repositoriesFolder, model.name), FS.DETECTED);
			long size = com.gitblit.utils.FileUtils.folderSize(gitDir);
			repositorySizeCache.updateObject(model.name, model.lastChange, size);
			return size;
			}

			/**
			* Ensure that a cached repository is completely closed and its resources
			* are properly released.
			*
			* @param repositoryName
			*/
			private void closeRepository(String repositoryName) {
			Repository repository = getRepository(repositoryName);
			if (repository == null) {
			return;
			}
			RepositoryCache.close(repository);

			// assume 2 uses in case reflection fails
			int uses = 2;
			try {
			// The FileResolver caches repositories which is very useful
			// for performance until you want to delete a repository.
			// I have to use reflection to call close() the correct
			// number of times to ensure that the object and ref databases
			// are properly closed before I can delete the repository from
			// the filesystem.
			Field useCnt = Repository.class.getDeclaredField("useCnt");
			useCnt.setAccessible(true);
			uses = ((AtomicInteger) useCnt.get(repository)).get();
			} catch (Exception e) {
			logger.warn(MessageFormat
			.format("Failed to reflectively determine use count for repository {0}",
			repositoryName), e);
			}
			if (uses > 0) {
			logger.info(MessageFormat
			.format("{0}.useCnt={1}, calling close() {2} time(s) to close object and ref databases",
			repositoryName, uses, uses));
			for (int i = 0; i < uses; i++) {
			repository.close();
			}
			}

			// close any open index writer/searcher in the Lucene executor
			luceneExecutor.close(repositoryName);
			}

			/**
			* Returns the metrics for the default branch of the specified repository.
			* This method builds a metrics cache. The cache is updated if the
			* repository is updated. A new copy of the metrics list is returned on each
			* call so that modifications to the list are non-destructive.
			*
			* @param model
			* @param repository
			* @return a new array list of metrics
			*/
			public List<Metric> getRepositoryDefaultMetrics(RepositoryModel model, Repository repository) {
			if (repositoryMetricsCache.hasCurrent(model.name, model.lastChange)) {
			return new ArrayList<Metric>(repositoryMetricsCache.getObject(model.name));
			}
			List<Metric> metrics = MetricUtils.getDateMetrics(repository, null, true, null, getTimezone());
			repositoryMetricsCache.updateObject(model.name, model.lastChange, metrics);
			return new ArrayList<Metric>(metrics);
			}

			/**
			* Returns the gitblit string value for the specified key. If key is not
			* set, returns defaultValue.
			*
			* @param config
			* @param field
			* @param defaultValue
			* @return field value or defaultValue
			*/
			private String getConfig(StoredConfig config, String field, String defaultValue) {
			String value = config.getString(Constants.CONFIG_GITBLIT, null, field);
			if (StringUtils.isEmpty(value)) {
			return defaultValue;
			}
			return value;
			}

			/**
			* Returns the gitblit boolean value for the specified key. If key is not
			* set, returns defaultValue.
			*
			* @param config
			* @param field
			* @param defaultValue
			* @return field value or defaultValue
			*/
			private boolean getConfig(StoredConfig config, String field, boolean defaultValue) {
			return config.getBoolean(Constants.CONFIG_GITBLIT, field, defaultValue);
			}

			/**
			* Returns the gitblit string value for the specified key. If key is not
			* set, returns defaultValue.
			*
			* @param config
			* @param field
			* @param defaultValue
			* @return field value or defaultValue
			*/
			private int getConfig(StoredConfig config, String field, int defaultValue) {
			String value = config.getString(Constants.CONFIG_GITBLIT, null, field);
			if (StringUtils.isEmpty(value)) {
			return defaultValue;
			}
			try {
			return Integer.parseInt(value);
			} catch (Exception e) {
			}
			return defaultValue;
			}

			/**
			* Creates/updates the repository model keyed by reopsitoryName. Saves all
			* repository settings in .git/config. This method allows for renaming
			* repositories and will update user access permissions accordingly.
			*
			* All repositories created by this method are bare and automatically have
			* .git appended to their names, which is the standard convention for bare
			* repositories.
			*
			* @param repositoryName
			* @param repository
			* @param isCreate
			* @throws GitBlitException
			*/
			public void updateRepositoryModel(String repositoryName, RepositoryModel repository,
			boolean isCreate) throws GitBlitException {
			if (gcExecutor.isCollectingGarbage(repositoryName)) {
			throw new GitBlitException(MessageFormat.format("sorry, Gitblit is busy collecting garbage in {0}",
			repositoryName));
			}
			Repository r = null;
			String projectPath = StringUtils.getFirstPathElement(repository.name);
			if (!StringUtils.isEmpty(projectPath)) {
			if (projectPath.equalsIgnoreCase(getString(Keys.web.repositoryRootGroupName, "main"))) {
			// strip leading group name
			repository.name = repository.name.substring(projectPath.length() + 1);
			}
			}
			if (isCreate) {
			// ensure created repository name ends with .git
			if (!repository.name.toLowerCase().endsWith(org.eclipse.jgit.lib.Constants.DOT_GIT_EXT)) {
			repository.name += org.eclipse.jgit.lib.Constants.DOT_GIT_EXT;
			}
			if (hasRepository(repository.name)) {
			throw new GitBlitException(MessageFormat.format(
			"Can not create repository ''{0}'' because it already exists.",
			repository.name));
			}
			// create repository
			logger.info("create repository " + repository.name);
			r = JGitUtils.createRepository(repositoriesFolder, repository.name);
			} else {
			// rename repository
			if (!repositoryName.equalsIgnoreCase(repository.name)) {
			if (!repository.name.toLowerCase().endsWith(
			org.eclipse.jgit.lib.Constants.DOT_GIT_EXT)) {
			repository.name += org.eclipse.jgit.lib.Constants.DOT_GIT_EXT;
			}
			if (new File(repositoriesFolder, repository.name).exists()) {
			throw new GitBlitException(MessageFormat.format(
			"Failed to rename ''{0}'' because ''{1}'' already exists.",
			repositoryName, repository.name));
			}
			closeRepository(repositoryName);
			File folder = new File(repositoriesFolder, repositoryName);
			File destFolder = new File(repositoriesFolder, repository.name);
			if (destFolder.exists()) {
			throw new GitBlitException(
			MessageFormat
			.format("Can not rename repository ''{0}'' to ''{1}'' because ''{1}'' already exists.",
			repositoryName, repository.name));
			}
			File parentFile = destFolder.getParentFile();
			if (!parentFile.exists() && !parentFile.mkdirs()) {
			throw new GitBlitException(MessageFormat.format(
			"Failed to create folder ''{0}''", parentFile.getAbsolutePath()));
			}
			if (!folder.renameTo(destFolder)) {
			throw new GitBlitException(MessageFormat.format(
			"Failed to rename repository ''{0}'' to ''{1}''.", repositoryName,
			repository.name));
			}
			// rename the roles
			if (!userService.renameRepositoryRole(repositoryName, repository.name)) {
			throw new GitBlitException(MessageFormat.format(
			"Failed to rename repository permissions ''{0}'' to ''{1}''.",
			repositoryName, repository.name));
			}

			// rename fork origins in their configs
			if (!ArrayUtils.isEmpty(repository.forks)) {
			for (String fork : repository.forks) {
			Repository rf = getRepository(fork);
			try {
			StoredConfig config = rf.getConfig();
			String origin = config.getString("remote", "origin", "url");
			origin = origin.replace(repositoryName, repository.name);
			config.setString("remote", "origin", "url", origin);
			config.save();
			} catch (Exception e) {
			logger.error("Failed to update repository fork config for " + fork, e);
			}
			rf.close();
			}
			}

			// remove this repository from any origin model's fork list
			if (!StringUtils.isEmpty(repository.originRepository)) {
			RepositoryModel origin = repositoryListCache.get(repository.originRepository);
			if (origin != null && !ArrayUtils.isEmpty(origin.forks)) {
			origin.forks.remove(repositoryName);
			}
			}

			// clear the cache
			clearRepositoryMetadataCache(repositoryName);
			repository.resetDisplayName();
			}

			// load repository
			logger.info("edit repository " + repository.name);
			r = getRepository(repository.name);
			}

			// update settings
			if (r != null) {
			updateConfiguration(r, repository);
			// only update symbolic head if it changes
			String currentRef = JGitUtils.getHEADRef(r);
			if (!StringUtils.isEmpty(repository.HEAD) && !repository.HEAD.equals(currentRef)) {
			logger.info(MessageFormat.format("Relinking {0} HEAD from {1} to {2}",
			repository.name, currentRef, repository.HEAD));
			if (JGitUtils.setHEADtoRef(r, repository.HEAD)) {
			// clear the cache
			clearRepositoryMetadataCache(repository.name);
			}
			}

			// close the repository object
			r.close();
			}

			// update repository cache
			removeFromCachedRepositoryList(repositoryName);
			// model will actually be replaced on next load because config is stale
			addToCachedRepositoryList(repository);
			}

			/**
			* Updates the Gitblit configuration for the specified repository.
			*
			* @param r
			* the Git repository
			* @param repository
			* the Gitblit repository model
			*/
			public void updateConfiguration(Repository r, RepositoryModel repository) {
			StoredConfig config = r.getConfig();
			config.setString(Constants.CONFIG_GITBLIT, null, "description", repository.description);
			config.setString(Constants.CONFIG_GITBLIT, null, "owner", ArrayUtils.toString(repository.owners));
			config.setBoolean(Constants.CONFIG_GITBLIT, null, "useTickets", repository.useTickets);
			config.setBoolean(Constants.CONFIG_GITBLIT, null, "useDocs", repository.useDocs);
			config.setBoolean(Constants.CONFIG_GITBLIT, null, "useIncrementalPushTags", repository.useIncrementalPushTags);
			if (StringUtils.isEmpty(repository.incrementalPushTagPrefix) \|\|
			repository.incrementalPushTagPrefix.equals(settings.getString(Keys.git.defaultIncrementalPushTagPrefix, "r"))) {
			config.unset(Constants.CONFIG_GITBLIT, null, "incrementalPushTagPrefix");
			} else {
			config.setString(Constants.CONFIG_GITBLIT, null, "incrementalPushTagPrefix", repository.incrementalPushTagPrefix);
			}
			config.setBoolean(Constants.CONFIG_GITBLIT, null, "allowForks", repository.allowForks);
			config.setString(Constants.CONFIG_GITBLIT, null, "accessRestriction", repository.accessRestriction.name());
			config.setString(Constants.CONFIG_GITBLIT, null, "authorizationControl", repository.authorizationControl.name());
			config.setBoolean(Constants.CONFIG_GITBLIT, null, "verifyCommitter", repository.verifyCommitter);
			config.setBoolean(Constants.CONFIG_GITBLIT, null, "showRemoteBranches", repository.showRemoteBranches);
			config.setBoolean(Constants.CONFIG_GITBLIT, null, "isFrozen", repository.isFrozen);
			config.setBoolean(Constants.CONFIG_GITBLIT, null, "showReadme", repository.showReadme);
			config.setBoolean(Constants.CONFIG_GITBLIT, null, "skipSizeCalculation", repository.skipSizeCalculation);
			config.setBoolean(Constants.CONFIG_GITBLIT, null, "skipSummaryMetrics", repository.skipSummaryMetrics);
			config.setString(Constants.CONFIG_GITBLIT, null, "federationStrategy",
			repository.federationStrategy.name());
			config.setBoolean(Constants.CONFIG_GITBLIT, null, "isFederated", repository.isFederated);
			config.setString(Constants.CONFIG_GITBLIT, null, "gcThreshold", repository.gcThreshold);
			if (repository.gcPeriod == settings.getInteger(Keys.git.defaultGarbageCollectionPeriod, 7)) {
			// use default from config
			config.unset(Constants.CONFIG_GITBLIT, null, "gcPeriod");
			} else {
			config.setInt(Constants.CONFIG_GITBLIT, null, "gcPeriod", repository.gcPeriod);
			}
			if (repository.lastGC != null) {
			config.setString(Constants.CONFIG_GITBLIT, null, "lastGC", new SimpleDateFormat(Constants.ISO8601).format(repository.lastGC));
			}
			if (repository.maxActivityCommits == settings.getInteger(Keys.web.maxActivityCommits, 0)) {
			// use default from config
			config.unset(Constants.CONFIG_GITBLIT, null, "maxActivityCommits");
			} else {
			config.setInt(Constants.CONFIG_GITBLIT, null, "maxActivityCommits", repository.maxActivityCommits);
			}

			updateList(config, "federationSets", repository.federationSets);
			updateList(config, "preReceiveScript", repository.preReceiveScripts);
			updateList(config, "postReceiveScript", repository.postReceiveScripts);
			updateList(config, "mailingList", repository.mailingLists);
			updateList(config, "indexBranch", repository.indexedBranches);

			// User Defined Properties
			if (repository.customFields != null) {
			if (repository.customFields.size() == 0) {
			// clear section
			config.unsetSection(Constants.CONFIG_GITBLIT, Constants.CONFIG_CUSTOM_FIELDS);
			} else {
			for (Entry<String, String> property : repository.customFields.entrySet()) {
			// set field
			String key = property.getKey();
			String value = property.getValue();
			config.setString(Constants.CONFIG_GITBLIT, Constants.CONFIG_CUSTOM_FIELDS, key, value);
			}
			}
			}

			try {
			config.save();
			} catch (IOException e) {
			logger.error("Failed to save repository config!", e);
			}
			}

			private void updateList(StoredConfig config, String field, List<String> list) {
			// a null list is skipped, not cleared
			// this is for RPC administration where an older manager might be used
			if (list == null) {
			return;
			}
			if (ArrayUtils.isEmpty(list)) {
			config.unset(Constants.CONFIG_GITBLIT, null, field);
			} else {
			config.setStringList(Constants.CONFIG_GITBLIT, null, field, list);
			}
			}

			/**
			* Deletes the repository from the file system and removes the repository
			* permission from all repository users.
			*
			* @param model
			* @return true if successful
			*/
			public boolean deleteRepositoryModel(RepositoryModel model) {
			return deleteRepository(model.name);
			}

			/**
			* Deletes the repository from the file system and removes the repository
			* permission from all repository users.
			*
			* @param repositoryName
			* @return true if successful
			*/
			public boolean deleteRepository(String repositoryName) {
			try {
			closeRepository(repositoryName);
			// clear the repository cache
			clearRepositoryMetadataCache(repositoryName);

			RepositoryModel model = removeFromCachedRepositoryList(repositoryName);
			if (model != null && !ArrayUtils.isEmpty(model.forks)) {
			resetRepositoryListCache();
			}

			File folder = new File(repositoriesFolder, repositoryName);
			if (folder.exists() && folder.isDirectory()) {
			FileUtils.delete(folder, FileUtils.RECURSIVE \| FileUtils.RETRY);
			if (userService.deleteRepositoryRole(repositoryName)) {
			logger.info(MessageFormat.format("Repository \"{0}\" deleted", repositoryName));
			return true;
			}
			}
			} catch (Throwable t) {
			logger.error(MessageFormat.format("Failed to delete repository {0}", repositoryName), t);
			}
			return false;
			}

			/**
			* Returns an html version of the commit message with any global or
			* repository-specific regular expression substitution applied.
			*
			* @param repositoryName
			* @param text
			* @return html version of the commit message
			*/
			public String processCommitMessage(String repositoryName, String text) {
			String html = StringUtils.breakLinesForHtml(text);
			Map<String, String> map = new HashMap<String, String>();
			// global regex keys
			if (settings.getBoolean(Keys.regex.global, false)) {
			for (String key : settings.getAllKeys(Keys.regex.global)) {
			if (!key.equals(Keys.regex.global)) {
			String subKey = key.substring(key.lastIndexOf('.') + 1);
			map.put(subKey, settings.getString(key, ""));
			}
			}
			}

			// repository-specific regex keys
			List<String> keys = settings.getAllKeys(Keys.regex._ROOT + "."
			+ repositoryName.toLowerCase());
			for (String key : keys) {
			String subKey = key.substring(key.lastIndexOf('.') + 1);
			map.put(subKey, settings.getString(key, ""));
			}

			for (Entry<String, String> entry : map.entrySet()) {
			String definition = entry.getValue().trim();
			String[] chunks = definition.split("!!!");
			if (chunks.length == 2) {
			html = html.replaceAll(chunks[0], chunks[1]);
			} else {
			logger.warn(entry.getKey()
			+ " improperly formatted. Use !!! to separate match from replacement: "
			+ definition);
			}
			}
			return html;
			}

			/**
			* Returns Gitblit's scheduled executor service for scheduling tasks.
			*
			* @return scheduledExecutor
			*/
			public ScheduledExecutorService executor() {
			return scheduledExecutor;
			}

			public static boolean canFederate() {
			String passphrase = getString(Keys.federation.passphrase, "");
			return !StringUtils.isEmpty(passphrase);
			}

			/**
			* Configures this Gitblit instance to pull any registered federated gitblit
			* instances.
			*/
			private void configureFederation() {
			boolean validPassphrase = true;
			String passphrase = settings.getString(Keys.federation.passphrase, "");
			if (StringUtils.isEmpty(passphrase)) {
			logger.warn("Federation passphrase is blank! This server can not be PULLED from.");
			validPassphrase = false;
			}
			if (validPassphrase) {
			// standard tokens
			for (FederationToken tokenType : FederationToken.values()) {
			logger.info(MessageFormat.format("Federation {0} token = {1}", tokenType.name(),
			getFederationToken(tokenType)));
			}

			// federation set tokens
			for (String set : settings.getStrings(Keys.federation.sets)) {
			logger.info(MessageFormat.format("Federation Set {0} token = {1}", set,
			getFederationToken(set)));
			}
			}

			// Schedule the federation executor
			List<FederationModel> registrations = getFederationRegistrations();
			if (registrations.size() > 0) {
			FederationPullExecutor executor = new FederationPullExecutor(registrations, true);
			scheduledExecutor.schedule(executor, 1, TimeUnit.MINUTES);
			}
			}

			/**
			* Returns the list of federated gitblit instances that this instance will
			* try to pull.
			*
			* @return list of registered gitblit instances
			*/
			public List<FederationModel> getFederationRegistrations() {
			if (federationRegistrations.isEmpty()) {
			federationRegistrations.addAll(FederationUtils.getFederationRegistrations(settings));
			}
			return federationRegistrations;
			}

			/**
			* Retrieve the specified federation registration.
			*
			* @param name
			* the name of the registration
			* @return a federation registration
			*/
			public FederationModel getFederationRegistration(String url, String name) {
			// check registrations
			for (FederationModel r : getFederationRegistrations()) {
			if (r.name.equals(name) && r.url.equals(url)) {
			return r;
			}
			}

			// check the results
			for (FederationModel r : getFederationResultRegistrations()) {
			if (r.name.equals(name) && r.url.equals(url)) {
			return r;
			}
			}
			return null;
			}

			/**
			* Returns the list of federation sets.
			*
			* @return list of federation sets
			*/
			public List<FederationSet> getFederationSets(String gitblitUrl) {
			List<FederationSet> list = new ArrayList<FederationSet>();
			// generate standard tokens
			for (FederationToken type : FederationToken.values()) {
			FederationSet fset = new FederationSet(type.toString(), type, getFederationToken(type));
			fset.repositories = getRepositories(gitblitUrl, fset.token);
			list.add(fset);
			}
			// generate tokens for federation sets
			for (String set : settings.getStrings(Keys.federation.sets)) {
			FederationSet fset = new FederationSet(set, FederationToken.REPOSITORIES,
			getFederationToken(set));
			fset.repositories = getRepositories(gitblitUrl, fset.token);
			list.add(fset);
			}
			return list;
			}

			/**
			* Returns the list of possible federation tokens for this Gitblit instance.
			*
			* @return list of federation tokens
			*/
			public List<String> getFederationTokens() {
			List<String> tokens = new ArrayList<String>();
			// generate standard tokens
			for (FederationToken type : FederationToken.values()) {
			tokens.add(getFederationToken(type));
			}
			// generate tokens for federation sets
			for (String set : settings.getStrings(Keys.federation.sets)) {
			tokens.add(getFederationToken(set));
			}
			return tokens;
			}

			/**
			* Returns the specified federation token for this Gitblit instance.
			*
			* @param type
			* @return a federation token
			*/
			public String getFederationToken(FederationToken type) {
			return getFederationToken(type.name());
			}

			/**
			* Returns the specified federation token for this Gitblit instance.
			*
			* @param value
			* @return a federation token
			*/
			public String getFederationToken(String value) {
			String passphrase = settings.getString(Keys.federation.passphrase, "");
			return StringUtils.getSHA1(passphrase + "-" + value);
			}

			/**
			* Compares the provided token with this Gitblit instance's tokens and
			* determines if the requested permission may be granted to the token.
			*
			* @param req
			* @param token
			* @return true if the request can be executed
			*/
			public boolean validateFederationRequest(FederationRequest req, String token) {
			String all = getFederationToken(FederationToken.ALL);
			String unr = getFederationToken(FederationToken.USERS_AND_REPOSITORIES);
			String jur = getFederationToken(FederationToken.REPOSITORIES);
			switch (req) {
			case PULL_REPOSITORIES:
			return token.equals(all) \|\| token.equals(unr) \|\| token.equals(jur);
			case PULL_USERS:
			case PULL_TEAMS:
			return token.equals(all) \|\| token.equals(unr);
			case PULL_SETTINGS:
			case PULL_SCRIPTS:
			return token.equals(all);
			default:
			break;
			}
			return false;
			}

			/**
			* Acknowledge and cache the status of a remote Gitblit instance.
			*
			* @param identification
			* the identification of the pulling Gitblit instance
			* @param registration
			* the registration from the pulling Gitblit instance
			* @return true if acknowledged
			*/
			public boolean acknowledgeFederationStatus(String identification, FederationModel registration) {
			// reset the url to the identification of the pulling Gitblit instance
			registration.url = identification;
			String id = identification;
			if (!StringUtils.isEmpty(registration.folder)) {
			id += "-" + registration.folder;
			}
			federationPullResults.put(id, registration);
			return true;
			}

			/**
			* Returns the list of registration results.
			*
			* @return the list of registration results
			*/
			public List<FederationModel> getFederationResultRegistrations() {
			return new ArrayList<FederationModel>(federationPullResults.values());
			}

			/**
			* Submit a federation proposal. The proposal is cached locally and the
			* Gitblit administrator(s) are notified via email.
			*
			* @param proposal
			* the proposal
			* @param gitblitUrl
			* the url of your gitblit instance to send an email to
			* administrators
			* @return true if the proposal was submitted
			*/
			public boolean submitFederationProposal(FederationProposal proposal, String gitblitUrl) {
			// convert proposal to json
			String json = JsonUtils.toJsonString(proposal);

			try {
			// make the proposals folder
			File proposalsFolder = getProposalsFolder();
			proposalsFolder.mkdirs();

			// cache json to a file
			File file = new File(proposalsFolder, proposal.token + Constants.PROPOSAL_EXT);
			com.gitblit.utils.FileUtils.writeContent(file, json);
			} catch (Exception e) {
			logger.error(MessageFormat.format("Failed to cache proposal from {0}", proposal.url), e);
			}

			// send an email, if possible
			sendMailToAdministrators("Federation proposal from " + proposal.url,
			"Please review the proposal @ " + gitblitUrl + "/proposal/" + proposal.token);
			return true;
			}

			/**
			* Returns the list of pending federation proposals
			*
			* @return list of federation proposals
			*/
			public List<FederationProposal> getPendingFederationProposals() {
			List<FederationProposal> list = new ArrayList<FederationProposal>();
			File folder = getProposalsFolder();
			if (folder.exists()) {
			File[] files = folder.listFiles(new FileFilter() {
			@Override
			public boolean accept(File file) {
			return file.isFile()
			&& file.getName().toLowerCase().endsWith(Constants.PROPOSAL_EXT);
			}
			});
			for (File file : files) {
			String json = com.gitblit.utils.FileUtils.readContent(file, null);
			FederationProposal proposal = JsonUtils.fromJsonString(json,
			FederationProposal.class);
			list.add(proposal);
			}
			}
			return list;
			}

			/**
			* Get repositories for the specified token.
			*
			* @param gitblitUrl
			* the base url of this gitblit instance
			* @param token
			* the federation token
			* @return a map of <cloneurl, RepositoryModel>
			*/
			public Map<String, RepositoryModel> getRepositories(String gitblitUrl, String token) {
			Map<String, String> federationSets = new HashMap<String, String>();
			for (String set : getStrings(Keys.federation.sets)) {
			federationSets.put(getFederationToken(set), set);
			}

			// Determine the Gitblit clone url
			StringBuilder sb = new StringBuilder();
			sb.append(gitblitUrl);
			sb.append(Constants.GIT_PATH);
			sb.append("{0}");
			String cloneUrl = sb.toString();

			// Retrieve all available repositories
			UserModel user = new UserModel(Constants.FEDERATION_USER);
			user.canAdmin = true;
			List<RepositoryModel> list = getRepositoryModels(user);

			// create the [cloneurl, repositoryModel] map
			Map<String, RepositoryModel> repositories = new HashMap<String, RepositoryModel>();
			for (RepositoryModel model : list) {
			// by default, setup the url for THIS repository
			String url = MessageFormat.format(cloneUrl, model.name);
			switch (model.federationStrategy) {
			case EXCLUDE:
			// skip this repository
			continue;
			case FEDERATE_ORIGIN:
			// federate the origin, if it is defined
			if (!StringUtils.isEmpty(model.origin)) {
			url = model.origin;
			}
			break;
			default:
			break;
			}

			if (federationSets.containsKey(token)) {
			// include repositories only for federation set
			String set = federationSets.get(token);
			if (model.federationSets.contains(set)) {
			repositories.put(url, model);
			}
			} else {
			// standard federation token for ALL
			repositories.put(url, model);
			}
			}
			return repositories;
			}

			/**
			* Creates a proposal from the token.
			*
			* @param gitblitUrl
			* the url of this Gitblit instance
			* @param token
			* @return a potential proposal
			*/
			public FederationProposal createFederationProposal(String gitblitUrl, String token) {
			FederationToken tokenType = FederationToken.REPOSITORIES;
			for (FederationToken type : FederationToken.values()) {
			if (token.equals(getFederationToken(type))) {
			tokenType = type;
			break;
			}
			}
			Map<String, RepositoryModel> repositories = getRepositories(gitblitUrl, token);
			FederationProposal proposal = new FederationProposal(gitblitUrl, tokenType, token,
			repositories);
			return proposal;
			}

			/**
			* Returns the proposal identified by the supplied token.
			*
			* @param token
			* @return the specified proposal or null
			*/
			public FederationProposal getPendingFederationProposal(String token) {
			List<FederationProposal> list = getPendingFederationProposals();
			for (FederationProposal proposal : list) {
			if (proposal.token.equals(token)) {
			return proposal;
			}
			}
			return null;
			}

			/**
			* Deletes a pending federation proposal.
			*
			* @param a
			* proposal
			* @return true if the proposal was deleted
			*/
			public boolean deletePendingFederationProposal(FederationProposal proposal) {
			File folder = getProposalsFolder();
			File file = new File(folder, proposal.token + Constants.PROPOSAL_EXT);
			return file.delete();
			}

			/**
			* Returns the list of all Groovy push hook scripts. Script files must have
			* .groovy extension
			*
			* @return list of available hook scripts
			*/
			public List<String> getAllScripts() {
			File groovyFolder = getGroovyScriptsFolder();
			File[] files = groovyFolder.listFiles(new FileFilter() {
			@Override
			public boolean accept(File pathname) {
			return pathname.isFile() && pathname.getName().endsWith(".groovy");
			}
			});
			List<String> scripts = new ArrayList<String>();
			if (files != null) {
			for (File file : files) {
			String script = file.getName().substring(0, file.getName().lastIndexOf('.'));
			scripts.add(script);
			}
			}
			return scripts;
			}

			/**
			* Returns the list of pre-receive scripts the repository inherited from the
			* global settings and team affiliations.
			*
			* @param repository
			* if null only the globally specified scripts are returned
			* @return a list of scripts
			*/
			public List<String> getPreReceiveScriptsInherited(RepositoryModel repository) {
			Set<String> scripts = new LinkedHashSet<String>();
			// Globals
			for (String script : getStrings(Keys.groovy.preReceiveScripts)) {
			if (script.endsWith(".groovy")) {
			scripts.add(script.substring(0, script.lastIndexOf('.')));
			} else {
			scripts.add(script);
			}
			}

			// Team Scripts
			if (repository != null) {
			for (String teamname : userService.getTeamnamesForRepositoryRole(repository.name)) {
			TeamModel team = userService.getTeamModel(teamname);
			scripts.addAll(team.preReceiveScripts);
			}
			}
			return new ArrayList<String>(scripts);
			}

			/**
			* Returns the list of all available Groovy pre-receive push hook scripts
			* that are not already inherited by the repository. Script files must have
			* .groovy extension
			*
			* @param repository
			* optional parameter
			* @return list of available hook scripts
			*/
			public List<String> getPreReceiveScriptsUnused(RepositoryModel repository) {
			Set<String> inherited = new TreeSet<String>(getPreReceiveScriptsInherited(repository));

			// create list of available scripts by excluding inherited scripts
			List<String> scripts = new ArrayList<String>();
			for (String script : getAllScripts()) {
			if (!inherited.contains(script)) {
			scripts.add(script);
			}
			}
			return scripts;
			}

			/**
			* Returns the list of post-receive scripts the repository inherited from
			* the global settings and team affiliations.
			*
			* @param repository
			* if null only the globally specified scripts are returned
			* @return a list of scripts
			*/
			public List<String> getPostReceiveScriptsInherited(RepositoryModel repository) {
			Set<String> scripts = new LinkedHashSet<String>();
			// Global Scripts
			for (String script : getStrings(Keys.groovy.postReceiveScripts)) {
			if (script.endsWith(".groovy")) {
			scripts.add(script.substring(0, script.lastIndexOf('.')));
			} else {
			scripts.add(script);
			}
			}
			// Team Scripts
			if (repository != null) {
			for (String teamname : userService.getTeamnamesForRepositoryRole(repository.name)) {
			TeamModel team = userService.getTeamModel(teamname);
			scripts.addAll(team.postReceiveScripts);
			}
			}
			return new ArrayList<String>(scripts);
			}

			/**
			* Returns the list of unused Groovy post-receive push hook scripts that are
			* not already inherited by the repository. Script files must have .groovy
			* extension
			*
			* @param repository
			* optional parameter
			* @return list of available hook scripts
			*/
			public List<String> getPostReceiveScriptsUnused(RepositoryModel repository) {
			Set<String> inherited = new TreeSet<String>(getPostReceiveScriptsInherited(repository));

			// create list of available scripts by excluding inherited scripts
			List<String> scripts = new ArrayList<String>();
			for (String script : getAllScripts()) {
			if (!inherited.contains(script)) {
			scripts.add(script);
			}
			}
			return scripts;
			}

			/**
			* Search the specified repositories using the Lucene query.
			*
			* @param query
			* @param page
			* @param pageSize
			* @param repositories
			* @return
			*/
			public List<SearchResult> search(String query, int page, int pageSize, List<String> repositories) {
			List<SearchResult> srs = luceneExecutor.search(query, page, pageSize, repositories);
			return srs;
			}

			/**
			* Notify the administrators by email.
			*
			* @param subject
			* @param message
			*/
			public void sendMailToAdministrators(String subject, String message) {
			List<String> toAddresses = settings.getStrings(Keys.mail.adminAddresses);
			sendMail(subject, message, toAddresses);
			}

			/**
			* Notify users by email of something.
			*
			* @param subject
			* @param message
			* @param toAddresses
			*/
			public void sendMail(String subject, String message, Collection<String> toAddresses) {
			this.sendMail(subject, message, toAddresses.toArray(new String[0]));
			}

			/**
			* Notify users by email of something.
			*
			* @param subject
			* @param message
			* @param toAddresses
			*/
			public void sendMail(String subject, String message, String... toAddresses) {
			if (toAddresses == null \|\| toAddresses.length == 0) {
			logger.debug(MessageFormat.format("Dropping message {0} because there are no recipients", subject));
			return;
			}
			try {
			Message mail = mailExecutor.createMessage(toAddresses);
			if (mail != null) {
			mail.setSubject(subject);

			MimeBodyPart messagePart = new MimeBodyPart();
			messagePart.setText(message, "utf-8");
			messagePart.setHeader("Content-Type", "text/plain; charset=\"utf-8\"");
			messagePart.setHeader("Content-Transfer-Encoding", "quoted-printable");

			MimeMultipart multiPart = new MimeMultipart();
			multiPart.addBodyPart(messagePart);
			mail.setContent(multiPart);

			mailExecutor.queue(mail);
			}
			} catch (MessagingException e) {
			logger.error("Messaging error", e);
			}
			}

			/**
			* Notify users by email of something.
			*
			* @param subject
			* @param message
			* @param toAddresses
			*/
			public void sendHtmlMail(String subject, String message, Collection<String> toAddresses) {
			this.sendHtmlMail(subject, message, toAddresses.toArray(new String[0]));
			}

			/**
			* Notify users by email of something.
			*
			* @param subject
			* @param message
			* @param toAddresses
			*/
			public void sendHtmlMail(String subject, String message, String... toAddresses) {
			if (toAddresses == null \|\| toAddresses.length == 0) {
			logger.debug(MessageFormat.format("Dropping message {0} because there are no recipients", subject));
			return;
			}
			try {
			Message mail = mailExecutor.createMessage(toAddresses);
			if (mail != null) {
			mail.setSubject(subject);

			MimeBodyPart messagePart = new MimeBodyPart();
			messagePart.setText(message, "utf-8");
			messagePart.setHeader("Content-Type", "text/html; charset=\"utf-8\"");
			messagePart.setHeader("Content-Transfer-Encoding", "quoted-printable");

			MimeMultipart multiPart = new MimeMultipart();
			multiPart.addBodyPart(messagePart);
			mail.setContent(multiPart);

			mailExecutor.queue(mail);
			}
			} catch (MessagingException e) {
			logger.error("Messaging error", e);
			}
			}

			/**
			* Returns the descriptions/comments of the Gitblit config settings.
			*
			* @return SettingsModel
			*/
			public ServerSettings getSettingsModel() {
			// ensure that the current values are updated in the setting models
			for (String key : settings.getAllKeys(null)) {
			SettingModel setting = settingsModel.get(key);
			if (setting == null) {
			// unreferenced setting, create a setting model
			setting = new SettingModel();
			setting.name = key;
			settingsModel.add(setting);
			}
			setting.currentValue = settings.getString(key, "");
			}
			settingsModel.pushScripts = getAllScripts();
			return settingsModel;
			}

			/**
			* Parse the properties file and aggregate all the comments by the setting
			* key. A setting model tracks the current value, the default value, the
			* description of the setting and and directives about the setting.
			*
			* @return Map<String, SettingModel>
			*/
			private ServerSettings loadSettingModels(InputStream referencePropertiesInputStream) {
			ServerSettings settingsModel = new ServerSettings();
			settingsModel.supportsCredentialChanges = userService.supportsCredentialChanges();
			settingsModel.supportsDisplayNameChanges = userService.supportsDisplayNameChanges();
			settingsModel.supportsEmailAddressChanges = userService.supportsEmailAddressChanges();
			settingsModel.supportsTeamMembershipChanges = userService.supportsTeamMembershipChanges();
			try {
			// Read bundled Gitblit properties to extract setting descriptions.
			// This copy is pristine and only used for populating the setting
			// models map.
			InputStream is = referencePropertiesInputStream;
			BufferedReader propertiesReader = new BufferedReader(new InputStreamReader(is));
			StringBuilder description = new StringBuilder();
			SettingModel setting = new SettingModel();
			String line = null;
			while ((line = propertiesReader.readLine()) != null) {
			if (line.length() == 0) {
			description.setLength(0);
			setting = new SettingModel();
			} else {
			if (line.charAt(0) == '#') {
			if (line.length() > 1) {
			String text = line.substring(1).trim();
			if (SettingModel.CASE_SENSITIVE.equals(text)) {
			setting.caseSensitive = true;
			} else if (SettingModel.RESTART_REQUIRED.equals(text)) {
			setting.restartRequired = true;
			} else if (SettingModel.SPACE_DELIMITED.equals(text)) {
			setting.spaceDelimited = true;
			} else if (text.startsWith(SettingModel.SINCE)) {
			try {
			setting.since = text.split(" ")[1];
			} catch (Exception e) {
			setting.since = text;
			}
			} else {
			description.append(text);
			description.append('\n');
			}
			}
			} else {
			String[] kvp = line.split("=", 2);
			String key = kvp[0].trim();
			setting.name = key;
			setting.defaultValue = kvp[1].trim();
			setting.currentValue = setting.defaultValue;
			setting.description = description.toString().trim();
			settingsModel.add(setting);
			description.setLength(0);
			setting = new SettingModel();
			}
			}
			}
			propertiesReader.close();
			} catch (NullPointerException e) {
			logger.error("Failed to find resource copy of gitblit.properties");
			} catch (IOException e) {
			logger.error("Failed to load resource copy of gitblit.properties");
			}
			return settingsModel;
			}

			/**
			* Configure the Gitblit singleton with the specified settings source. This
			* source may be file settings (Gitblit GO) or may be web.xml settings
			* (Gitblit WAR).
			*
			* @param settings
			*/
			public void configureContext(IStoredSettings settings, File folder, boolean startFederation) {
			this.settings = settings;
			this.baseFolder = folder;

			repositoriesFolder = getRepositoriesFolder();

			logger.info("Gitblit base folder = " + folder.getAbsolutePath());
			logger.info("Git repositories folder = " + repositoriesFolder.getAbsolutePath());
			logger.info("Gitblit settings = " + settings.toString());

			// prepare service executors
			mailExecutor = new MailExecutor(settings);
			luceneExecutor = new LuceneExecutor(settings, repositoriesFolder);
			gcExecutor = new GCExecutor(settings);

			// calculate repository list settings checksum for future config changes
			repositoryListSettingsChecksum.set(getRepositoryListSettingsChecksum());

			// build initial repository list
			if (settings.getBoolean(Keys.git.cacheRepositoryList, true)) {
			logger.info("Identifying available repositories...");
			getRepositoryList();
			}

			logTimezone("JVM", TimeZone.getDefault());
			logTimezone(Constants.NAME, getTimezone());

			serverStatus = new ServerStatus(isGO());

			if (this.userService == null) {
			String realm = settings.getString(Keys.realm.userService, "${baseFolder}/users.properties");
			IUserService loginService = null;
			try {
			// check to see if this "file" is a login service class
			Class<?> realmClass = Class.forName(realm);
			loginService = (IUserService) realmClass.newInstance();
			} catch (Throwable t) {
			loginService = new GitblitUserService();
			}
			setUserService(loginService);
			}

			// load and cache the project metadata
			projectConfigs = new FileBasedConfig(getFileOrFolder(Keys.web.projectsFile, "${baseFolder}/projects.conf"), FS.detect());
			getProjectConfigs();

			configureMailExecutor();
			configureLuceneIndexing();
			configureGarbageCollector();
			if (startFederation) {
			configureFederation();
			}
			configureJGit();
			configureFanout();
			configureGitDaemon();

			ContainerUtils.CVE_2007_0450.test();
			}

			protected void configureMailExecutor() {
			if (mailExecutor.isReady()) {
			logger.info("Mail executor is scheduled to process the message queue every 2 minutes.");
			scheduledExecutor.scheduleAtFixedRate(mailExecutor, 1, 2, TimeUnit.MINUTES);
			} else {
			logger.warn("Mail server is not properly configured. Mail services disabled.");
			}
			}

			protected void configureLuceneIndexing() {
			scheduledExecutor.scheduleAtFixedRate(luceneExecutor, 1, 2, TimeUnit.MINUTES);
			logger.info("Lucene executor is scheduled to process indexed branches every 2 minutes.");
			}

			protected void configureGarbageCollector() {
			// schedule gc engine
			if (gcExecutor.isReady()) {
			logger.info("GC executor is scheduled to scan repositories every 24 hours.");
			Calendar c = Calendar.getInstance();
			c.set(Calendar.HOUR_OF_DAY, settings.getInteger(Keys.git.garbageCollectionHour, 0));
			c.set(Calendar.MINUTE, 0);
			c.set(Calendar.SECOND, 0);
			c.set(Calendar.MILLISECOND, 0);
			Date cd = c.getTime();
			Date now = new Date();
			int delay = 0;
			if (cd.before(now)) {
			c.add(Calendar.DATE, 1);
			cd = c.getTime();
			}
			delay = (int) ((cd.getTime() - now.getTime())/TimeUtils.MIN);
			String when = delay + " mins";
			if (delay > 60) {
			when = MessageFormat.format("{0,number,0.0} hours", ((float)delay)/60f);
			}
			logger.info(MessageFormat.format("Next scheculed GC scan is in {0}", when));
			scheduledExecutor.scheduleAtFixedRate(gcExecutor, delay, 60*24, TimeUnit.MINUTES);
			}
			}

			protected void configureJGit() {
			// Configure JGit
			WindowCacheConfig cfg = new WindowCacheConfig();

			cfg.setPackedGitWindowSize(settings.getFilesize(Keys.git.packedGitWindowSize, cfg.getPackedGitWindowSize()));
			cfg.setPackedGitLimit(settings.getFilesize(Keys.git.packedGitLimit, cfg.getPackedGitLimit()));
			cfg.setDeltaBaseCacheLimit(settings.getFilesize(Keys.git.deltaBaseCacheLimit, cfg.getDeltaBaseCacheLimit()));
			cfg.setPackedGitOpenFiles(settings.getFilesize(Keys.git.packedGitOpenFiles, cfg.getPackedGitOpenFiles()));
			cfg.setStreamFileThreshold(settings.getFilesize(Keys.git.streamFileThreshold, cfg.getStreamFileThreshold()));
			cfg.setPackedGitMMAP(settings.getBoolean(Keys.git.packedGitMmap, cfg.isPackedGitMMAP()));

			try {
			WindowCache.reconfigure(cfg);
			logger.debug(MessageFormat.format("{0} = {1,number,0}", Keys.git.packedGitWindowSize, cfg.getPackedGitWindowSize()));
			logger.debug(MessageFormat.format("{0} = {1,number,0}", Keys.git.packedGitLimit, cfg.getPackedGitLimit()));
			logger.debug(MessageFormat.format("{0} = {1,number,0}", Keys.git.deltaBaseCacheLimit, cfg.getDeltaBaseCacheLimit()));
			logger.debug(MessageFormat.format("{0} = {1,number,0}", Keys.git.packedGitOpenFiles, cfg.getPackedGitOpenFiles()));
			logger.debug(MessageFormat.format("{0} = {1,number,0}", Keys.git.streamFileThreshold, cfg.getStreamFileThreshold()));
			logger.debug(MessageFormat.format("{0} = {1}", Keys.git.packedGitMmap, cfg.isPackedGitMMAP()));
			} catch (IllegalArgumentException e) {
			logger.error("Failed to configure JGit parameters!", e);
			}
			}

			protected void configureFanout() {
			// startup Fanout PubSub service
			if (settings.getInteger(Keys.fanout.port, 0) > 0) {
			String bindInterface = settings.getString(Keys.fanout.bindInterface, null);
			int port = settings.getInteger(Keys.fanout.port, FanoutService.DEFAULT_PORT);
			boolean useNio = settings.getBoolean(Keys.fanout.useNio, true);
			int limit = settings.getInteger(Keys.fanout.connectionLimit, 0);

			if (useNio) {
			if (StringUtils.isEmpty(bindInterface)) {
			fanoutService = new FanoutNioService(port);
			} else {
			fanoutService = new FanoutNioService(bindInterface, port);
			}
			} else {
			if (StringUtils.isEmpty(bindInterface)) {
			fanoutService = new FanoutSocketService(port);
			} else {
			fanoutService = new FanoutSocketService(bindInterface, port);
			}
			}

			fanoutService.setConcurrentConnectionLimit(limit);
			fanoutService.setAllowAllChannelAnnouncements(false);
			fanoutService.start();
			}
			}

			protected void configureGitDaemon() {
			String bindInterface = settings.getString(Keys.git.daemonBindInterface, "localhost");
			int port = settings.getInteger(Keys.git.daemonPort, GitDaemon.DEFAULT_PORT);
			if (port > 0) {
			try {
			gitDaemon = new GitDaemon(bindInterface, port, getRepositoriesFolder());
			gitDaemon.start();
			logger.info(MessageFormat.format("Git daemon is listening on {0}:{1,number,0}", bindInterface, port));
			} catch (IOException e) {
			logger.error(MessageFormat.format("Failed to start Git daemon on {0}:{1,number.0}", bindInterface, port), e);
			}
			}
			}

			protected final Logger getLogger() {
			return logger;
			}

			protected final ScheduledExecutorService getScheduledExecutor() {
			return scheduledExecutor;
			}

			protected final LuceneExecutor getLuceneExecutor() {
			return luceneExecutor;
			}

			private void logTimezone(String type, TimeZone zone) {
			SimpleDateFormat df = new SimpleDateFormat("z Z");
			df.setTimeZone(zone);
			String offset = df.format(new Date());
			logger.info(type + " timezone is " + zone.getID() + " (" + offset + ")");
			}

			/**
			* Configure Gitblit from the web.xml, if no configuration has already been
			* specified.
			*
			* @see ServletContextListener.contextInitialize(ServletContextEvent)
			*/
			@Override
			public void contextInitialized(ServletContextEvent contextEvent) {
			contextInitialized(contextEvent, getClass().getResourceAsStream("/reference.properties"));
			}

			public void contextInitialized(ServletContextEvent contextEvent, InputStream referencePropertiesInputStream) {
			servletContext = contextEvent.getServletContext();
			if (settings == null) {
			// Gitblit is running in a servlet container
			ServletContext context = contextEvent.getServletContext();
			WebXmlSettings webxmlSettings = new WebXmlSettings(context);
			File contextFolder = new File(context.getRealPath("/"));
			String openShift = System.getenv("OPENSHIFT_DATA_DIR");

			if (!StringUtils.isEmpty(openShift)) {
			// Gitblit is running in OpenShift/JBoss
			File base = new File(openShift);
			logger.info("EXPRESS contextFolder is " + contextFolder.getAbsolutePath());

			// gitblit.properties setting overrides
			File overrideFile = new File(base, "gitblit.properties");
			webxmlSettings.applyOverrides(overrideFile);

			// Copy the included scripts to the configured groovy folder
			String path = webxmlSettings.getString(Keys.groovy.scriptsFolder, "groovy");
			File localScripts = com.gitblit.utils.FileUtils.resolveParameter(Constants.baseFolder$, base, path);
			if (!localScripts.exists()) {
			File warScripts = new File(contextFolder, "/WEB-INF/data/groovy");
			if (!warScripts.equals(localScripts)) {
			try {
			com.gitblit.utils.FileUtils.copy(localScripts, warScripts.listFiles());
			} catch (IOException e) {
			logger.error(MessageFormat.format(
			"Failed to copy included Groovy scripts from {0} to {1}",
			warScripts, localScripts));
			}
			}
			}

			// configure context using the web.xml
			configureContext(webxmlSettings, base, true);
			} else {
			// Gitblit is running in a standard servlet container
			logger.info("WAR contextFolder is " + contextFolder.getAbsolutePath());

			String path = webxmlSettings.getString(Constants.baseFolder, Constants.contextFolder$ + "/WEB-INF/data");
			File base = com.gitblit.utils.FileUtils.resolveParameter(Constants.contextFolder$, contextFolder, path);
			base.mkdirs();

			// try to copy the data folder contents to the baseFolder
			File localSettings = new File(base, "gitblit.properties");
			if (!localSettings.exists()) {
			File contextData = new File(contextFolder, "/WEB-INF/data");
			if (!base.equals(contextData)) {
			try {
			com.gitblit.utils.FileUtils.copy(base, contextData.listFiles());
			} catch (IOException e) {
			logger.error(MessageFormat.format(
			"Failed to copy included data from {0} to {1}",
			contextData, base));
			}
			}
			}

			// delegate all config to baseFolder/gitblit.properties file
			FileSettings settings = new FileSettings(localSettings.getAbsolutePath());
			configureContext(settings, base, true);
			}
			}

			settingsModel = loadSettingModels(referencePropertiesInputStream);
			serverStatus.servletContainer = servletContext.getServerInfo();
			}

			/**
			* Gitblit is being shutdown either because the servlet container is
			* shutting down or because the servlet container is re-deploying Gitblit.
			*/
			@Override
			public void contextDestroyed(ServletContextEvent contextEvent) {
			logger.info("Gitblit context destroyed by servlet container.");
			scheduledExecutor.shutdownNow();
			luceneExecutor.close();
			gcExecutor.close();
			if (fanoutService != null) {
			fanoutService.stop();
			}
			if (gitDaemon != null) {
			gitDaemon.stop();
			}
			}

			/**
			*
			* @return true if we are running the gc executor
			*/
			public boolean isCollectingGarbage() {
			return gcExecutor.isRunning();
			}

			/**
			* Returns true if Gitblit is actively collecting garbage in this repository.
			*
			* @param repositoryName
			* @return true if actively collecting garbage
			*/
			public boolean isCollectingGarbage(String repositoryName) {
			return gcExecutor.isCollectingGarbage(repositoryName);
			}

			/**
			* Creates a personal fork of the specified repository. The clone is view
			* restricted by default and the owner of the source repository is given
			* access to the clone.
			*
			* @param repository
			* @param user
			* @return the repository model of the fork, if successful
			* @throws GitBlitException
			*/
			public RepositoryModel fork(RepositoryModel repository, UserModel user) throws GitBlitException {
			String cloneName = MessageFormat.format("~{0}/{1}.git", user.username, StringUtils.stripDotGit(StringUtils.getLastPathElement(repository.name)));
			String fromUrl = MessageFormat.format("file://{0}/{1}", repositoriesFolder.getAbsolutePath(), repository.name);

			// clone the repository
			try {
			JGitUtils.cloneRepository(repositoriesFolder, cloneName, fromUrl, true, null);
			} catch (Exception e) {
			throw new GitBlitException(e);
			}

			// create a Gitblit repository model for the clone
			RepositoryModel cloneModel = repository.cloneAs(cloneName);
			// owner has REWIND/RW+ permissions
			cloneModel.addOwner(user.username);
			updateRepositoryModel(cloneName, cloneModel, false);

			// add the owner of the source repository to the clone's access list
			if (!ArrayUtils.isEmpty(repository.owners)) {
			for (String owner : repository.owners) {
			UserModel originOwner = getUserModel(owner);
			if (originOwner != null) {
			originOwner.setRepositoryPermission(cloneName, AccessPermission.CLONE);
			updateUserModel(originOwner.username, originOwner, false);
			}
			}
			}

			// grant origin's user list clone permission to fork
			List<String> users = getRepositoryUsers(repository);
			List<UserModel> cloneUsers = new ArrayList<UserModel>();
			for (String name : users) {
			if (!name.equalsIgnoreCase(user.username)) {
			UserModel cloneUser = getUserModel(name);
			if (cloneUser.canClone(repository)) {
			// origin user can clone origin, grant clone access to fork
			cloneUser.setRepositoryPermission(cloneName, AccessPermission.CLONE);
			}
			cloneUsers.add(cloneUser);
			}
			}
			userService.updateUserModels(cloneUsers);

			// grant origin's team list clone permission to fork
			List<String> teams = getRepositoryTeams(repository);
			List<TeamModel> cloneTeams = new ArrayList<TeamModel>();
			for (String name : teams) {
			TeamModel cloneTeam = getTeamModel(name);
			if (cloneTeam.canClone(repository)) {
			// origin team can clone origin, grant clone access to fork
			cloneTeam.setRepositoryPermission(cloneName, AccessPermission.CLONE);
			}
			cloneTeams.add(cloneTeam);
			}
			userService.updateTeamModels(cloneTeams);

			// add this clone to the cached model
			addToCachedRepositoryList(cloneModel);
			return cloneModel;
			}

			/**
			* Allow to understand if GitBlit supports and is configured to allow
			* cookie-based authentication.
			*
			* @return status of Cookie authentication enablement.
			*/
			public boolean allowCookieAuthentication() {
			return GitBlit.getBoolean(Keys.web.allowCookieAuthentication, true) && userService.supportsCookies();
			}
			}
			/*
			* Copyright 2013 gitblit.com.
			*
			* Licensed under the Apache License, Version 2.0 (the "License");
			* you may not use this file except in compliance with the License.
			* You may obtain a copy of the License at
			*
			* http://www.apache.org/licenses/LICENSE-2.0
			*
			* Unless required by applicable law or agreed to in writing, software
			* distributed under the License is distributed on an "AS IS" BASIS,
			* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
			* See the License for the specific language governing permissions and
			* limitations under the License.
			*/
			package com.gitblit;

			import com.gitblit.manager.GitblitManager;
			import com.gitblit.manager.IAuthenticationManager;
			import com.gitblit.manager.IFederationManager;
			import com.gitblit.manager.IFilestoreManager;
			import com.gitblit.manager.INotificationManager;
			import com.gitblit.manager.IPluginManager;
			import com.gitblit.manager.IProjectManager;
			import com.gitblit.manager.IRepositoryManager;
			import com.gitblit.manager.IRuntimeManager;
			import com.gitblit.manager.IUserManager;
			import com.gitblit.tickets.ITicketService;
			import com.gitblit.transport.ssh.IPublicKeyManager;
			import com.google.inject.Inject;
			import com.google.inject.Provider;
			import com.google.inject.Singleton;

			/**
			* GitBlit is the aggregate manager for the Gitblit webapp. The parent class provides all
			* functionality. This class exists to not break existing Groovy push hooks.
			*
			* @author James Moger
			*
			*/
			@Singleton
			@Deprecated
			public class GitBlit extends GitblitManager {

			@Inject
			public GitBlit(
			Provider<IPublicKeyManager> publicKeyManagerProvider,
			Provider<ITicketService> ticketServiceProvider,
			IRuntimeManager runtimeManager,
			IPluginManager pluginManager,
			INotificationManager notificationManager,
			IUserManager userManager,
			IAuthenticationManager authenticationManager,
			IRepositoryManager repositoryManager,
			IProjectManager projectManager,
			IFederationManager federationManager,
			IFilestoreManager filestoreManager) {

			super(
			publicKeyManagerProvider,
			ticketServiceProvider,
			runtimeManager,
			pluginManager,
			notificationManager,
			userManager,
			authenticationManager,
			repositoryManager,
			projectManager,
			federationManager,
			filestoreManager);
			}
			}