Ignore .gitignore files on git.overleaf.com repos (fix #1281)

services/git-bridge/src/main/java/uk/ac/ic/wlgitbridge/bridge/Bridge.java

@@ -6,6 +6,7 @@ import uk.ac.ic.wlgitbridge.bridge.db.DBStore;
 import uk.ac.ic.wlgitbridge.bridge.db.ProjectState;
 import uk.ac.ic.wlgitbridge.bridge.lock.LockGuard;
 import uk.ac.ic.wlgitbridge.bridge.lock.ProjectLock;
+import uk.ac.ic.wlgitbridge.bridge.repo.ProjectRepo;
 import uk.ac.ic.wlgitbridge.bridge.repo.RepoStore;
 import uk.ac.ic.wlgitbridge.bridge.resource.ResourceCache;
 import uk.ac.ic.wlgitbridge.bridge.resource.UrlResourceCache;

services/git-bridge/src/main/java/uk/ac/ic/wlgitbridge/bridge/GitProjectRepo.java → services/git-bridge/src/main/java/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepo.java

@@ -1,12 +1,12 @@
-package uk.ac.ic.wlgitbridge.bridge;
+package uk.ac.ic.wlgitbridge.bridge.repo;
 
 import com.google.common.base.Preconditions;
 import org.eclipse.jgit.api.Git;
+import org.eclipse.jgit.api.ResetCommand;
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.lib.PersonIdent;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
-import uk.ac.ic.wlgitbridge.bridge.repo.RepoStore;
 import uk.ac.ic.wlgitbridge.data.filestore.GitDirectoryContents;
 import uk.ac.ic.wlgitbridge.data.filestore.RawFile;
 import uk.ac.ic.wlgitbridge.git.exception.GitUserException;
@@ -80,10 +80,23 @@ public class GitProjectRepo implements ProjectRepo {
         }
     }
 
+    public void resetHard() throws IOException {
+        Git git = new Git(getJGitRepository());
+        try {
+            git.reset().setMode(ResetCommand.ResetType.HARD).call();
+        } catch (GitAPIException e) {
+            throw new IOException(e);
+        }
+    }
+
     public Repository getJGitRepository() {
         return repository.get();
     }
 
+    public File getDirectory() {
+        return getJGitRepository().getWorkTree();
+    }
+
     private void initRepositoryField(RepoStore repoStore) throws IOException {
         Preconditions.checkNotNull(repoStore);
         Preconditions.checkArgument(Project.isValidProjectName(projectName));
@@ -103,10 +116,11 @@ public class GitProjectRepo implements ProjectRepo {
             GitDirectoryContents contents
     ) throws IOException, GitAPIException {
         Preconditions.checkState(repository.isPresent());
+        Repository repo = getJGitRepository();
         String name = getProjectName();
         Log.info("[{}] Writing commit", name);
         contents.write();
-        Git git = new Git(repository.get());
+        Git git = new Git(getJGitRepository());
         Log.info("[{}] Getting missing files", name);
         Set<String> missingFiles = git.status().call().getMissing();
         for (String missing : missingFiles) {
@@ -114,7 +128,10 @@ public class GitProjectRepo implements ProjectRepo {
             git.rm().setCached(true).addFilepattern(missing).call();
         }
         Log.info("[{}] Calling Git add", name);
-        git.add().addFilepattern(".").call();
+        git.add(
+        ).setWorkingTreeIterator(
+                new NoGitignoreIterator(repo)
+        ).addFilepattern(".").call();
         Log.info("[{}] Calling Git commit", name);
         git.commit(
         ).setAuthor(

services/git-bridge/src/main/java/uk/ac/ic/wlgitbridge/bridge/repo/NoGitignoreIterator.java

@@ -0,0 +1,82 @@
+package uk.ac.ic.wlgitbridge.bridge.repo;
+
+import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.treewalk.FileTreeIterator;
+import org.eclipse.jgit.treewalk.WorkingTreeIterator;
+import org.eclipse.jgit.treewalk.WorkingTreeOptions;
+import org.eclipse.jgit.util.FS;
+
+import java.io.File;
+import java.lang.reflect.Field;
+
+/**
+ * Created by winston on 08/10/2016.
+ */
+public class NoGitignoreIterator extends FileTreeIterator {
+
+    private static final Field ignoreNodeField;
+
+    static {
+        try {
+            ignoreNodeField = WorkingTreeIterator.class.getDeclaredField(
+                    "ignoreNode"
+            );
+        } catch (NoSuchFieldException e) {
+            throw new RuntimeException(e);
+        }
+        ignoreNodeField.setAccessible(true);
+    }
+
+    public NoGitignoreIterator(Repository repo) {
+        super(repo);
+    }
+
+    public NoGitignoreIterator(
+            Repository repo,
+            FileModeStrategy fileModeStrategy
+    ) {
+        super(repo, fileModeStrategy);
+    }
+
+    public NoGitignoreIterator(File root, FS fs, WorkingTreeOptions options) {
+        super(root, fs, options);
+    }
+
+    public NoGitignoreIterator(
+            File root,
+            FS fs,
+            WorkingTreeOptions options,
+            FileModeStrategy fileModeStrategy
+    ) {
+        super(root, fs, options, fileModeStrategy);
+    }
+
+    @Deprecated
+    protected NoGitignoreIterator(WorkingTreeIterator p, File root, FS fs) {
+        super(p, root, fs);
+    }
+
+    protected NoGitignoreIterator(FileTreeIterator p, File root, FS fs) {
+        super(p, root, fs);
+    }
+
+    protected NoGitignoreIterator(
+            WorkingTreeIterator p,
+            File root,
+            FS fs,
+            FileModeStrategy fileModeStrategy
+    ) {
+        super(p, root, fs, fileModeStrategy);
+    }
+
+    @Override
+    protected void init(Entry[] list) {
+        super.init(list);
+        try {
+            ignoreNodeField.set(this, null);
+        } catch (IllegalAccessException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
+}

services/git-bridge/src/main/java/uk/ac/ic/wlgitbridge/bridge/ProjectRepo.java → services/git-bridge/src/main/java/uk/ac/ic/wlgitbridge/bridge/repo/ProjectRepo.java

@@ -1,4 +1,4 @@
-package uk.ac.ic.wlgitbridge.bridge;
+package uk.ac.ic.wlgitbridge.bridge.repo;
 
 import uk.ac.ic.wlgitbridge.bridge.repo.RepoStore;
 import uk.ac.ic.wlgitbridge.data.filestore.GitDirectoryContents;

services/git-bridge/src/main/java/uk/ac/ic/wlgitbridge/data/filestore/GitDirectoryContents.java

@@ -20,13 +20,38 @@ public class GitDirectoryContents {
     private final String commitMessage;
     private final Date when;
 
-    public GitDirectoryContents(List<RawFile> files, File rootGitDirectory, String projectName, Snapshot snapshot) {
+    public GitDirectoryContents(
+            List<RawFile> files,
+            File rootGitDirectory,
+            String projectName,
+            String userName,
+            String userEmail,
+            String commitMessage,
+            Date when
+    ) {
         this.files = files;
-        gitDirectory = new File(rootGitDirectory, projectName);
-        userName = snapshot.getUserName();
-        userEmail = snapshot.getUserEmail();
-        commitMessage = snapshot.getComment();
-        when = snapshot.getCreatedAt();
+        this.gitDirectory = new File(rootGitDirectory, projectName);
+        this.userName = userName;
+        this.userEmail = userEmail;
+        this.commitMessage = commitMessage;
+        this.when = when;
+    }
+
+    public GitDirectoryContents(
+            List<RawFile> files,
+            File rootGitDirectory,
+            String projectName,
+            Snapshot snapshot
+    ) {
+        this(
+                files,
+                rootGitDirectory,
+                projectName,
+                snapshot.getUserName(),
+                snapshot.getUserEmail(),
+                snapshot.getComment(),
+                snapshot.getCreatedAt()
+        );
     }
 
     public void write() throws IOException {

services/git-bridge/src/main/java/uk/ac/ic/wlgitbridge/data/filestore/RawFile.java

@@ -32,7 +32,8 @@ public abstract class RawFile {
             return false;
         }
         RawFile that = (RawFile) obj;
-        return getPath().equals(that.getPath()) && Arrays.equals(getContents(), that.getContents());
+        return getPath().equals(that.getPath())
+                && Arrays.equals(getContents(), that.getContents());
     }
 
 }

services/git-bridge/src/main/java/uk/ac/ic/wlgitbridge/git/handler/WLRepositoryResolver.java

@@ -8,7 +8,7 @@ import org.eclipse.jgit.transport.resolver.RepositoryResolver;
 import org.eclipse.jgit.transport.resolver.ServiceNotAuthorizedException;
 import org.eclipse.jgit.transport.resolver.ServiceNotEnabledException;
 import uk.ac.ic.wlgitbridge.bridge.Bridge;
-import uk.ac.ic.wlgitbridge.bridge.GitProjectRepo;
+import uk.ac.ic.wlgitbridge.bridge.repo.GitProjectRepo;
 import uk.ac.ic.wlgitbridge.git.exception.GitUserException;
 import uk.ac.ic.wlgitbridge.server.Oauth2Filter;
 import uk.ac.ic.wlgitbridge.snapshot.base.ForbiddenException;

services/git-bridge/src/test/java/uk/ac/ic/wlgitbridge/bridge/BridgeTest.java

@@ -5,6 +5,7 @@ import org.junit.Test;
 import uk.ac.ic.wlgitbridge.bridge.db.DBStore;
 import uk.ac.ic.wlgitbridge.bridge.db.ProjectState;
 import uk.ac.ic.wlgitbridge.bridge.lock.ProjectLock;
+import uk.ac.ic.wlgitbridge.bridge.repo.ProjectRepo;
 import uk.ac.ic.wlgitbridge.bridge.repo.RepoStore;
 import uk.ac.ic.wlgitbridge.bridge.resource.ResourceCache;
 import uk.ac.ic.wlgitbridge.bridge.snapshot.SnapshotAPI;

services/git-bridge/src/test/java/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepoTest.java

@@ -0,0 +1,124 @@
+package uk.ac.ic.wlgitbridge.bridge.repo;
+
+import com.google.api.client.repackaged.com.google.common.base.Preconditions;
+import org.apache.commons.io.FileUtils;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
+import uk.ac.ic.wlgitbridge.data.filestore.GitDirectoryContents;
+import uk.ac.ic.wlgitbridge.data.filestore.RawFile;
+import uk.ac.ic.wlgitbridge.data.filestore.RepositoryFile;
+import uk.ac.ic.wlgitbridge.util.Files;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.*;
+
+import static org.junit.Assert.assertEquals;
+
+/**
+ * Created by winston on 08/10/2016.
+ */
+public class GitProjectRepoTest {
+
+    public static File makeTempRepoDir(
+            TemporaryFolder tmpFolder,
+            String name
+    ) throws IOException {
+        File tmp = tmpFolder.newFolder(name);
+        Path rootdir = Paths.get(
+                "src/test/resources/uk/ac/ic/wlgitbridge/"
+                        + "bridge/repo/GitProjectRepoTest/rootdir"
+        );
+        FileUtils.copyDirectory(rootdir.toFile(), tmp);
+        Files.renameAll(tmp, "DOTgit", ".git");
+        return tmp;
+    }
+
+    private File rootdir;
+    FSGitRepoStore repoStore;
+    GitProjectRepo repo;
+
+    @Before
+    public void setup() throws IOException {
+        TemporaryFolder tmpFolder = new TemporaryFolder();
+        tmpFolder.create();
+        rootdir = makeTempRepoDir(tmpFolder, "rootdir");
+        repoStore = new FSGitRepoStore(rootdir.getAbsolutePath());
+        repo = new GitProjectRepo("repo");
+        repo.useExistingRepository(repoStore);
+    }
+
+    private GitDirectoryContents makeDirContents(
+            String... contents
+    ) {
+        Preconditions.checkArgument(contents.length % 2 == 0);
+        List<RawFile> files = new ArrayList<>(contents.length / 2);
+        for (int i = 0; i + 1 < contents.length; i += 2) {
+            files.add(
+                    new RepositoryFile(
+                            contents[i],
+                            contents[i + 1].getBytes(StandardCharsets.UTF_8)
+                    )
+            );
+        }
+        return new GitDirectoryContents(
+                files,
+                repoStore.getRootDirectory(),
+                "repo",
+                "Winston Li",
+                "git@winston.li",
+                "Commit Message",
+                new Date()
+        );
+    }
+
+    @Test
+    public void deletingIgnoredFileOnAppDeletesFromTheRepo(
+    ) throws IOException {
+        GitDirectoryContents contents = makeDirContents(
+                ".gitignore",
+                "*.ignored\n"
+        );
+        repo.commitAndGetMissing(contents);
+        repo.resetHard();
+        File dir = repo.getDirectory();
+        assertEquals(
+                new HashSet<String>(Arrays.asList(".git", ".gitignore")),
+                new HashSet<String>(Arrays.asList(dir.list()))
+        );
+    }
+
+    @Test
+    public void addingIgnoredFilesOnAppAddsToTheRepo() throws IOException {
+        GitDirectoryContents contents = makeDirContents(
+                ".gitignore",
+                "*.ignored\n",
+                "file1.ignored",
+                "",
+                "file1.txt",
+                "",
+                "file2.txt",
+                "",
+                "added.ignored",
+                ""
+        );
+        repo.commitAndGetMissing(contents);
+        repo.resetHard();
+        assertEquals(
+                new HashSet<String>(Arrays.asList(
+                        ".git",
+                        ".gitignore",
+                        "file1.ignored",
+                        "file1.txt",
+                        "file2.txt",
+                        "added.ignored"
+                )),
+                new HashSet<String>(Arrays.asList(repo.getDirectory().list()))
+        );
+    }
+
+}

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepoTest/rootdir/repo/.gitignore

@@ -0,0 +1,2 @@
+*.ignored
+

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepoTest/rootdir/repo/DOTgit/COMMIT_EDITMSG

@@ -0,0 +1 @@
+Add ignored file

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepoTest/rootdir/repo/DOTgit/HEAD

@@ -0,0 +1 @@
+ref: refs/heads/master

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepoTest/rootdir/repo/DOTgit/config

@@ -0,0 +1,7 @@
+[core]
+	repositoryformatversion = 0
+	filemode = true
+	bare = false
+	logallrefupdates = true
+	ignorecase = true
+	precomposeunicode = true

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepoTest/rootdir/repo/DOTgit/description

@@ -0,0 +1 @@
+Unnamed repository; edit this file 'description' to name the repository.

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepoTest/rootdir/repo/DOTgit/hooks/applypatch-msg.sample

@@ -0,0 +1,15 @@
+#!/bin/sh
+#
+# An example hook script to check the commit log message taken by
+# applypatch from an e-mail message.
+#
+# The hook should exit with non-zero status after issuing an
+# appropriate message if it wants to stop the commit.  The hook is
+# allowed to edit the commit message file.
+#
+# To enable this hook, rename this file to "applypatch-msg".
+
+. git-sh-setup
+commitmsg="$(git rev-parse --git-path hooks/commit-msg)"
+test -x "$commitmsg" && exec "$commitmsg" ${1+"$@"}
+:

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepoTest/rootdir/repo/DOTgit/hooks/commit-msg.sample

@@ -0,0 +1,24 @@
+#!/bin/sh
+#
+# An example hook script to check the commit log message.
+# Called by "git commit" with one argument, the name of the file
+# that has the commit message.  The hook should exit with non-zero
+# status after issuing an appropriate message if it wants to stop the
+# commit.  The hook is allowed to edit the commit message file.
+#
+# To enable this hook, rename this file to "commit-msg".
+
+# Uncomment the below to add a Signed-off-by line to the message.
+# Doing this in a hook is a bad idea in general, but the prepare-commit-msg
+# hook is more suited to it.
+#
+# SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^\(.*>\).*$/Signed-off-by: \1/p')
+# grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1"
+
+# This example catches duplicate Signed-off-by lines.
+
+test "" = "$(grep '^Signed-off-by: ' "$1" |
+	 sort | uniq -c | sed -e '/^[ 	]*1[ 	]/d')" || {
+	echo >&2 Duplicate Signed-off-by lines.
+	exit 1
+}

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepoTest/rootdir/repo/DOTgit/hooks/post-update.sample

@@ -0,0 +1,8 @@
+#!/bin/sh
+#
+# An example hook script to prepare a packed repository for use over
+# dumb transports.
+#
+# To enable this hook, rename this file to "post-update".
+
+exec git update-server-info

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepoTest/rootdir/repo/DOTgit/hooks/pre-applypatch.sample

@@ -0,0 +1,14 @@
+#!/bin/sh
+#
+# An example hook script to verify what is about to be committed
+# by applypatch from an e-mail message.
+#
+# The hook should exit with non-zero status after issuing an
+# appropriate message if it wants to stop the commit.
+#
+# To enable this hook, rename this file to "pre-applypatch".
+
+. git-sh-setup
+precommit="$(git rev-parse --git-path hooks/pre-commit)"
+test -x "$precommit" && exec "$precommit" ${1+"$@"}
+:

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepoTest/rootdir/repo/DOTgit/hooks/pre-commit.sample

@@ -0,0 +1,49 @@
+#!/bin/sh
+#
+# An example hook script to verify what is about to be committed.
+# Called by "git commit" with no arguments.  The hook should
+# exit with non-zero status after issuing an appropriate message if
+# it wants to stop the commit.
+#
+# To enable this hook, rename this file to "pre-commit".
+
+if git rev-parse --verify HEAD >/dev/null 2>&1
+then
+	against=HEAD
+else
+	# Initial commit: diff against an empty tree object
+	against=4b825dc642cb6eb9a060e54bf8d69288fbee4904
+fi
+
+# If you want to allow non-ASCII filenames set this variable to true.
+allownonascii=$(git config --bool hooks.allownonascii)
+
+# Redirect output to stderr.
+exec 1>&2
+
+# Cross platform projects tend to avoid non-ASCII filenames; prevent
+# them from being added to the repository. We exploit the fact that the
+# printable range starts at the space character and ends with tilde.
+if [ "$allownonascii" != "true" ] &&
+	# Note that the use of brackets around a tr range is ok here, (it's
+	# even required, for portability to Solaris 10's /usr/bin/tr), since
+	# the square bracket bytes happen to fall in the designated range.
+	test $(git diff --cached --name-only --diff-filter=A -z $against |
+	  LC_ALL=C tr -d '[ -~]\0' | wc -c) != 0
+then
+	cat <<\EOF
+Error: Attempt to add a non-ASCII file name.
+
+This can cause problems if you want to work with people on other platforms.
+
+To be portable it is advisable to rename the file.
+
+If you know what you are doing you can disable this check using:
+
+  git config hooks.allownonascii true
+EOF
+	exit 1
+fi
+
+# If there are whitespace errors, print the offending file names and fail.
+exec git diff-index --check --cached $against --

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepoTest/rootdir/repo/DOTgit/hooks/pre-push.sample

@@ -0,0 +1,53 @@
+#!/bin/sh
+
+# An example hook script to verify what is about to be pushed.  Called by "git
+# push" after it has checked the remote status, but before anything has been
+# pushed.  If this script exits with a non-zero status nothing will be pushed.
+#
+# This hook is called with the following parameters:
+#
+# $1 -- Name of the remote to which the push is being done
+# $2 -- URL to which the push is being done
+#
+# If pushing without using a named remote those arguments will be equal.
+#
+# Information about the commits which are being pushed is supplied as lines to
+# the standard input in the form:
+#
+#   <local ref> <local sha1> <remote ref> <remote sha1>
+#
+# This sample shows how to prevent push of commits where the log message starts
+# with "WIP" (work in progress).
+
+remote="$1"
+url="$2"
+
+z40=0000000000000000000000000000000000000000
+
+while read local_ref local_sha remote_ref remote_sha
+do
+	if [ "$local_sha" = $z40 ]
+	then
+		# Handle delete
+		:
+	else
+		if [ "$remote_sha" = $z40 ]
+		then
+			# New branch, examine all commits
+			range="$local_sha"
+		else
+			# Update to existing branch, examine new commits
+			range="$remote_sha..$local_sha"
+		fi
+
+		# Check for WIP commit
+		commit=`git rev-list -n 1 --grep '^WIP' "$range"`
+		if [ -n "$commit" ]
+		then
+			echo >&2 "Found WIP commit in $local_ref, not pushing"
+			exit 1
+		fi
+	fi
+done
+
+exit 0

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepoTest/rootdir/repo/DOTgit/hooks/pre-rebase.sample

@@ -0,0 +1,169 @@
+#!/bin/sh
+#
+# Copyright (c) 2006, 2008 Junio C Hamano
+#
+# The "pre-rebase" hook is run just before "git rebase" starts doing
+# its job, and can prevent the command from running by exiting with
+# non-zero status.
+#
+# The hook is called with the following parameters:
+#
+# $1 -- the upstream the series was forked from.
+# $2 -- the branch being rebased (or empty when rebasing the current branch).
+#
+# This sample shows how to prevent topic branches that are already
+# merged to 'next' branch from getting rebased, because allowing it
+# would result in rebasing already published history.
+
+publish=next
+basebranch="$1"
+if test "$#" = 2
+then
+	topic="refs/heads/$2"
+else
+	topic=`git symbolic-ref HEAD` ||
+	exit 0 ;# we do not interrupt rebasing detached HEAD
+fi
+
+case "$topic" in
+refs/heads/??/*)
+	;;
+*)
+	exit 0 ;# we do not interrupt others.
+	;;
+esac
+
+# Now we are dealing with a topic branch being rebased
+# on top of master.  Is it OK to rebase it?
+
+# Does the topic really exist?
+git show-ref -q "$topic" || {
+	echo >&2 "No such branch $topic"
+	exit 1
+}
+
+# Is topic fully merged to master?
+not_in_master=`git rev-list --pretty=oneline ^master "$topic"`
+if test -z "$not_in_master"
+then
+	echo >&2 "$topic is fully merged to master; better remove it."
+	exit 1 ;# we could allow it, but there is no point.
+fi
+
+# Is topic ever merged to next?  If so you should not be rebasing it.
+only_next_1=`git rev-list ^master "^$topic" ${publish} | sort`
+only_next_2=`git rev-list ^master           ${publish} | sort`
+if test "$only_next_1" = "$only_next_2"
+then
+	not_in_topic=`git rev-list "^$topic" master`
+	if test -z "$not_in_topic"
+	then
+		echo >&2 "$topic is already up-to-date with master"
+		exit 1 ;# we could allow it, but there is no point.
+	else
+		exit 0
+	fi
+else
+	not_in_next=`git rev-list --pretty=oneline ^${publish} "$topic"`
+	/usr/bin/perl -e '
+		my $topic = $ARGV[0];
+		my $msg = "* $topic has commits already merged to public branch:\n";
+		my (%not_in_next) = map {
+			/^([0-9a-f]+) /;
+			($1 => 1);
+		} split(/\n/, $ARGV[1]);
+		for my $elem (map {
+				/^([0-9a-f]+) (.*)$/;
+				[$1 => $2];
+			} split(/\n/, $ARGV[2])) {
+			if (!exists $not_in_next{$elem->[0]}) {
+				if ($msg) {
+					print STDERR $msg;
+					undef $msg;
+				}
+				print STDERR " $elem->[1]\n";
+			}
+		}
+	' "$topic" "$not_in_next" "$not_in_master"
+	exit 1
+fi
+
+exit 0
+
+################################################################
+
+This sample hook safeguards topic branches that have been
+published from being rewound.
+
+The workflow assumed here is:
+
+ * Once a topic branch forks from "master", "master" is never
+   merged into it again (either directly or indirectly).
+
+ * Once a topic branch is fully cooked and merged into "master",
+   it is deleted.  If you need to build on top of it to correct
+   earlier mistakes, a new topic branch is created by forking at
+   the tip of the "master".  This is not strictly necessary, but
+   it makes it easier to keep your history simple.
+
+ * Whenever you need to test or publish your changes to topic
+   branches, merge them into "next" branch.
+
+The script, being an example, hardcodes the publish branch name
+to be "next", but it is trivial to make it configurable via
+$GIT_DIR/config mechanism.
+
+With this workflow, you would want to know:
+
+(1) ... if a topic branch has ever been merged to "next".  Young
+    topic branches can have stupid mistakes you would rather
+    clean up before publishing, and things that have not been
+    merged into other branches can be easily rebased without
+    affecting other people.  But once it is published, you would
+    not want to rewind it.
+
+(2) ... if a topic branch has been fully merged to "master".
+    Then you can delete it.  More importantly, you should not
+    build on top of it -- other people may already want to
+    change things related to the topic as patches against your
+    "master", so if you need further changes, it is better to
+    fork the topic (perhaps with the same name) afresh from the
+    tip of "master".
+
+Let's look at this example:
+
+		   o---o---o---o---o---o---o---o---o---o "next"
+		  /       /           /           /
+		 /   a---a---b A     /           /
+		/   /               /           /
+	       /   /   c---c---c---c B         /
+	      /   /   /             \         /
+	     /   /   /   b---b C     \       /
+	    /   /   /   /             \     /
+    ---o---o---o---o---o---o---o---o---o---o---o "master"
+
+
+A, B and C are topic branches.
+
+ * A has one fix since it was merged up to "next".
+
+ * B has finished.  It has been fully merged up to "master" and "next",
+   and is ready to be deleted.
+
+ * C has not merged to "next" at all.
+
+We would want to allow C to be rebased, refuse A, and encourage
+B to be deleted.
+
+To compute (1):
+
+	git rev-list ^master ^topic next
+	git rev-list ^master        next
+
+	if these match, topic has not merged in next at all.
+
+To compute (2):
+
+	git rev-list master..topic
+
+	if this is empty, it is fully merged to "master".

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepoTest/rootdir/repo/DOTgit/hooks/prepare-commit-msg.sample

@@ -0,0 +1,36 @@
+#!/bin/sh
+#
+# An example hook script to prepare the commit log message.
+# Called by "git commit" with the name of the file that has the
+# commit message, followed by the description of the commit
+# message's source.  The hook's purpose is to edit the commit
+# message file.  If the hook fails with a non-zero status,
+# the commit is aborted.
+#
+# To enable this hook, rename this file to "prepare-commit-msg".
+
+# This hook includes three examples.  The first comments out the
+# "Conflicts:" part of a merge commit.
+#
+# The second includes the output of "git diff --name-status -r"
+# into the message, just before the "git status" output.  It is
+# commented because it doesn't cope with --amend or with squashed
+# commits.
+#
+# The third example adds a Signed-off-by line to the message, that can
+# still be edited.  This is rarely a good idea.
+
+case "$2,$3" in
+  merge,)
+    /usr/bin/perl -i.bak -ne 's/^/# /, s/^# #/#/ if /^Conflicts/ .. /#/; print' "$1" ;;
+
+# ,|template,)
+#   /usr/bin/perl -i.bak -pe '
+#      print "\n" . `git diff --cached --name-status -r`
+#	 if /^#/ && $first++ == 0' "$1" ;;
+
+  *) ;;
+esac
+
+# SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^\(.*>\).*$/Signed-off-by: \1/p')
+# grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1"

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepoTest/rootdir/repo/DOTgit/hooks/update.sample

@@ -0,0 +1,128 @@
+#!/bin/sh
+#
+# An example hook script to block unannotated tags from entering.
+# Called by "git receive-pack" with arguments: refname sha1-old sha1-new
+#
+# To enable this hook, rename this file to "update".
+#
+# Config
+# ------
+# hooks.allowunannotated
+#   This boolean sets whether unannotated tags will be allowed into the
+#   repository.  By default they won't be.
+# hooks.allowdeletetag
+#   This boolean sets whether deleting tags will be allowed in the
+#   repository.  By default they won't be.
+# hooks.allowmodifytag
+#   This boolean sets whether a tag may be modified after creation. By default
+#   it won't be.
+# hooks.allowdeletebranch
+#   This boolean sets whether deleting branches will be allowed in the
+#   repository.  By default they won't be.
+# hooks.denycreatebranch
+#   This boolean sets whether remotely creating branches will be denied
+#   in the repository.  By default this is allowed.
+#
+
+# --- Command line
+refname="$1"
+oldrev="$2"
+newrev="$3"
+
+# --- Safety check
+if [ -z "$GIT_DIR" ]; then
+	echo "Don't run this script from the command line." >&2
+	echo " (if you want, you could supply GIT_DIR then run" >&2
+	echo "  $0 <ref> <oldrev> <newrev>)" >&2
+	exit 1
+fi
+
+if [ -z "$refname" -o -z "$oldrev" -o -z "$newrev" ]; then
+	echo "usage: $0 <ref> <oldrev> <newrev>" >&2
+	exit 1
+fi
+
+# --- Config
+allowunannotated=$(git config --bool hooks.allowunannotated)
+allowdeletebranch=$(git config --bool hooks.allowdeletebranch)
+denycreatebranch=$(git config --bool hooks.denycreatebranch)
+allowdeletetag=$(git config --bool hooks.allowdeletetag)
+allowmodifytag=$(git config --bool hooks.allowmodifytag)
+
+# check for no description
+projectdesc=$(sed -e '1q' "$GIT_DIR/description")
+case "$projectdesc" in
+"Unnamed repository"* | "")
+	echo "*** Project description file hasn't been set" >&2
+	exit 1
+	;;
+esac
+
+# --- Check types
+# if $newrev is 0000...0000, it's a commit to delete a ref.
+zero="0000000000000000000000000000000000000000"
+if [ "$newrev" = "$zero" ]; then
+	newrev_type=delete
+else
+	newrev_type=$(git cat-file -t $newrev)
+fi
+
+case "$refname","$newrev_type" in
+	refs/tags/*,commit)
+		# un-annotated tag
+		short_refname=${refname##refs/tags/}
+		if [ "$allowunannotated" != "true" ]; then
+			echo "*** The un-annotated tag, $short_refname, is not allowed in this repository" >&2
+			echo "*** Use 'git tag [ -a | -s ]' for tags you want to propagate." >&2
+			exit 1
+		fi
+		;;
+	refs/tags/*,delete)
+		# delete tag
+		if [ "$allowdeletetag" != "true" ]; then
+			echo "*** Deleting a tag is not allowed in this repository" >&2
+			exit 1
+		fi
+		;;
+	refs/tags/*,tag)
+		# annotated tag
+		if [ "$allowmodifytag" != "true" ] && git rev-parse $refname > /dev/null 2>&1
+		then
+			echo "*** Tag '$refname' already exists." >&2
+			echo "*** Modifying a tag is not allowed in this repository." >&2
+			exit 1
+		fi
+		;;
+	refs/heads/*,commit)
+		# branch
+		if [ "$oldrev" = "$zero" -a "$denycreatebranch" = "true" ]; then
+			echo "*** Creating a branch is not allowed in this repository" >&2
+			exit 1
+		fi
+		;;
+	refs/heads/*,delete)
+		# delete branch
+		if [ "$allowdeletebranch" != "true" ]; then
+			echo "*** Deleting a branch is not allowed in this repository" >&2
+			exit 1
+		fi
+		;;
+	refs/remotes/*,commit)
+		# tracking branch
+		;;
+	refs/remotes/*,delete)
+		# delete tracking branch
+		if [ "$allowdeletebranch" != "true" ]; then
+			echo "*** Deleting a tracking branch is not allowed in this repository" >&2
+			exit 1
+		fi
+		;;
+	*)
+		# Anything else (is there anything else?)
+		echo "*** Update hook: unknown type of update to ref $refname of type $newrev_type" >&2
+		exit 1
+		;;
+esac
+
+# --- Finished
+exit 0

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepoTest/rootdir/repo/DOTgit/info/exclude

@@ -0,0 +1,6 @@
+# git ls-files --others --exclude-from=.git/info/exclude
+# Lines that start with '#' are comments.
+# For a project mostly in C, the following would be a good set of
+# exclude patterns (uncomment them if you want to use them):
+# *.[oa]
+# *~

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepoTest/rootdir/repo/DOTgit/logs/HEAD

@@ -0,0 +1,2 @@
+0000000000000000000000000000000000000000 4a64431a59519ff25eff2cd94a561081146059b7 Winston Li <git@winston.li> 1475933347 +0100	commit (initial): Initial commit
+4a64431a59519ff25eff2cd94a561081146059b7 71ebe5d70c8634f7531cc09c1cad5dae951a9052 Winston Li <git@winston.li> 1475933399 +0100	commit: Add ignored file

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepoTest/rootdir/repo/DOTgit/logs/refs/heads/master

@@ -0,0 +1,2 @@
+0000000000000000000000000000000000000000 4a64431a59519ff25eff2cd94a561081146059b7 Winston Li <git@winston.li> 1475933347 +0100	commit (initial): Initial commit
+4a64431a59519ff25eff2cd94a561081146059b7 71ebe5d70c8634f7531cc09c1cad5dae951a9052 Winston Li <git@winston.li> 1475933399 +0100	commit: Add ignored file

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepoTest/rootdir/repo/DOTgit/objects/4a/64431a59519ff25eff2cd94a561081146059b7

@@ -0,0 +1,3 @@
+x
•ΝΑ
+!€αΞ>Εάƒpt"Ίέ;«i
μ*l½~Π>AΗ�πρ—±,,€w²Φ
+6�¦­qƒkΥ`Ι!"Oχ�Γ”I'BίZTι-Ο±Β�ϋKF‡+ΓρΑrώl}�ω8y­µ“‡½F­UωΝ¤ώΙΤ¥³p�aσκ�6>

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/bridge/repo/GitProjectRepoTest/rootdir/repo/DOTgit/refs/heads/master

@@ -0,0 +1 @@
+71ebe5d70c8634f7531cc09c1cad5dae951a9052