thodg/libgit2

diff --git a/include/git2/config.h b/include/git2/config.h
index f415fbd..21d8a0b 100644
--- a/include/git2/config.h
+++ b/include/git2/config.h
@@ -80,15 +80,16 @@ GIT_EXTERN(int) git_config_find_global(char *global_config_path, size_t length);
 GIT_EXTERN(int) git_config_find_system(char *system_config_path, size_t length);
 
 /**
- * Open the global configuration file
+ * Open the global and system configuration files
  *
- * Utility wrapper that calls `git_config_find_global`
- * and opens the located file, if it exists.
+ * Utility wrapper that finds the global and system configuration files
+ * and opens them into a single prioritized config object that can be
+ * used when accessing default config data outside a repository.
  *
  * @param out Pointer to store the config instance
  * @return 0 or an error code
  */
-GIT_EXTERN(int) git_config_open_global(git_config **out);
+GIT_EXTERN(int) git_config_open_default(git_config **out);
 
 /**
  * Create a configuration file backend for ondisk files
diff --git a/include/git2/repository.h b/include/git2/repository.h
index e727ff3..f520d54 100644
--- a/include/git2/repository.h
+++ b/include/git2/repository.h
@@ -83,6 +83,18 @@ GIT_EXTERN(int) git_repository_discover(
 		int across_fs,
 		const char *ceiling_dirs);
 
+/**
+ * Option flags for `git_repository_open_ext`.
+ *
+ * * GIT_REPOSITORY_OPEN_NO_SEARCH - Only open the repository if it can be
+ *   immediately found in the start_path.  Do not walk up from the
+ *   start_path looking at parent directories.
+ * * GIT_REPOSITORY_OPEN_CROSS_FS - Unless this flag is set, open will not
+ *   continue searching across filesystem boundaries (i.e. when `st_dev`
+ *   changes from the `stat` system call).  (E.g. Searching in a user's home
+ *   directory "/home/user/source/" will not return "/.git/" as the found
+ *   repo if "/" is a different filesystem than "/home".)
+ */
 enum {
 	GIT_REPOSITORY_OPEN_NO_SEARCH = (1 << 0),
 	GIT_REPOSITORY_OPEN_CROSS_FS  = (1 << 1),
@@ -90,6 +102,20 @@ enum {
 
 /**
  * Find and open a repository with extended controls.
+ *
+ * @param repo_out Pointer to the repo which will be opened.  This can
+ *        actually be NULL if you only want to use the error code to
+ *        see if a repo at this path could be opened.
+ * @param start_path Path to open as git repository.  If the flags
+ *        permit "searching", then this can be a path to a subdirectory
+ *        inside the working directory of the repository.
+ * @param flags A combination of the GIT_REPOSITORY_OPEN flags above.
+ * @param ceiling_dirs A GIT_PATH_LIST_SEPARATOR delimited list of path
+ *        prefixes at which the search for a containing repository should
+ *        terminate.
+ * @return 0 on success, GIT_ENOTFOUND if no repository could be found,
+ *        or -1 if there was a repository but open failed for some reason
+ *        (such as repo corruption or system errors).
  */
 GIT_EXTERN(int) git_repository_open_ext(
 	git_repository **repo,
@@ -118,13 +144,127 @@ GIT_EXTERN(void) git_repository_free(git_repository *repo);
  *
  * @param repo_out pointer to the repo which will be created or reinitialized
  * @param path the path to the repository
- * @param is_bare if true, a Git repository without a working directory is created
- *		at the pointed path. If false, provided path will be considered as the working
- *		directory into which the .git directory will be created.
+ * @param is_bare if true, a Git repository without a working directory is
+ *		created at the pointed path. If false, provided path will be
+ *		considered as the working directory into which the .git directory
+ *		will be created.
  *
  * @return 0 or an error code
  */
-GIT_EXTERN(int) git_repository_init(git_repository **repo_out, const char *path, unsigned is_bare);
+GIT_EXTERN(int) git_repository_init(
+	git_repository **repo_out,
+	const char *path,
+	unsigned is_bare);
+
+/**
+ * Option flags for `git_repository_init_ext`.
+ *
+ * These flags configure extra behaviors to `git_repository_init_ext`.
+ * In every case, the default behavior is the zero value (i.e. flag is
+ * not set).  Just OR the flag values together for the `flags` parameter
+ * when initializing a new repo.  Details of individual values are:
+ *
+ * * BARE   - Create a bare repository with no working directory.
+ * * NO_REINIT - Return an EEXISTS error if the repo_path appears to
+ *        already be an git repository.
+ * * NO_DOTGIT_DIR - Normally a "/.git/" will be appended to the repo
+ *        path for non-bare repos (if it is not already there), but
+ *        passing this flag prevents that behavior.
+ * * MKDIR  - Make the repo_path (and workdir_path) as needed.  Init is
+ *        always willing to create the ".git" directory even without this
+ *        flag.  This flag tells init to create the trailing component of
+ *        the repo and workdir paths as needed.
+ * * MKPATH - Recursively make all components of the repo and workdir
+ *        paths as necessary.
+ * * EXTERNAL_TEMPLATE - libgit2 normally uses internal templates to
+ *        initialize a new repo.  This flags enables external templates,
+ *        looking the "template_path" from the options if set, or the
+ *        `init.templatedir` global config if not, or falling back on
+ *        "/usr/share/git-core/templates" if it exists.
+ */
+enum {
+	GIT_REPOSITORY_INIT_BARE              = (1u << 0),
+	GIT_REPOSITORY_INIT_NO_REINIT         = (1u << 1),
+	GIT_REPOSITORY_INIT_NO_DOTGIT_DIR     = (1u << 2),
+	GIT_REPOSITORY_INIT_MKDIR             = (1u << 3),
+	GIT_REPOSITORY_INIT_MKPATH            = (1u << 4),
+	GIT_REPOSITORY_INIT_EXTERNAL_TEMPLATE = (1u << 5),
+};
+
+/**
+ * Mode options for `git_repository_init_ext`.
+ *
+ * Set the mode field of the `git_repository_init_options` structure
+ * either to the custom mode that you would like, or to one of the
+ * following modes:
+ *
+ * * SHARED_UMASK - Use permissions configured by umask - the default.
+ * * SHARED_GROUP - Use "--shared=group" behavior, chmod'ing the new repo
+ *        to be group writable and "g+sx" for sticky group assignment.
+ * * SHARED_ALL - Use "--shared=all" behavior, adding world readability.
+ * * Anything else - Set to custom value.
+ */
+enum {
+	GIT_REPOSITORY_INIT_SHARED_UMASK = 0,
+	GIT_REPOSITORY_INIT_SHARED_GROUP = 0002775,
+	GIT_REPOSITORY_INIT_SHARED_ALL   = 0002777,
+};
+
+/**
+ * Extended options structure for `git_repository_init_ext`.
+ *
+ * This contains extra options for `git_repository_init_ext` that enable
+ * additional initialization features.  The fields are:
+ *
+ * * flags - Combination of GIT_REPOSITORY_INIT flags above.
+ * * mode  - Set to one of the standard GIT_REPOSITORY_INIT_SHARED_...
+ *        constants above, or to a custom value that you would like.
+ * * workdir_path - The path to the working dir or NULL for default (i.e.
+ *        repo_path parent on non-bare repos).  IF THIS IS RELATIVE PATH,
+ *        IT WILL BE EVALUATED RELATIVE TO THE REPO_PATH.  If this is not
+ *        the "natural" working directory, a .git gitlink file will be
+ *        created here linking to the repo_path.
+ * * description - If set, this will be used to initialize the "description"
+ *        file in the repository, instead of using the template content.
+ * * template_path - When GIT_REPOSITORY_INIT_EXTERNAL_TEMPLATE is set,
+ *        this contains the path to use for the template directory.  If
+ *        this is NULL, the config or default directory options will be
+ *        used instead.
+ * * initial_head - The name of the head to point HEAD at.  If NULL, then
+ *        this will be treated as "master" and the HEAD ref will be set
+ *        to "refs/heads/master".  If this begins with "refs/" it will be
+ *        used verbatim; otherwise "refs/heads/" will be prefixed.
+ * * origin_url - If this is non-NULL, then after the rest of the
+ *        repository initialization is completed, an "origin" remote
+ *        will be added pointing to this URL.
+ */
+typedef struct {
+	uint32_t    flags;
+	uint32_t    mode;
+	const char *workdir_path;
+	const char *description;
+	const char *template_path;
+	const char *initial_head;
+	const char *origin_url;
+} git_repository_init_options;
+
+/**
+ * Create a new Git repository in the given folder with extended controls.
+ *
+ * This will initialize a new git repository (creating the repo_path
+ * if requested by flags) and working directory as needed.  It will
+ * auto-detect the case sensitivity of the file system and if the
+ * file system supports file mode bits correctly.
+ *
+ * @param repo_out Pointer to the repo which will be created or reinitialized.
+ * @param repo_path The path to the repository.
+ * @param opts Pointer to git_repository_init_options struct.
+ * @return 0 or an error code on failure.
+ */
+GIT_EXTERN(int) git_repository_init_ext(
+	git_repository **repo_out,
+	const char *repo_path,
+	git_repository_init_options *opts);
 
 /**
  * Retrieve and resolve the reference pointed at by HEAD.
@@ -326,6 +466,11 @@ GIT_EXTERN(void) git_repository_set_index(git_repository *repo, git_index *index
  *
  * Use this function to get the contents of this file. Don't forget to
  * remove the file after you create the commit.
+ *
+ * @param buffer Buffer to write data into or NULL to just read required size
+ * @param len Length of buffer in bytes
+ * @param repo Repository to read prepared message from
+ * @return Bytes written to buffer, GIT_ENOTFOUND if no message, or -1 on error
  */
 GIT_EXTERN(int) git_repository_message(char *buffer, size_t len, git_repository *repo);
 
diff --git a/src/attr_file.c b/src/attr_file.c
index 20b3cf6..b2f312e 100644
--- a/src/attr_file.c
+++ b/src/attr_file.c
@@ -250,18 +250,15 @@ git_attr_assignment *git_attr_rule__lookup_assignment(
 int git_attr_path__init(
 	git_attr_path *info, const char *path, const char *base)
 {
+	ssize_t root;
+
 	/* build full path as best we can */
 	git_buf_init(&info->full, 0);
 
-	if (base != NULL && git_path_root(path) < 0) {
-		if (git_buf_joinpath(&info->full, base, path) < 0)
-			return -1;
-		info->path = info->full.ptr + strlen(base);
-	} else {
-		if (git_buf_sets(&info->full, path) < 0)
-			return -1;
-		info->path = info->full.ptr;
-	}
+	if (git_path_join_unrooted(&info->full, path, base, &root) < 0)
+		return -1;
+
+	info->path = info->full.ptr + root;
 
 	/* remove trailing slashes */
 	while (info->full.size > 0) {
diff --git a/src/config.c b/src/config.c
index 44cfe76..277daaa 100644
--- a/src/config.c
+++ b/src/config.c
@@ -501,17 +501,28 @@ int git_config_find_system(char *system_config_path, size_t length)
 	return 0;
 }
 
-int git_config_open_global(git_config **out)
+int git_config_open_default(git_config **out)
 {
 	int error;
-	git_buf path = GIT_BUF_INIT;
+	git_config *cfg = NULL;
+	git_buf buf = GIT_BUF_INIT;
 
-	if ((error = git_config_find_global_r(&path)) < 0)
-		return error;
+	error = git_config_new(&cfg);
 
-	error = git_config_open_ondisk(out, git_buf_cstr(&path));
-	git_buf_free(&path);
+	if (!error && !git_config_find_global_r(&buf))
+		error = git_config_add_file_ondisk(cfg, buf.ptr, 2);
+
+	if (!error && !git_config_find_system_r(&buf))
+		error = git_config_add_file_ondisk(cfg, buf.ptr, 1);
+
+	git_buf_free(&buf);
+
+	if (error && cfg) {
+		git_config_free(cfg);
+		cfg = NULL;
+	}
+
+	*out = cfg;
 
 	return error;
 }
-
diff --git a/src/fileops.c b/src/fileops.c
index 4de58b0..5df3123 100644
--- a/src/fileops.c
+++ b/src/fileops.c
@@ -10,19 +10,8 @@
 
 int git_futils_mkpath2file(const char *file_path, const mode_t mode)
 {
-	int result = 0;
-	git_buf target_folder = GIT_BUF_INIT;
-
-	if (git_path_dirname_r(&target_folder, file_path) < 0)
-		return -1;
-
-	/* Does the containing folder exist? */
-	if (git_path_isdir(target_folder.ptr) == false)
-		/* Let's create the tree structure */
-		result = git_futils_mkdir_r(target_folder.ptr, NULL, mode);
-
-	git_buf_free(&target_folder);
-	return result;
+	return git_futils_mkdir(
+		file_path, NULL, mode, GIT_MKDIR_PATH | GIT_MKDIR_SKIP_LAST);
 }
 
 int git_futils_mktmp(git_buf *path_out, const char *filename)
@@ -239,66 +228,92 @@ void git_futils_mmap_free(git_map *out)
 	p_munmap(out);
 }
 
-int git_futils_mkdir_r(const char *path, const char *base, const mode_t mode)
+int git_futils_mkdir(
+	const char *path,
+	const char *base,
+	mode_t mode,
+	uint32_t flags)
 {
 	git_buf make_path = GIT_BUF_INIT;
-	size_t start = 0;
-	char *pp, *sp;
-	bool failed = false;
-
-	if (base != NULL) {
-		/*
-		 * when a base is being provided, it is supposed to already exist.
-		 * Therefore, no attempt is being made to recursively create this leading path
-		 * segment. It's just skipped. */
-		start = strlen(base);
-		if (git_buf_joinpath(&make_path, base, path) < 0)
-			return -1;
-	} else {
-		int root_path_offset;
+	ssize_t root = 0;
+	char lastch, *tail;
 
-		if (git_buf_puts(&make_path, path) < 0)
-			return -1;
+	/* build path and find "root" where we should start calling mkdir */
+	if (git_path_join_unrooted(&make_path, path, base, &root) < 0)
+		return -1;
 
-		root_path_offset = git_path_root(make_path.ptr);
-		if (root_path_offset > 0) {
-			 /*
-			  * On Windows, will skip the drive name (eg. C: or D:)
-			  * or the leading part of a network path (eg. //computer_name ) */
-			start = root_path_offset;
-		}
+	if (make_path.size == 0) {
+		giterr_set(GITERR_OS, "Attempt to create empty path");
+		goto fail;
 	}
 
-	pp = make_path.ptr + start;
-
-	while (!failed && (sp = strchr(pp, '/')) != NULL) {
-		if (sp != pp && git_path_isdir(make_path.ptr) == false) {
-			*sp = 0;
-
-			/* Do not choke while trying to recreate an existing directory */
-			if (p_mkdir(make_path.ptr, mode) < 0 && errno != EEXIST)
-				failed = true;
+	/* remove trailing slashes on path */
+	while (make_path.ptr[make_path.size - 1] == '/') {
+		make_path.size--;
+		make_path.ptr[make_path.size] = '\0';
+	}
 
-			*sp = '/';
+	/* if we are not supposed to made the last element, truncate it */
+	if ((flags & GIT_MKDIR_SKIP_LAST) != 0)
+		git_buf_rtruncate_at_char(&make_path, '/');
+
+	/* if we are not supposed to make the whole path, reset root */
+	if ((flags & GIT_MKDIR_PATH) == 0)
+		root = git_buf_rfind(&make_path, '/');
+
+	/* clip root to make_path length */
+	if (root >= (ssize_t)make_path.size)
+		root = (ssize_t)make_path.size - 1;
+	if (root < 0)
+		root = 0;
+
+	tail = & make_path.ptr[root];
+
+	while (*tail) {
+		/* advance tail to include next path component */
+		while (*tail == '/')
+			tail++;
+		while (*tail && *tail != '/')
+			tail++;
+
+		/* truncate path at next component */
+		lastch = *tail;
+		*tail = '\0';
+
+		/* make directory */
+		if (p_mkdir(make_path.ptr, mode) < 0 &&
+			(errno != EEXIST || (flags & GIT_MKDIR_EXCL) != 0))
+		{
+			giterr_set(GITERR_OS, "Failed to make directory '%s'",
+				make_path.ptr);
+			goto fail;
 		}
 
-		pp = sp + 1;
-	}
+		/* chmod if requested */
+		if ((flags & GIT_MKDIR_CHMOD_PATH) != 0 ||
+			((flags & GIT_MKDIR_CHMOD) != 0 && lastch == '\0'))
+		{
+			if (p_chmod(make_path.ptr, mode) < 0) {
+				giterr_set(GITERR_OS, "Failed to set permissions on '%s'",
+					make_path.ptr);
+				goto fail;
+			}
+		}
 
-	if (*pp != '\0' && !failed) {
-		if (p_mkdir(make_path.ptr, mode) < 0 && errno != EEXIST)
-			failed = true;
+		*tail = lastch;
 	}
 
 	git_buf_free(&make_path);
+	return 0;
 
-	if (failed) {
-		giterr_set(GITERR_OS,
-			"Failed to create directory structure at '%s'", path);
-		return -1;
-	}
+fail:
+	git_buf_free(&make_path);
+	return -1;
+}
 
-	return 0;
+int git_futils_mkdir_r(const char *path, const char *base, const mode_t mode)
+{
+	return git_futils_mkdir(path, base, mode, GIT_MKDIR_PATH);
 }
 
 static int _rmdir_recurs_foreach(void *opaque, git_buf *path)
@@ -495,3 +510,196 @@ int git_futils_fake_symlink(const char *old, const char *new)
 	}
 	return retcode;
 }
+
+static int cp_by_fd(int ifd, int ofd, bool close_fd_when_done)
+{
+	int error = 0;
+	char buffer[4096];
+	ssize_t len = 0;
+
+	while (!error && (len = p_read(ifd, buffer, sizeof(buffer))) > 0)
+		/* p_write() does not have the same semantics as write().  It loops
+		 * internally and will return 0 when it has completed writing.
+		 */
+		error = p_write(ofd, buffer, len);
+
+	if (len < 0) {
+		giterr_set(GITERR_OS, "Read error while copying file");
+		error = (int)len;
+	}
+
+	if (close_fd_when_done) {
+		p_close(ifd);
+		p_close(ofd);
+	}
+
+	return error;
+}
+
+int git_futils_cp(const char *from, const char *to, mode_t filemode)
+{
+	int ifd, ofd;
+
+	if ((ifd = git_futils_open_ro(from)) < 0)
+		return ifd;
+
+	if ((ofd = p_open(to, O_WRONLY | O_CREAT | O_EXCL, filemode)) < 0) {
+		if (errno == ENOENT || errno == ENOTDIR)
+			ofd = GIT_ENOTFOUND;
+		giterr_set(GITERR_OS, "Failed to open '%s' for writing", to);
+		p_close(ifd);
+		return ofd;
+	}
+
+	return cp_by_fd(ifd, ofd, true);
+}
+
+static int cp_link(const char *from, const char *to, size_t link_size)
+{
+	int error = 0;
+	ssize_t read_len;
+	char *link_data = git__malloc(link_size + 1);
+	GITERR_CHECK_ALLOC(link_data);
+
+	read_len = p_readlink(from, link_data, link_size);
+	if (read_len != (ssize_t)link_size) {
+		giterr_set(GITERR_OS, "Failed to read symlink data for '%s'", from);
+		error = -1;
+	}
+	else {
+		link_data[read_len] = '\0';
+
+		if (p_symlink(link_data, to) < 0) {
+			giterr_set(GITERR_OS, "Could not symlink '%s' as '%s'",
+				link_data, to);
+			error = -1;
+		}
+	}
+
+	git__free(link_data);
+	return error;
+}
+
+typedef struct {
+	const char *to_root;
+	git_buf to;
+	ssize_t from_prefix;
+	uint32_t flags;
+	uint32_t mkdir_flags;
+	mode_t dirmode;
+} cp_r_info;
+
+static int _cp_r_callback(void *ref, git_buf *from)
+{
+	cp_r_info *info = ref;
+	struct stat from_st, to_st;
+	bool exists = false;
+
+	if ((info->flags & GIT_CPDIR_COPY_DOTFILES) == 0 &&
+		from->ptr[git_path_basename_offset(from)] == '.')
+		return 0;
+
+	if (git_buf_joinpath(
+			&info->to, info->to_root, from->ptr + info->from_prefix) < 0)
+		return -1;
+
+	if (p_lstat(info->to.ptr, &to_st) < 0) {
+		if (errno != ENOENT) {
+			giterr_set(GITERR_OS,
+				"Could not access %s while copying files", info->to.ptr);
+			return -1;
+		}
+	} else
+		exists = true;
+
+	if (git_path_lstat(from->ptr, &from_st) < 0)
+		return -1;
+
+	if (S_ISDIR(from_st.st_mode)) {
+		int error = 0;
+		mode_t oldmode = info->dirmode;
+
+		/* if we are not chmod'ing, then overwrite dirmode */
+		if ((info->flags & GIT_CPDIR_CHMOD) == 0)
+			info->dirmode = from_st.st_mode;
+
+		/* make directory now if CREATE_EMPTY_DIRS is requested and needed */
+		if (!exists && (info->flags & GIT_CPDIR_CREATE_EMPTY_DIRS) != 0)
+			error = git_futils_mkdir(
+				info->to.ptr, NULL, info->dirmode, info->mkdir_flags);
+
+		/* recurse onto target directory */
+		if (!exists || S_ISDIR(to_st.st_mode))
+			error = git_path_direach(from, _cp_r_callback, info);
+
+		if (oldmode != 0)
+			info->dirmode = oldmode;
+
+		return error;
+	}
+
+	if (exists) {
+		if ((info->flags & GIT_CPDIR_OVERWRITE) == 0)
+			return 0;
+
+		if (p_unlink(info->to.ptr) < 0) {
+			giterr_set(GITERR_OS, "Cannot overwrite existing file '%s'",
+				info->to.ptr);
+			return -1;
+		}
+	}
+
+	/* Done if this isn't a regular file or a symlink */
+	if (!S_ISREG(from_st.st_mode) &&
+		(!S_ISLNK(from_st.st_mode) ||
+		 (info->flags & GIT_CPDIR_COPY_SYMLINKS) == 0))
+		return 0;
+
+	/* Make container directory on demand if needed */
+	if ((info->flags & GIT_CPDIR_CREATE_EMPTY_DIRS) == 0 &&
+		git_futils_mkdir(
+			info->to.ptr, NULL, info->dirmode, info->mkdir_flags) < 0)
+		return -1;
+
+	/* make symlink or regular file */
+	if (S_ISLNK(from_st.st_mode))
+		return cp_link(from->ptr, info->to.ptr, (size_t)from_st.st_size);
+	else
+		return git_futils_cp(from->ptr, info->to.ptr, from_st.st_mode);
+}
+
+int git_futils_cp_r(
+	const char *from,
+	const char *to,
+	uint32_t flags,
+	mode_t dirmode)
+{
+	int error;
+	git_buf path = GIT_BUF_INIT;
+	cp_r_info info;
+
+	if (git_buf_sets(&path, from) < 0)
+		return -1;
+
+	info.to_root = to;
+	info.flags   = flags;
+	info.dirmode = dirmode;
+	info.from_prefix = path.size;
+	git_buf_init(&info.to, 0);
+
+	/* precalculate mkdir flags */
+	if ((flags & GIT_CPDIR_CREATE_EMPTY_DIRS) == 0) {
+		info.mkdir_flags = GIT_MKDIR_PATH | GIT_MKDIR_SKIP_LAST;
+		if ((flags & GIT_CPDIR_CHMOD) != 0)
+			info.mkdir_flags |= GIT_MKDIR_CHMOD_PATH;
+	} else {
+		info.mkdir_flags =
+			((flags & GIT_CPDIR_CHMOD) != 0) ? GIT_MKDIR_CHMOD : 0;
+	}
+
+	error = _cp_r_callback(&info, &path);
+
+	git_buf_free(&path);
+
+	return error;
+}
diff --git a/src/fileops.h b/src/fileops.h
index 594eacb..5c23ce3 100644
--- a/src/fileops.h
+++ b/src/fileops.h
@@ -50,12 +50,47 @@ extern int git_futils_creat_locked_withpath(const char *path, const mode_t dirmo
 /**
  * Create a path recursively
  *
- * If a base parameter is being passed, it's expected to be valued with a path pointing to an already
- * exisiting directory.
+ * If a base parameter is being passed, it's expected to be valued with a
+ * path pointing to an already existing directory.
  */
 extern int git_futils_mkdir_r(const char *path, const char *base, const mode_t mode);
 
 /**
+ * Flags to pass to `git_futils_mkdir`.
+ *
+ * * GIT_MKDIR_EXCL is "exclusive" - i.e. generate an error if dir exists.
+ * * GIT_MKDIR_PATH says to make all components in the path.
+ * * GIT_MKDIR_CHMOD says to chmod the final directory entry after creation
+ * * GIT_MKDIR_CHMOD_PATH says to chmod each directory component in the path
+ * * GIT_MKDIR_SKIP_LAST says to leave off the last element of the path
+ *
+ * Note that the chmod options will be executed even if the directory already
+ * exists, unless GIT_MKDIR_EXCL is given.
+ */
+typedef enum {
+	GIT_MKDIR_EXCL = 1,
+	GIT_MKDIR_PATH = 2,
+	GIT_MKDIR_CHMOD = 4,
+	GIT_MKDIR_CHMOD_PATH = 8,
+	GIT_MKDIR_SKIP_LAST = 16
+} git_futils_mkdir_flags;
+
+/**
+ * Create a directory or entire path.
+ *
+ * This makes a directory (and the entire path leading up to it if requested),
+ * and optionally chmods the directory immediately after (or each part of the
+ * path if requested).
+ *
+ * @param path The path to create.
+ * @param base Root for relative path.  These directories will never be made.
+ * @param mode The mode to use for created directories.
+ * @param flags Combination of the mkdir flags above.
+ * @return 0 on success, else error code
+ */
+extern int git_futils_mkdir(const char *path, const char *base, mode_t mode, uint32_t flags);
+
+/**
  * Create all the folders required to contain
  * the full path of a file
  */
@@ -95,6 +130,45 @@ extern int git_futils_mktmp(git_buf *path_out, const char *filename);
 extern int git_futils_mv_withpath(const char *from, const char *to, const mode_t dirmode);
 
 /**
+ * Copy a file
+ *
+ * The filemode will be used for the newly created file.
+ */
+extern int git_futils_cp(
+	const char *from,
+	const char *to,
+	mode_t filemode);
+
+/**
+ * Flags that can be passed to `git_futils_cp_r`.
+ */
+typedef enum {
+	GIT_CPDIR_CREATE_EMPTY_DIRS = 1,
+	GIT_CPDIR_COPY_SYMLINKS = 2,
+	GIT_CPDIR_COPY_DOTFILES = 4,
+	GIT_CPDIR_OVERWRITE = 8,
+	GIT_CPDIR_CHMOD = 16
+} git_futils_cpdir_flags;
+
+/**
+ * Copy a directory tree.
+ *
+ * This copies directories and files from one root to another.  You can
+ * pass a combinationof GIT_CPDIR flags as defined above.
+ *
+ * If you pass the CHMOD flag, then the dirmode will be applied to all
+ * directories that are created during the copy, overiding the natural
+ * permissions.  If you do not pass the CHMOD flag, then the dirmode
+ * will actually be copied from the source files and the `dirmode` arg
+ * will be ignored.
+ */
+extern int git_futils_cp_r(
+	const char *from,
+	const char *to,
+	uint32_t flags,
+	mode_t dirmode);
+
+/**
  * Open a file readonly and set error if needed.
  */
 extern int git_futils_open_ro(const char *path);
diff --git a/src/message.c b/src/message.c
index e6dedc9..791b694 100644
--- a/src/message.c
+++ b/src/message.c
@@ -82,5 +82,5 @@ int git_message_prettify(char *message_out, size_t buffer_size, const char *mess
 
 done:
 	git_buf_free(&buf);
-	return out_size;
+	return (int)out_size;
 }
diff --git a/src/path.c b/src/path.c
index 22391c5..1518885 100644
--- a/src/path.c
+++ b/src/path.c
@@ -147,6 +147,20 @@ char *git_path_basename(const char *path)
 	return basename;
 }
 
+size_t git_path_basename_offset(git_buf *buffer)
+{
+	ssize_t slash;
+
+	if (!buffer || buffer->size <= 0)
+		return 0;
+
+	slash = git_buf_rfind_next(buffer, '/');
+
+	if (slash >= 0 && buffer->ptr[slash] == '/')
+		return (size_t)(slash + 1);
+
+	return 0;
+}
 
 const char *git_path_topdir(const char *path)
 {
@@ -193,6 +207,31 @@ int git_path_root(const char *path)
 	return -1;	/* Not a real error - signals that path is not rooted */
 }
 
+int git_path_join_unrooted(
+	git_buf *path_out, const char *path, const char *base, ssize_t *root_at)
+{
+	int error, root;
+
+	assert(path && path_out);
+
+	root = git_path_root(path);
+
+	if (base != NULL && root < 0) {
+		error = git_buf_joinpath(path_out, base, path);
+
+		if (root_at)
+			*root_at = (ssize_t)strlen(base);
+	}
+	else {
+		error = git_buf_sets(path_out, path);
+
+		if (root_at)
+			*root_at = (root < 0) ? 0 : (ssize_t)root;
+	}
+
+	return error;
+}
+
 int git_path_prettify(git_buf *path_out, const char *path, const char *base)
 {
 	char buf[GIT_PATH_MAX];
@@ -502,12 +541,7 @@ bool git_path_contains_file(git_buf *base, const char *file)
 
 int git_path_find_dir(git_buf *dir, const char *path, const char *base)
 {
-	int error;
-
-	if (base != NULL && git_path_root(path) < 0)
-		error = git_buf_joinpath(dir, base, path);
-	else
-		error = git_buf_sets(dir, path);
+	int error = git_path_join_unrooted(dir, path, base, NULL);
 
 	if (!error) {
 		char buf[GIT_PATH_MAX];
diff --git a/src/path.h b/src/path.h
index 14618b2..b629227 100644
--- a/src/path.h
+++ b/src/path.h
@@ -58,6 +58,11 @@ extern int git_path_dirname_r(git_buf *buffer, const char *path);
 extern char *git_path_basename(const char *path);
 extern int git_path_basename_r(git_buf *buffer, const char *path);
 
+/* Return the offset of the start of the basename.  Unlike the other
+ * basename functions, this returns 0 if the path is empty.
+ */
+extern size_t git_path_basename_offset(git_buf *buffer);
+
 extern const char *git_path_topdir(const char *path);
 
 /**
@@ -186,6 +191,15 @@ extern bool git_path_contains_dir(git_buf *parent, const char *subdir);
 extern bool git_path_contains_file(git_buf *dir, const char *file);
 
 /**
+ * Prepend base to unrooted path or just copy path over.
+ *
+ * This will optionally return the index into the path where the "root"
+ * is, either the end of the base directory prefix or the path root.
+ */
+extern int git_path_join_unrooted(
+	git_buf *path_out, const char *path, const char *base, ssize_t *root_at);
+
+/**
  * Clean up path, prepending base if it is not already rooted.
  */
 extern int git_path_prettify(git_buf *path_out, const char *path, const char *base);
diff --git a/src/posix.h b/src/posix.h
index d35fe08..71bb822 100644
--- a/src/posix.h
+++ b/src/posix.h
@@ -11,8 +11,15 @@
 #include <fcntl.h>
 #include <time.h>
 
+#ifndef S_IFGITLINK
 #define S_IFGITLINK 0160000
 #define S_ISGITLINK(m) (((m) & S_IFMT) == S_IFGITLINK)
+#endif
+
+/* if S_ISGID is not defined, then don't try to set it */
+#ifndef S_ISGID
+#define S_ISGID 0
+#endif
 
 #if !defined(O_BINARY)
 #define O_BINARY 0
diff --git a/src/repo_template.h b/src/repo_template.h
new file mode 100644
index 0000000..ae5a969
--- /dev/null
+++ b/src/repo_template.h
@@ -0,0 +1,58 @@
+/*
+ * Copyright (C) 2012 the libgit2 contributors
+ *
+ * This file is part of libgit2, distributed under the GNU GPL v2 with
+ * a Linking Exception. For full terms see the included COPYING file.
+ */
+#ifndef INCLUDE_repo_template_h__
+#define INCLUDE_repo_template_h__
+
+#define GIT_OBJECTS_INFO_DIR GIT_OBJECTS_DIR "info/"
+#define GIT_OBJECTS_PACK_DIR GIT_OBJECTS_DIR "pack/"
+
+#define GIT_HOOKS_DIR "hooks/"
+#define GIT_HOOKS_DIR_MODE 0755
+
+#define GIT_HOOKS_README_FILE GIT_HOOKS_DIR "README.sample"
+#define GIT_HOOKS_README_MODE 0755
+#define GIT_HOOKS_README_CONTENT \
+"#!/bin/sh\n"\
+"#\n"\
+"# Place appropriately named executable hook scripts into this directory\n"\
+"# to intercept various actions that git takes.  See `git help hooks` for\n"\
+"# more information.\n"
+
+#define GIT_INFO_DIR "info/"
+#define GIT_INFO_DIR_MODE 0755
+
+#define GIT_INFO_EXCLUDE_FILE GIT_INFO_DIR "exclude"
+#define GIT_INFO_EXCLUDE_MODE 0644
+#define GIT_INFO_EXCLUDE_CONTENT \
+"# File patterns to ignore; see `git help ignore` for more information.\n"\
+"# Lines that start with '#' are comments.\n"
+
+#define GIT_DESC_FILE "description"
+#define GIT_DESC_MODE 0644
+#define GIT_DESC_CONTENT \
+"Unnamed repository; edit this file 'description' to name the repository.\n"
+
+typedef struct {
+	const char *path;
+	mode_t mode;
+	const char *content;
+} repo_template_item;
+
+static repo_template_item repo_template[] = {
+	{ GIT_OBJECTS_INFO_DIR, GIT_OBJECT_DIR_MODE, NULL }, /* '/objects/info/' */
+	{ GIT_OBJECTS_PACK_DIR, GIT_OBJECT_DIR_MODE, NULL }, /* '/objects/pack/' */
+	{ GIT_REFS_HEADS_DIR, GIT_REFS_DIR_MODE, NULL },     /* '/refs/heads/' */
+	{ GIT_REFS_TAGS_DIR, GIT_REFS_DIR_MODE, NULL },      /* '/refs/tags/' */
+	{ GIT_HOOKS_DIR, GIT_HOOKS_DIR_MODE, NULL },         /* '/hooks/' */
+	{ GIT_INFO_DIR, GIT_INFO_DIR_MODE, NULL },           /* '/info/' */
+	{ GIT_DESC_FILE, GIT_DESC_MODE, GIT_DESC_CONTENT },
+	{ GIT_HOOKS_README_FILE, GIT_HOOKS_README_MODE, GIT_HOOKS_README_CONTENT },
+	{ GIT_INFO_EXCLUDE_FILE, GIT_INFO_EXCLUDE_MODE, GIT_INFO_EXCLUDE_CONTENT },
+	{ NULL, 0, NULL }
+};
+
+#endif
diff --git a/src/repository.c b/src/repository.c
index 6f1f434..bf19d07 100644
--- a/src/repository.c
+++ b/src/repository.c
@@ -18,15 +18,14 @@
 #include "config.h"
 #include "refs.h"
 
-#define GIT_OBJECTS_INFO_DIR GIT_OBJECTS_DIR "info/"
-#define GIT_OBJECTS_PACK_DIR GIT_OBJECTS_DIR "pack/"
-
 #define GIT_FILE_CONTENT_PREFIX "gitdir:"
 
 #define GIT_BRANCH_MASTER "master"
 
 #define GIT_REPO_VERSION 0
 
+#define GIT_TEMPLATE_DIR "/usr/share/git-core/templates"
+
 static void drop_odb(git_repository *repo)
 {
 	if (repo->_odb != NULL) {
@@ -238,16 +237,17 @@ static int read_gitfile(git_buf *path_out, const char *file_path)
 
 	git_buf_rtrim(&file);
 
-	if (file.size <= prefix_len ||
-		memcmp(file.ptr, GIT_FILE_CONTENT_PREFIX, prefix_len) != 0)
+	if (git_buf_len(&file) <= prefix_len ||
+		memcmp(git_buf_cstr(&file), GIT_FILE_CONTENT_PREFIX, prefix_len) != 0)
 	{
 		giterr_set(GITERR_REPOSITORY, "The `.git` file at '%s' is malformed", file_path);
 		error = -1;
 	}
 	else if ((error = git_path_dirname_r(path_out, file_path)) >= 0) {
-		const char *gitlink = ((const char *)file.ptr) + prefix_len;
+		const char *gitlink = git_buf_cstr(&file) + prefix_len;
 		while (*gitlink && git__isspace(*gitlink)) gitlink++;
-		error = git_path_prettify_dir(path_out, gitlink, path_out->ptr);
+		error = git_path_prettify_dir(
+			path_out, gitlink, git_buf_cstr(path_out));
 	}
 
 	git_buf_free(&file);
@@ -359,9 +359,11 @@ int git_repository_open_ext(
 	git_buf path = GIT_BUF_INIT, parent = GIT_BUF_INIT;
 	git_repository *repo;
 
-	*repo_ptr = NULL;
+	if (repo_ptr)
+		*repo_ptr = NULL;
 
-	if ((error = find_repo(&path, &parent, start_path, flags, ceiling_dirs)) < 0)
+	error = find_repo(&path, &parent, start_path, flags, ceiling_dirs);
+	if (error < 0 || !repo_ptr)
 		return error;
 
 	repo = repository_alloc();
@@ -632,19 +634,35 @@ static int check_repositoryformatversion(git_config *config)
 	return 0;
 }
 
-static int repo_init_createhead(const char *git_dir)
+static int repo_init_create_head(const char *git_dir, const char *ref_name)
 {
 	git_buf ref_path = GIT_BUF_INIT;
 	git_filebuf ref = GIT_FILEBUF_INIT;
+	const char *fmt;
 
 	if (git_buf_joinpath(&ref_path, git_dir, GIT_HEAD_FILE) < 0 ||
-		git_filebuf_open(&ref, ref_path.ptr, 0) < 0 ||
-		git_filebuf_printf(&ref, "ref: refs/heads/master\n") < 0 ||
+		git_filebuf_open(&ref, ref_path.ptr, 0) < 0)
+		goto fail;
+
+	if (!ref_name)
+		ref_name = GIT_BRANCH_MASTER;
+
+	if (git__prefixcmp(ref_name, "refs/") == 0)
+		fmt = "ref: %s\n";
+	else
+		fmt = "ref: refs/heads/%s\n";
+
+	if (git_filebuf_printf(&ref, fmt, ref_name) < 0 ||
 		git_filebuf_commit(&ref, GIT_REFS_FILE_MODE) < 0)
-		return -1;
+		goto fail;
 
 	git_buf_free(&ref_path);
 	return 0;
+
+fail:
+	git_buf_free(&ref_path);
+	git_filebuf_cleanup(&ref);
+	return -1;
 }
 
 static bool is_chmod_supported(const char *file_path)
@@ -665,6 +683,7 @@ static bool is_chmod_supported(const char *file_path)
 		return false;
 
 	_is_supported = (st1.st_mode != st2.st_mode);
+
 	return _is_supported;
 }
 
@@ -686,19 +705,45 @@ cleanup:
 	return _is_insensitive;
 }
 
-static int repo_init_config(const char *git_dir, bool is_bare, bool is_reinit)
+static bool are_symlinks_supported(const char *wd_path)
+{
+	git_buf path = GIT_BUF_INIT;
+	int fd;
+	struct stat st;
+	static int _symlinks_supported = -1;
+
+	if (_symlinks_supported > -1)
+		return _symlinks_supported;
+
+	if ((fd = git_futils_mktmp(&path, wd_path)) < 0 ||
+		p_close(fd) < 0 ||
+		p_unlink(path.ptr) < 0 ||
+		p_symlink("testing", path.ptr) < 0 ||
+		p_lstat(path.ptr, &st) < 0)
+		_symlinks_supported = false;
+	else
+		_symlinks_supported = (S_ISLNK(st.st_mode) != 0);
+
+	(void)p_unlink(path.ptr);
+	git_buf_free(&path);
+
+	return _symlinks_supported;
+}
+
+static int repo_init_config(
+	const char *repo_dir,
+	const char *work_dir,
+	git_repository_init_options *opts)
 {
+	int error = 0;
 	git_buf cfg_path = GIT_BUF_INIT;
 	git_config *config = NULL;
 
-#define SET_REPO_CONFIG(type, name, val) {\
-	if (git_config_set_##type(config, name, val) < 0) { \
-		git_buf_free(&cfg_path); \
-		git_config_free(config); \
-		return -1; } \
-}
+#define SET_REPO_CONFIG(TYPE, NAME, VAL) do {\
+	if ((error = git_config_set_##TYPE(config, NAME, VAL)) < 0) \
+		goto cleanup; } while (0)
 
-	if (git_buf_joinpath(&cfg_path, git_dir, GIT_CONFIG_FILENAME_INREPO) < 0)
+	if (git_buf_joinpath(&cfg_path, repo_dir, GIT_CONFIG_FILENAME_INREPO) < 0)
 		return -1;
 
 	if (git_config_open_ondisk(&config, git_buf_cstr(&cfg_path)) < 0) {
@@ -706,58 +751,61 @@ static int repo_init_config(const char *git_dir, bool is_bare, bool is_reinit)
 		return -1;
 	}
 
-	if (is_reinit && check_repositoryformatversion(config) < 0) {
-		git_buf_free(&cfg_path);
-		git_config_free(config);
-		return -1;
-	}
+	if ((opts->flags & GIT_REPOSITORY_INIT__IS_REINIT) != 0 &&
+		(error = check_repositoryformatversion(config)) < 0)
+		goto cleanup;
 
-	SET_REPO_CONFIG(bool, "core.bare", is_bare);
-	SET_REPO_CONFIG(int32, "core.repositoryformatversion", GIT_REPO_VERSION);
-	SET_REPO_CONFIG(bool, "core.filemode", is_chmod_supported(git_buf_cstr(&cfg_path)));
-	
-	if (!is_bare)
+	SET_REPO_CONFIG(
+		bool, "core.bare", (opts->flags & GIT_REPOSITORY_INIT_BARE) != 0);
+	SET_REPO_CONFIG(
+		int32, "core.repositoryformatversion", GIT_REPO_VERSION);
+	SET_REPO_CONFIG(
+		bool, "core.filemode", is_chmod_supported(git_buf_cstr(&cfg_path)));
+
+	if (!(opts->flags & GIT_REPOSITORY_INIT_BARE)) {
 		SET_REPO_CONFIG(bool, "core.logallrefupdates", true);
 
-	if (!is_reinit && is_filesystem_case_insensitive(git_dir))
-		SET_REPO_CONFIG(bool, "core.ignorecase", true);
-	/* TODO: what other defaults? */
+		if (!are_symlinks_supported(work_dir))
+			SET_REPO_CONFIG(bool, "core.symlinks", false);
 
-	git_buf_free(&cfg_path);
-	git_config_free(config);
-	return 0;
-}
-
-#define GIT_HOOKS_DIR "hooks/"
-#define GIT_HOOKS_DIR_MODE 0755
+		if (!(opts->flags & GIT_REPOSITORY_INIT__NATURAL_WD)) {
+			SET_REPO_CONFIG(string, "core.worktree", work_dir);
+		}
+		else if ((opts->flags & GIT_REPOSITORY_INIT__IS_REINIT) != 0) {
+			if ((error = git_config_delete(config, "core.worktree")) < 0)
+				goto cleanup;
+		}
+	} else {
+		if (!are_symlinks_supported(repo_dir))
+			SET_REPO_CONFIG(bool, "core.symlinks", false);
+	}
 
-#define GIT_HOOKS_README_FILE GIT_HOOKS_DIR "README.sample"
-#define GIT_HOOKS_README_MODE 0755
-#define GIT_HOOKS_README_CONTENT \
-"#!/bin/sh\n"\
-"#\n"\
-"# Place appropriately named executable hook scripts into this directory\n"\
-"# to intercept various actions that git takes.  See `git help hooks` for\n"\
-"# more information.\n"
+	if (!(opts->flags & GIT_REPOSITORY_INIT__IS_REINIT) &&
+		is_filesystem_case_insensitive(repo_dir))
+		SET_REPO_CONFIG(bool, "core.ignorecase", true);
 
-#define GIT_INFO_DIR "info/"
-#define GIT_INFO_DIR_MODE 0755
+	if (opts->mode == GIT_REPOSITORY_INIT_SHARED_GROUP) {
+		SET_REPO_CONFIG(int32, "core.sharedrepository", 1);
+		SET_REPO_CONFIG(bool, "receive.denyNonFastforwards", true);
+	}
+	else if (opts->mode == GIT_REPOSITORY_INIT_SHARED_ALL) {
+		SET_REPO_CONFIG(int32, "core.sharedrepository", 2);
+		SET_REPO_CONFIG(bool, "receive.denyNonFastforwards", true);
+	}
 
-#define GIT_INFO_EXCLUDE_FILE GIT_INFO_DIR "exclude"
-#define GIT_INFO_EXCLUDE_MODE 0644
-#define GIT_INFO_EXCLUDE_CONTENT \
-"# File patterns to ignore; see `git help ignore` for more information.\n"\
-"# Lines that start with '#' are comments.\n"
+cleanup:
+	git_buf_free(&cfg_path);
+	git_config_free(config);
 
-#define GIT_DESC_FILE "description"
-#define GIT_DESC_MODE 0644
-#define GIT_DESC_CONTENT "Unnamed repository; edit this file 'description' to name the repository.\n"
+	return error;
+}
 
 static int repo_write_template(
 	const char *git_dir,
 	bool allow_overwrite,
 	const char *file,
 	mode_t mode,
+	bool hidden,
 	const char *content)
 {
 	git_buf path = GIT_BUF_INIT;
@@ -781,6 +829,15 @@ static int repo_write_template(
 	else if (errno != EEXIST)
 		error = fd;
 
+#ifdef GIT_WIN32
+	if (!error && hidden) {
+		if (p_hide_directory__w32(path.ptr) < 0)
+			error = -1;
+	}
+#else
+	GIT_UNUSED(hidden);
+#endif
+
 	git_buf_free(&path);
 
 	if (error)
@@ -790,86 +847,316 @@ static int repo_write_template(
 	return error;
 }
 
-static int repo_init_structure(const char *git_dir, int is_bare)
+static int repo_write_gitlink(
+	const char *in_dir, const char *to_repo)
 {
-	int i;
-	struct { const char *dir; mode_t mode; } dirs[] = {
-		{ GIT_OBJECTS_INFO_DIR, GIT_OBJECT_DIR_MODE }, /* '/objects/info/' */
-		{ GIT_OBJECTS_PACK_DIR, GIT_OBJECT_DIR_MODE }, /* '/objects/pack/' */
-		{ GIT_REFS_HEADS_DIR, GIT_REFS_DIR_MODE },     /* '/refs/heads/' */
-		{ GIT_REFS_TAGS_DIR, GIT_REFS_DIR_MODE },      /* '/refs/tags/' */
-		{ GIT_HOOKS_DIR, GIT_HOOKS_DIR_MODE },         /* '/hooks/' */
-		{ GIT_INFO_DIR, GIT_INFO_DIR_MODE },           /* '/info/' */
-		{ NULL, 0 }
-	};
-	struct { const char *file; mode_t mode; const char *content; } tmpl[] = {
-		{ GIT_DESC_FILE, GIT_DESC_MODE, GIT_DESC_CONTENT },
-		{ GIT_HOOKS_README_FILE, GIT_HOOKS_README_MODE, GIT_HOOKS_README_CONTENT },
-		{ GIT_INFO_EXCLUDE_FILE, GIT_INFO_EXCLUDE_MODE, GIT_INFO_EXCLUDE_CONTENT },
-		{ NULL, 0, NULL }
-	};
-
-	/* Make the base directory */
-	if (git_futils_mkdir_r(git_dir, NULL, is_bare ? GIT_BARE_DIR_MODE : GIT_DIR_MODE) < 0)
+	int error;
+	git_buf buf = GIT_BUF_INIT;
+	struct stat st;
+
+	git_path_dirname_r(&buf, to_repo);
+	git_path_to_dir(&buf);
+	if (git_buf_oom(&buf))
 		return -1;
 
-	/* Hides the ".git" directory */
-	if (!is_bare) {
+	/* don't write gitlink to natural workdir */
+	if (git__suffixcmp(to_repo, "/" DOT_GIT "/") == 0 &&
+		strcmp(in_dir, buf.ptr) == 0)
+	{
+		error = GIT_PASSTHROUGH;
+		goto cleanup;
+	}
+
+	if ((error = git_buf_joinpath(&buf, in_dir, DOT_GIT)) < 0)
+		goto cleanup;
+
+	if (!p_stat(buf.ptr, &st) && !S_ISREG(st.st_mode)) {
+		giterr_set(GITERR_REPOSITORY,
+			"Cannot overwrite gitlink file into path '%s'", in_dir);
+		error = GIT_EEXISTS;
+		goto cleanup;
+	}
+
+	git_buf_clear(&buf);
+
+	error = git_buf_printf(&buf, "%s %s", GIT_FILE_CONTENT_PREFIX, to_repo);
+
+	if (!error)
+		error = repo_write_template(in_dir, true, DOT_GIT, 0644, true, buf.ptr);
+
+cleanup:
+	git_buf_free(&buf);
+	return error;
+}
+
+static mode_t pick_dir_mode(git_repository_init_options *opts)
+{
+	if (opts->mode == GIT_REPOSITORY_INIT_SHARED_UMASK)
+		return 0755;
+	if (opts->mode == GIT_REPOSITORY_INIT_SHARED_GROUP)
+		return (0775 | S_ISGID);
+	if (opts->mode == GIT_REPOSITORY_INIT_SHARED_ALL)
+		return (0777 | S_ISGID);
+	return opts->mode;
+}
+
+#include "repo_template.h"
+
+static int repo_init_structure(
+	const char *repo_dir,
+	const char *work_dir,
+	git_repository_init_options *opts)
+{
+	int error = 0;
+	repo_template_item *tpl;
+	bool external_tpl =
+		((opts->flags & GIT_REPOSITORY_INIT_EXTERNAL_TEMPLATE) != 0);
+	mode_t dmode = pick_dir_mode(opts);
+
+	/* Hide the ".git" directory */
+	if ((opts->flags & GIT_REPOSITORY_INIT_BARE) != 0) {
 #ifdef GIT_WIN32
-		if (p_hide_directory__w32(git_dir) < 0) {
+		if (p_hide_directory__w32(repo_dir) < 0) {
 			giterr_set(GITERR_REPOSITORY,
 				"Failed to mark Git repository folder as hidden");
 			return -1;
 		}
 #endif
 	}
-
-	/* Make subdirectories as needed */
-	for (i = 0; dirs[i].dir != NULL; ++i) {
-		if (git_futils_mkdir_r(dirs[i].dir, git_dir, dirs[i].mode) < 0)
+	/* Create .git gitlink if appropriate */
+	else if ((opts->flags & GIT_REPOSITORY_INIT__NATURAL_WD) == 0) {
+		if (repo_write_gitlink(work_dir, repo_dir) < 0)
 			return -1;
 	}
 
-	/* Make template files as needed */
-	for (i = 0; tmpl[i].file != NULL; ++i) {
-		if (repo_write_template(
-				git_dir, false, tmpl[i].file, tmpl[i].mode, tmpl[i].content) < 0)
+	/* Copy external template if requested */
+	if (external_tpl) {
+		git_config *cfg;
+		const char *tdir;
+
+		if (opts->template_path)
+			tdir = opts->template_path;
+		else if ((error = git_config_open_default(&cfg)) < 0)
+			return error;
+		else {
+			error = git_config_get_string(&tdir, cfg, "init.templatedir");
+
+			git_config_free(cfg);
+
+			if (error && error != GIT_ENOTFOUND)
+				return error;
+
+			giterr_clear();
+			tdir = GIT_TEMPLATE_DIR;
+		}
+
+		error = git_futils_cp_r(tdir, repo_dir,
+			GIT_CPDIR_COPY_SYMLINKS | GIT_CPDIR_CHMOD, dmode);
+
+		if (error < 0) {
+			if (strcmp(tdir, GIT_TEMPLATE_DIR) != 0)
+				return error;
+
+			/* if template was default, ignore error and use internal */
+			giterr_clear();
+			external_tpl = false;
+		}
+	}
+
+	/* Copy internal template
+	 * - always ensure existence of dirs
+	 * - only create files if no external template was specified
+	 */
+	for (tpl = repo_template; !error && tpl->path; ++tpl) {
+		if (!tpl->content)
+			error = git_futils_mkdir(
+				tpl->path, repo_dir, dmode, GIT_MKDIR_PATH | GIT_MKDIR_CHMOD);
+		else if (!external_tpl) {
+			const char *content = tpl->content;
+
+			if (opts->description && strcmp(tpl->path, GIT_DESC_FILE) == 0)
+				content = opts->description;
+
+			error = repo_write_template(
+				repo_dir, false, tpl->path, tpl->mode, false, content);
+		}
+	}
+
+	return error;
+}
+
+static int repo_init_directories(
+	git_buf *repo_path,
+	git_buf *wd_path,
+	const char *given_repo,
+	git_repository_init_options *opts)
+{
+	int error = 0;
+	bool add_dotgit, has_dotgit, natural_wd;
+	mode_t dirmode;
+
+	/* set up repo path */
+
+	add_dotgit =
+		(opts->flags & GIT_REPOSITORY_INIT_NO_DOTGIT_DIR) == 0 &&
+		(opts->flags & GIT_REPOSITORY_INIT_BARE) == 0 &&
+		git__suffixcmp(given_repo, "/" DOT_GIT) != 0 &&
+		git__suffixcmp(given_repo, "/" GIT_DIR) != 0;
+
+	if (git_buf_joinpath(repo_path, given_repo, add_dotgit ? GIT_DIR : "") < 0)
+		return -1;
+
+	has_dotgit = (git__suffixcmp(repo_path->ptr, "/" GIT_DIR) == 0);
+	if (has_dotgit)
+		opts->flags |= GIT_REPOSITORY_INIT__HAS_DOTGIT;
+
+	/* set up workdir path */
+
+	if ((opts->flags & GIT_REPOSITORY_INIT_BARE) == 0) {
+		if (opts->workdir_path) {
+			if (git_path_join_unrooted(
+					wd_path, opts->workdir_path, repo_path->ptr, NULL) < 0)
+				return -1;
+		} else if (has_dotgit) {
+			if (git_path_dirname_r(wd_path, repo_path->ptr) < 0)
+				return -1;
+		} else {
+			giterr_set(GITERR_REPOSITORY, "Cannot pick working directory"
+				" for non-bare repository that isn't a '.git' directory");
+			return -1;
+		}
+
+		if (git_path_to_dir(wd_path) < 0)
 			return -1;
+	} else {
+		git_buf_clear(wd_path);
 	}
 
-	return 0;
+	natural_wd =
+		has_dotgit &&
+		wd_path->size > 0 &&
+		wd_path->size + strlen(GIT_DIR) == repo_path->size &&
+		memcmp(repo_path->ptr, wd_path->ptr, wd_path->size) == 0;
+	if (natural_wd)
+		opts->flags |= GIT_REPOSITORY_INIT__NATURAL_WD;
+
+	/* create directories as needed / requested */
+
+	dirmode = pick_dir_mode(opts);
+
+	if ((opts->flags & GIT_REPOSITORY_INIT_MKDIR) != 0 && has_dotgit) {
+		git_buf p = GIT_BUF_INIT;
+		if ((error = git_path_dirname_r(&p, repo_path->ptr)) >= 0)
+			error = git_futils_mkdir(p.ptr, NULL, dirmode, 0);
+		git_buf_free(&p);
+	}
+
+	if ((opts->flags & GIT_REPOSITORY_INIT_MKDIR) != 0 ||
+		(opts->flags & GIT_REPOSITORY_INIT_MKPATH) != 0 ||
+		has_dotgit)
+	{
+		uint32_t mkflag = GIT_MKDIR_CHMOD;
+		if ((opts->flags & GIT_REPOSITORY_INIT_MKPATH) != 0)
+			mkflag |= GIT_MKDIR_PATH;
+		error = git_futils_mkdir(repo_path->ptr, NULL, dirmode, mkflag);
+	}
+
+	if (wd_path->size > 0 &&
+		!natural_wd &&
+		((opts->flags & GIT_REPOSITORY_INIT_MKDIR) != 0 ||
+		 (opts->flags & GIT_REPOSITORY_INIT_MKPATH) != 0))
+		error = git_futils_mkdir(wd_path->ptr, NULL, dirmode & ~S_ISGID,
+			(opts->flags & GIT_REPOSITORY_INIT_MKPATH) ? GIT_MKDIR_PATH : 0);
+
+	/* prettify both directories now that they are created */
+
+	if (!error) {
+		error = git_path_prettify_dir(repo_path, repo_path->ptr, NULL);
+
+		if (!error && wd_path->size > 0)
+			error = git_path_prettify_dir(wd_path, wd_path->ptr, NULL);
+	}
+
+	return error;
 }
 
-int git_repository_init(git_repository **repo_out, const char *path, unsigned is_bare)
+static int repo_init_create_origin(git_repository *repo, const char *url)
 {
-	git_buf repository_path = GIT_BUF_INIT;
-	bool is_reinit;
-	int result = -1;
+	int error;
+	git_remote *remote;
 
-	assert(repo_out && path);
+	if (!(error = git_remote_add(&remote, repo, "origin", url))) {
+		error = git_remote_save(remote);
+		git_remote_free(remote);
+	}
 
-	if (git_buf_joinpath(&repository_path, path, is_bare ? "" : GIT_DIR) < 0)
-		goto cleanup;
+	return error;
+}
 
-	is_reinit = git_path_isdir(repository_path.ptr) && valid_repository_path(&repository_path);
+int git_repository_init(
+	git_repository **repo_out, const char *path, unsigned is_bare)
+{
+	git_repository_init_options opts;
 
-	if (is_reinit) {
-		/* TODO: reinitialize the templates */
+	memset(&opts, 0, sizeof(opts));
+	opts.flags = GIT_REPOSITORY_INIT_MKPATH; /* don't love this default */
+	if (is_bare)
+		opts.flags |= GIT_REPOSITORY_INIT_BARE;
 
-		if (repo_init_config(repository_path.ptr, is_bare, is_reinit) < 0)
-			goto cleanup;
+	return git_repository_init_ext(repo_out, path, &opts);
+}
 
-	} else if (repo_init_structure(repository_path.ptr, is_bare) < 0 ||
-		repo_init_config(repository_path.ptr, is_bare, is_reinit) < 0 || 
-		repo_init_createhead(repository_path.ptr) < 0) {
+int git_repository_init_ext(
+	git_repository **repo_out,
+	const char *given_repo,
+	git_repository_init_options *opts)
+{
+	int error;
+	git_buf repo_path = GIT_BUF_INIT, wd_path = GIT_BUF_INIT;
+
+	assert(repo_out && given_repo && opts);
+
+	error = repo_init_directories(&repo_path, &wd_path, given_repo, opts);
+	if (error < 0)
 		goto cleanup;
+
+	if (valid_repository_path(&repo_path)) {
+
+		if ((opts->flags & GIT_REPOSITORY_INIT_NO_REINIT) != 0) {
+			giterr_set(GITERR_REPOSITORY,
+				"Attempt to reinitialize '%s'", given_repo);
+			error = GIT_EEXISTS;
+			goto cleanup;
+		}
+
+		opts->flags |= GIT_REPOSITORY_INIT__IS_REINIT;
+
+		error = repo_init_config(
+			git_buf_cstr(&repo_path), git_buf_cstr(&wd_path), opts);
+
+		/* TODO: reinitialize the templates */
+	}
+	else {
+		if (!(error = repo_init_structure(
+				git_buf_cstr(&repo_path), git_buf_cstr(&wd_path), opts)) &&
+			!(error = repo_init_config(
+				git_buf_cstr(&repo_path), git_buf_cstr(&wd_path), opts)))
+			error = repo_init_create_head(
+				git_buf_cstr(&repo_path), opts->initial_head);
 	}
+	if (error < 0)
+		goto cleanup;
+
+	error = git_repository_open(repo_out, git_buf_cstr(&repo_path));
 
-	result = git_repository_open(repo_out, repository_path.ptr);
+	if (!error && opts->origin_url)
+		error = repo_init_create_origin(*repo_out, opts->origin_url);
 
 cleanup:
-	git_buf_free(&repository_path);
-	return result;
+	git_buf_free(&repo_path);
+	git_buf_free(&wd_path);
+
+	return error;
 }
 
 int git_repository_head_detached(git_repository *repo)
@@ -965,43 +1252,6 @@ const char *git_repository_workdir(git_repository *repo)
 	return repo->workdir;
 }
 
-static int write_gitlink(
-	const char *in_dir, const char *to_repo)
-{
-	int error;
-	git_buf buf = GIT_BUF_INIT;
-	struct stat st;
-
-	if (git_path_dirname_r(&buf, to_repo) < 0 ||
-		git_path_to_dir(&buf) < 0)
-		return -1;
-
-	/* don't write gitlink to natural workdir */
-	if (git__suffixcmp(to_repo, "/" DOT_GIT "/") == 0 &&
-		strcmp(in_dir, buf.ptr) == 0)
-		return GIT_PASSTHROUGH;
-
-	if (git_buf_joinpath(&buf, in_dir, DOT_GIT) < 0)
-		return -1;
-
-	if (!p_stat(buf.ptr, &st) && !S_ISREG(st.st_mode)) {
-		giterr_set(GITERR_REPOSITORY,
-			"Cannot overwrite gitlink file into path '%s'", in_dir);
-		return GIT_EEXISTS;
-	}
-
-	git_buf_clear(&buf);
-
-	if (git_buf_printf(&buf, "%s %s", GIT_FILE_CONTENT_PREFIX, to_repo) < 0)
-		return -1;
-
-	error = repo_write_template(in_dir, true, DOT_GIT, 0644, buf.ptr);
-
-	git_buf_free(&buf);
-
-	return error;
-}
-
 int git_repository_set_workdir(
 	git_repository *repo, const char *workdir, int update_gitlink)
 {
@@ -1022,7 +1272,7 @@ int git_repository_set_workdir(
 		if (git_repository_config__weakptr(&config, repo) < 0)
 			return -1;
 
-		error = write_gitlink(path.ptr, git_repository_path(repo));
+		error = repo_write_gitlink(path.ptr, git_repository_path(repo));
 
 		/* passthrough error means gitlink is unnecessary */
 		if (error == GIT_PASSTHROUGH)
@@ -1078,39 +1328,27 @@ int git_repository_message(char *buffer, size_t len, git_repository *repo)
 {
 	git_buf buf = GIT_BUF_INIT, path = GIT_BUF_INIT;
 	struct stat st;
-	ssize_t size;
 	int error;
 
 	if (git_buf_joinpath(&path, repo->path_repository, MERGE_MSG_FILE) < 0)
 		return -1;
 
-	error = p_stat(git_buf_cstr(&path), &st);
-	if (error < 0) {
+	if ((error = p_stat(git_buf_cstr(&path), &st)) < 0) {
 		if (errno == ENOENT)
 			error = GIT_ENOTFOUND;
-
-		git_buf_free(&path);
-		return error;
 	}
-
-	if (buffer == NULL) {
-		git_buf_free(&path);
-		return (int)st.st_size;
+	else if (buffer != NULL) {
+		error = git_futils_readbuffer(&buf, git_buf_cstr(&path));
+		git_buf_copy_cstr(buffer, len, &buf);
 	}
 
-	if (git_futils_readbuffer(&buf, git_buf_cstr(&path)) < 0)
-		goto on_error;
-
-	memcpy(buffer, git_buf_cstr(&buf), len);
-	size = git_buf_len(&buf);
-
 	git_buf_free(&path);
 	git_buf_free(&buf);
-	return size;
 
-on_error:
-	git_buf_free(&path);
-	return -1;
+	if (!error)
+		error = (int)st.st_size + 1; /* add 1 for NUL byte */
+
+	return error;
 }
 
 int git_repository_message_remove(git_repository *repo)
diff --git a/src/repository.h b/src/repository.h
index 4e03e63..4695edf 100644
--- a/src/repository.h
+++ b/src/repository.h
@@ -68,6 +68,13 @@ typedef enum {
 	GIT_EOL_DEFAULT = GIT_EOL_NATIVE
 } git_cvar_value;
 
+/* internal repository init flags */
+enum {
+	GIT_REPOSITORY_INIT__HAS_DOTGIT = (1u << 16),
+	GIT_REPOSITORY_INIT__NATURAL_WD = (1u << 17),
+	GIT_REPOSITORY_INIT__IS_REINIT  = (1u << 18),
+};
+
 /** Base git object for inheritance */
 struct git_object {
 	git_cached_obj cached;
@@ -75,6 +82,7 @@ struct git_object {
 	git_otype type;
 };
 
+/** Internal structure for repository object */
 struct git_repository {
 	git_odb *_odb;
 	git_config *_config;
@@ -94,8 +102,7 @@ struct git_repository {
 	git_cvar_value cvar_cache[GIT_CVAR_CACHE_MAX];
 };
 
-/* fully free the object; internal method, do not
- * export */
+/* fully free the object; internal method, DO NOT EXPORT */
 void git_object__free(void *object);
 
 GIT_INLINE(int) git_object__dup(git_object **dest, git_object *source)
diff --git a/src/transports/http.c b/src/transports/http.c
index 85fec41..ce382c3 100644
--- a/src/transports/http.c
+++ b/src/transports/http.c
@@ -233,7 +233,7 @@ static int http_recv_cb(gitno_buffer *buf)
 	if (t->error < 0)
 		return t->error;
 
-	return buf->offset - old_len;
+	return (int)(buf->offset - old_len);
 }
 
 /* Set up the gitno_buffer so calling gitno_recv() grabs data from the HTTP response */
diff --git a/src/unix/posix.h b/src/unix/posix.h
index 7a3a388..25038c8 100644
--- a/src/unix/posix.h
+++ b/src/unix/posix.h
@@ -18,8 +18,8 @@
 
 #define p_lstat(p,b) lstat(p,b)
 #define p_readlink(a, b, c) readlink(a, b, c)
+#define p_symlink(o,n) symlink(o, n)
 #define p_link(o,n) link(o, n)
-#define p_symlink(o,n) symlink(o,n)
 #define p_unlink(p) unlink(p)
 #define p_mkdir(p,m) mkdir(p, m)
 #define p_fsync(fd) fsync(fd)
diff --git a/tests-clar/checkout/checkout.c b/tests-clar/checkout/checkout.c
index d6b79b4..ba14194 100644
--- a/tests-clar/checkout/checkout.c
+++ b/tests-clar/checkout/checkout.c
@@ -33,7 +33,7 @@ static void test_file_contents(const char *path, const char *expectedcontents)
 	actuallen = p_read(fd, buffer, 1024);
 	cl_git_pass(p_close(fd));
 
-	cl_assert_equal_i(actuallen, expectedlen);
+	cl_assert_equal_sz(actuallen, expectedlen);
 	cl_assert_equal_s(buffer, expectedcontents);
 }
 
diff --git a/tests-clar/clar_libgit2.h b/tests-clar/clar_libgit2.h
index eab6c3d..b4ee74c 100644
--- a/tests-clar/clar_libgit2.h
+++ b/tests-clar/clar_libgit2.h
@@ -25,6 +25,8 @@
  */
 #define cl_git_fail(expr) cl_must_fail(expr)
 
+#define cl_assert_equal_sz(sz1,sz2) cl_assert((sz1) == (sz2))
+
 /*
  * Some utility macros for building long strings
  */
diff --git a/tests-clar/core/buffer.c b/tests-clar/core/buffer.c
index b6274b0..972567e 100644
--- a/tests-clar/core/buffer.c
+++ b/tests-clar/core/buffer.c
@@ -665,7 +665,7 @@ static void assert_unescape(char *expected, char *to_unescape) {
 	cl_git_pass(git_buf_sets(&buf, to_unescape));
 	git_buf_unescape(&buf);
 	cl_assert_equal_s(expected, buf.ptr);
-	cl_assert_equal_i(strlen(expected), buf.size);
+	cl_assert_equal_sz(strlen(expected), buf.size);
 
 	git_buf_free(&buf);
 }
diff --git a/tests-clar/core/copy.c b/tests-clar/core/copy.c
new file mode 100644
index 0000000..2fdfed8
--- /dev/null
+++ b/tests-clar/core/copy.c
@@ -0,0 +1,126 @@
+#include "clar_libgit2.h"
+#include "fileops.h"
+#include "path.h"
+#include "posix.h"
+
+void test_core_copy__file(void)
+{
+	struct stat st;
+	const char *content = "This is some stuff to copy\n";
+
+	cl_git_mkfile("copy_me", content);
+
+	cl_git_pass(git_futils_cp("copy_me", "copy_me_two", 0664));
+
+	cl_git_pass(git_path_lstat("copy_me_two", &st));
+	cl_assert(S_ISREG(st.st_mode));
+	cl_assert(strlen(content) == (size_t)st.st_size);
+
+	cl_git_pass(p_unlink("copy_me_two"));
+	cl_git_pass(p_unlink("copy_me"));
+}
+
+void test_core_copy__file_in_dir(void)
+{
+	struct stat st;
+	const char *content = "This is some other stuff to copy\n";
+
+	cl_git_pass(git_futils_mkdir("an_dir/in_a_dir", NULL, 0775, GIT_MKDIR_PATH));
+	cl_git_mkfile("an_dir/in_a_dir/copy_me", content);
+	cl_assert(git_path_isdir("an_dir"));
+
+	cl_git_pass(git_futils_mkpath2file
+		("an_dir/second_dir/and_more/copy_me_two", 0775));
+
+	cl_git_pass(git_futils_cp
+		("an_dir/in_a_dir/copy_me",
+		 "an_dir/second_dir/and_more/copy_me_two",
+		 0664));
+
+	cl_git_pass(git_path_lstat("an_dir/second_dir/and_more/copy_me_two", &st));
+	cl_assert(S_ISREG(st.st_mode));
+	cl_assert(strlen(content) == (size_t)st.st_size);
+
+	cl_git_pass(git_futils_rmdir_r("an_dir", GIT_DIRREMOVAL_FILES_AND_DIRS));
+	cl_assert(!git_path_isdir("an_dir"));
+}
+
+void test_core_copy__tree(void)
+{
+	struct stat st;
+	const char *content = "File content\n";
+
+	cl_git_pass(git_futils_mkdir("src/b", NULL, 0775, GIT_MKDIR_PATH));
+	cl_git_pass(git_futils_mkdir("src/c/d", NULL, 0775, GIT_MKDIR_PATH));
+	cl_git_pass(git_futils_mkdir("src/c/e", NULL, 0775, GIT_MKDIR_PATH));
+
+	cl_git_mkfile("src/f1", content);
+	cl_git_mkfile("src/b/f2", content);
+	cl_git_mkfile("src/c/f3", content);
+	cl_git_mkfile("src/c/d/f4", content);
+	cl_git_mkfile("src/c/d/.f5", content);
+
+#ifndef GIT_WIN32
+	cl_assert(p_symlink("../../b/f2", "src/c/d/l1") == 0);
+#endif
+
+	cl_assert(git_path_isdir("src"));
+	cl_assert(git_path_isdir("src/b"));
+	cl_assert(git_path_isdir("src/c/d"));
+	cl_assert(git_path_isfile("src/c/d/f4"));
+
+	/* copy with no empty dirs, yes links, no dotfiles, no overwrite */
+
+	cl_git_pass(
+		git_futils_cp_r("src", "t1", GIT_CPDIR_COPY_SYMLINKS, 0) );
+
+	cl_assert(git_path_isdir("t1"));
+	cl_assert(git_path_isdir("t1/b"));
+	cl_assert(git_path_isdir("t1/c"));
+	cl_assert(git_path_isdir("t1/c/d"));
+	cl_assert(!git_path_isdir("t1/c/e"));
+
+	cl_assert(git_path_isfile("t1/f1"));
+	cl_assert(git_path_isfile("t1/b/f2"));
+	cl_assert(git_path_isfile("t1/c/f3"));
+	cl_assert(git_path_isfile("t1/c/d/f4"));
+	cl_assert(!git_path_isfile("t1/c/d/.f5"));
+
+	cl_git_pass(git_path_lstat("t1/c/f3", &st));
+	cl_assert(S_ISREG(st.st_mode));
+	cl_assert(strlen(content) == (size_t)st.st_size);
+
+#ifndef GIT_WIN32
+	cl_git_pass(git_path_lstat("t1/c/d/l1", &st));
+	cl_assert(S_ISLNK(st.st_mode));
+#endif
+
+	cl_git_pass(git_futils_rmdir_r("t1", GIT_DIRREMOVAL_FILES_AND_DIRS));
+	cl_assert(!git_path_isdir("t1"));
+
+	/* copy with empty dirs, no links, yes dotfiles, no overwrite */
+
+	cl_git_pass(
+		git_futils_cp_r("src", "t2", GIT_CPDIR_CREATE_EMPTY_DIRS | GIT_CPDIR_COPY_DOTFILES, 0) );
+
+	cl_assert(git_path_isdir("t2"));
+	cl_assert(git_path_isdir("t2/b"));
+	cl_assert(git_path_isdir("t2/c"));
+	cl_assert(git_path_isdir("t2/c/d"));
+	cl_assert(git_path_isdir("t2/c/e"));
+
+	cl_assert(git_path_isfile("t2/f1"));
+	cl_assert(git_path_isfile("t2/b/f2"));
+	cl_assert(git_path_isfile("t2/c/f3"));
+	cl_assert(git_path_isfile("t2/c/d/f4"));
+	cl_assert(git_path_isfile("t2/c/d/.f5"));
+
+#ifndef GIT_WIN32
+	cl_git_fail(git_path_lstat("t2/c/d/l1", &st));
+#endif
+
+	cl_git_pass(git_futils_rmdir_r("t2", GIT_DIRREMOVAL_FILES_AND_DIRS));
+	cl_assert(!git_path_isdir("t2"));
+
+	cl_git_pass(git_futils_rmdir_r("src", GIT_DIRREMOVAL_FILES_AND_DIRS));
+}
diff --git a/tests-clar/core/mkdir.c b/tests-clar/core/mkdir.c
new file mode 100644
index 0000000..d7723be
--- /dev/null
+++ b/tests-clar/core/mkdir.c
@@ -0,0 +1,172 @@
+#include "clar_libgit2.h"
+#include "fileops.h"
+#include "path.h"
+#include "posix.h"
+
+static void cleanup_basic_dirs(void *ref)
+{
+	GIT_UNUSED(ref);
+	git_futils_rmdir_r("d0", GIT_DIRREMOVAL_EMPTY_HIERARCHY);
+	git_futils_rmdir_r("d1", GIT_DIRREMOVAL_EMPTY_HIERARCHY);
+	git_futils_rmdir_r("d2", GIT_DIRREMOVAL_EMPTY_HIERARCHY);
+	git_futils_rmdir_r("d3", GIT_DIRREMOVAL_EMPTY_HIERARCHY);
+	git_futils_rmdir_r("d4", GIT_DIRREMOVAL_EMPTY_HIERARCHY);
+}
+
+void test_core_mkdir__basic(void)
+{
+	cl_set_cleanup(cleanup_basic_dirs, NULL);
+
+	/* make a directory */
+	cl_assert(!git_path_isdir("d0"));
+	cl_git_pass(git_futils_mkdir("d0", NULL, 0755, 0));
+	cl_assert(git_path_isdir("d0"));
+
+	/* make a path */
+	cl_assert(!git_path_isdir("d1"));
+	cl_git_pass(git_futils_mkdir("d1/d1.1/d1.2", NULL, 0755, GIT_MKDIR_PATH));
+	cl_assert(git_path_isdir("d1"));
+	cl_assert(git_path_isdir("d1/d1.1"));
+	cl_assert(git_path_isdir("d1/d1.1/d1.2"));
+
+	/* make a dir exclusively */
+	cl_assert(!git_path_isdir("d2"));
+	cl_git_pass(git_futils_mkdir("d2", NULL, 0755, GIT_MKDIR_EXCL));
+	cl_assert(git_path_isdir("d2"));
+
+	/* make exclusive failure */
+	cl_git_fail(git_futils_mkdir("d2", NULL, 0755, GIT_MKDIR_EXCL));
+
+	/* make a path exclusively */
+	cl_assert(!git_path_isdir("d3"));
+	cl_git_pass(git_futils_mkdir("d3/d3.1/d3.2", NULL, 0755, GIT_MKDIR_PATH | GIT_MKDIR_EXCL));
+	cl_assert(git_path_isdir("d3"));
+	cl_assert(git_path_isdir("d3/d3.1/d3.2"));
+
+	/* make exclusive path failure */
+	cl_git_fail(git_futils_mkdir("d3/d3.1/d3.2", NULL, 0755, GIT_MKDIR_PATH | GIT_MKDIR_EXCL));
+	/* ??? Should EXCL only apply to the last item in the path? */
+
+	/* path with trailing slash? */
+	cl_assert(!git_path_isdir("d4"));
+	cl_git_pass(git_futils_mkdir("d4/d4.1/", NULL, 0755, GIT_MKDIR_PATH));
+	cl_assert(git_path_isdir("d4/d4.1"));
+}
+
+static void cleanup_basedir(void *ref)
+{
+	GIT_UNUSED(ref);
+	git_futils_rmdir_r("base", GIT_DIRREMOVAL_EMPTY_HIERARCHY);
+}
+
+void test_core_mkdir__with_base(void)
+{
+#define BASEDIR "base/dir/here"
+
+	cl_set_cleanup(cleanup_basedir, NULL);
+
+	cl_git_pass(git_futils_mkdir(BASEDIR, NULL, 0755, GIT_MKDIR_PATH));
+
+	cl_git_pass(git_futils_mkdir("a", BASEDIR, 0755, 0));
+	cl_assert(git_path_isdir(BASEDIR "/a"));
+
+	cl_git_pass(git_futils_mkdir("b/b1/b2", BASEDIR, 0755, GIT_MKDIR_PATH));
+	cl_assert(git_path_isdir(BASEDIR "/b/b1/b2"));
+
+	/* exclusive with existing base */
+	cl_git_pass(git_futils_mkdir("c/c1/c2", BASEDIR, 0755, GIT_MKDIR_PATH | GIT_MKDIR_EXCL));
+
+	/* fail: exclusive with duplicated suffix */
+	cl_git_fail(git_futils_mkdir("c/c1/c3", BASEDIR, 0755, GIT_MKDIR_PATH | GIT_MKDIR_EXCL));
+
+	/* fail: exclusive with any duplicated component */
+	cl_git_fail(git_futils_mkdir("c/cz/cz", BASEDIR, 0755, GIT_MKDIR_PATH | GIT_MKDIR_EXCL));
+
+	/* success: exclusive without path */
+	cl_git_pass(git_futils_mkdir("c/c1/c3", BASEDIR, 0755, GIT_MKDIR_EXCL));
+
+	/* path with shorter base and existing dirs */
+	cl_git_pass(git_futils_mkdir("dir/here/d/", "base", 0755, GIT_MKDIR_PATH));
+	cl_assert(git_path_isdir("base/dir/here/d"));
+
+	/* fail: path with shorter base and existing dirs */
+	cl_git_fail(git_futils_mkdir("dir/here/e/", "base", 0755, GIT_MKDIR_PATH | GIT_MKDIR_EXCL));
+
+	/* fail: base with missing components */
+	cl_git_fail(git_futils_mkdir("f/", "base/missing", 0755, GIT_MKDIR_PATH));
+
+	/* success: shift missing component to path */
+	cl_git_pass(git_futils_mkdir("missing/f/", "base/", 0755, GIT_MKDIR_PATH));
+}
+
+static void cleanup_chmod_root(void *ref)
+{
+	mode_t *mode = ref;
+
+	if (*mode != 0) {
+		(void)p_umask(*mode);
+		git__free(mode);
+	}
+
+	git_futils_rmdir_r("r", GIT_DIRREMOVAL_EMPTY_HIERARCHY);
+}
+
+void test_core_mkdir__chmods(void)
+{
+	struct stat st;
+	mode_t *old = git__malloc(sizeof(mode_t));
+	*old = p_umask(022);
+
+	cl_set_cleanup(cleanup_chmod_root, old);
+
+	cl_git_pass(git_futils_mkdir("r", NULL, 0777, 0));
+
+	cl_git_pass(git_futils_mkdir("mode/is/important", "r", 0777, GIT_MKDIR_PATH));
+
+	cl_git_pass(git_path_lstat("r/mode", &st));
+	cl_assert((st.st_mode & 0777) == 0755);
+	cl_git_pass(git_path_lstat("r/mode/is", &st));
+	cl_assert((st.st_mode & 0777) == 0755);
+	cl_git_pass(git_path_lstat("r/mode/is/important", &st));
+	cl_assert((st.st_mode & 0777) == 0755);
+
+	cl_git_pass(git_futils_mkdir("mode2/is2/important2", "r", 0777, GIT_MKDIR_PATH | GIT_MKDIR_CHMOD));
+
+	cl_git_pass(git_path_lstat("r/mode2", &st));
+	cl_assert((st.st_mode & 0777) == 0755);
+	cl_git_pass(git_path_lstat("r/mode2/is2", &st));
+	cl_assert((st.st_mode & 0777) == 0755);
+	cl_git_pass(git_path_lstat("r/mode2/is2/important2", &st));
+	cl_assert((st.st_mode & 0777) == 0777);
+
+	cl_git_pass(git_futils_mkdir("mode3/is3/important3", "r", 0777, GIT_MKDIR_PATH | GIT_MKDIR_CHMOD_PATH));
+
+	cl_git_pass(git_path_lstat("r/mode3", &st));
+	cl_assert((st.st_mode & 0777) == 0777);
+	cl_git_pass(git_path_lstat("r/mode3/is3", &st));
+	cl_assert((st.st_mode & 0777) == 0777);
+	cl_git_pass(git_path_lstat("r/mode3/is3/important3", &st));
+	cl_assert((st.st_mode & 0777) == 0777);
+
+	/* test that we chmod existing dir */
+
+	cl_git_pass(git_futils_mkdir("mode/is/important", "r", 0777, GIT_MKDIR_PATH | GIT_MKDIR_CHMOD));
+
+	cl_git_pass(git_path_lstat("r/mode", &st));
+	cl_assert((st.st_mode & 0777) == 0755);
+	cl_git_pass(git_path_lstat("r/mode/is", &st));
+	cl_assert((st.st_mode & 0777) == 0755);
+	cl_git_pass(git_path_lstat("r/mode/is/important", &st));
+	cl_assert((st.st_mode & 0777) == 0777);
+
+	/* test that we chmod even existing dirs if CHMOD_PATH is set */
+
+	cl_git_pass(git_futils_mkdir("mode2/is2/important2.1", "r", 0777, GIT_MKDIR_PATH | GIT_MKDIR_CHMOD_PATH));
+
+	cl_git_pass(git_path_lstat("r/mode2", &st));
+	cl_assert((st.st_mode & 0777) == 0777);
+	cl_git_pass(git_path_lstat("r/mode2/is2", &st));
+	cl_assert((st.st_mode & 0777) == 0777);
+	cl_git_pass(git_path_lstat("r/mode2/is2/important2.1", &st));
+	cl_assert((st.st_mode & 0777) == 0777);
+}
diff --git a/tests-clar/refs/list.c b/tests-clar/refs/list.c
index ac3cc00..f92bf48 100644
--- a/tests-clar/refs/list.c
+++ b/tests-clar/refs/list.c
@@ -36,7 +36,7 @@ void test_refs_list__all(void)
 	/* We have exactly 9 refs in total if we include the packed ones:
 	 * there is a reference that exists both in the packfile and as
 	 * loose, but we only list it once */
-	cl_assert_equal_i(ref_list.count, 10);
+	cl_assert_equal_i((int)ref_list.count, 10);
 
 	git_strarray_free(&ref_list);
 }
diff --git a/tests-clar/repo/init.c b/tests-clar/repo/init.c
index 3d37c37..9cbc02b 100644
--- a/tests-clar/repo/init.c
+++ b/tests-clar/repo/init.c
@@ -2,6 +2,7 @@
 #include "fileops.h"
 #include "repository.h"
 #include "config.h"
+#include "path.h"
 
 enum repo_mode {
 	STANDARD_REPOSITORY = 0,
@@ -83,7 +84,7 @@ void test_repo_init__bare_repo_escaping_current_workdir(void)
 	git_buf path_current_workdir = GIT_BUF_INIT;
 
 	cl_git_pass(git_path_prettify_dir(&path_current_workdir, ".", NULL));
-	
+
 	cl_git_pass(git_buf_joinpath(&path_repository, git_buf_cstr(&path_current_workdir), "a/b/c"));
 	cl_git_pass(git_futils_mkdir_r(git_buf_cstr(&path_repository), NULL, GIT_DIR_MODE));
 
@@ -295,3 +296,82 @@ void test_repo_init__sets_logAllRefUpdates_according_to_type_of_repository(void)
 	git_repository_free(_repo);
 	assert_config_entry_on_init_bytype("core.logallrefupdates", true, false);
 }
+
+void test_repo_init__extended_0(void)
+{
+	git_repository_init_options opts;
+	memset(&opts, 0, sizeof(opts));
+
+	/* without MKDIR this should fail */
+	cl_git_fail(git_repository_init_ext(&_repo, "extended", &opts));
+
+	/* make the directory first, then it should succeed */
+	cl_git_pass(git_futils_mkdir("extended", NULL, 0775, 0));
+	cl_git_pass(git_repository_init_ext(&_repo, "extended", &opts));
+
+	cl_assert(!git__suffixcmp(git_repository_workdir(_repo), "/extended/"));
+	cl_assert(!git__suffixcmp(git_repository_path(_repo), "/extended/.git/"));
+	cl_assert(!git_repository_is_bare(_repo));
+	cl_assert(git_repository_is_empty(_repo));
+
+	cleanup_repository("extended");
+}
+
+void test_repo_init__extended_1(void)
+{
+	git_reference *ref;
+	git_remote *remote;
+	struct stat st;
+	git_repository_init_options opts;
+	memset(&opts, 0, sizeof(opts));
+
+	opts.flags = GIT_REPOSITORY_INIT_MKPATH |
+		GIT_REPOSITORY_INIT_NO_DOTGIT_DIR;
+	opts.mode = GIT_REPOSITORY_INIT_SHARED_GROUP;
+	opts.workdir_path = "../c_wd";
+	opts.description = "Awesomest test repository evah";
+	opts.initial_head = "development";
+	opts.origin_url = "https://github.com/libgit2/libgit2.git";
+
+	cl_git_pass(git_repository_init_ext(&_repo, "root/b/c.git", &opts));
+
+	cl_assert(!git__suffixcmp(git_repository_workdir(_repo), "/c_wd/"));
+	cl_assert(!git__suffixcmp(git_repository_path(_repo), "/c.git/"));
+	cl_assert(git_path_isfile("root/b/c_wd/.git"));
+	cl_assert(!git_repository_is_bare(_repo));
+	/* repo will not be counted as empty because we set head to "development" */
+	cl_assert(!git_repository_is_empty(_repo));
+
+	cl_git_pass(git_path_lstat(git_repository_path(_repo), &st));
+	cl_assert(S_ISDIR(st.st_mode));
+	cl_assert((S_ISGID & st.st_mode) == S_ISGID);
+
+	cl_git_pass(git_reference_lookup(&ref, _repo, "HEAD"));
+	cl_assert(git_reference_type(ref) == GIT_REF_SYMBOLIC);
+	cl_assert_equal_s("refs/heads/development", git_reference_target(ref));
+	git_reference_free(ref);
+
+	cl_git_pass(git_remote_load(&remote, _repo, "origin"));
+	cl_assert_equal_s("origin", git_remote_name(remote));
+	cl_assert_equal_s(opts.origin_url, git_remote_url(remote));
+	git_remote_free(remote);
+
+	git_repository_free(_repo);
+	cl_fixture_cleanup("root");
+}
+
+void test_repo_init__extended_with_template(void)
+{
+	git_repository_init_options opts;
+	memset(&opts, 0, sizeof(opts));
+
+	opts.flags = GIT_REPOSITORY_INIT_MKPATH | GIT_REPOSITORY_INIT_BARE;
+	opts.template_path = cl_fixture("template");
+
+	cl_git_pass(git_repository_init_ext(&_repo, "templated.git", &opts));
+
+	cl_assert(git_repository_is_bare(_repo));
+	cl_assert(!git__suffixcmp(git_repository_path(_repo), "/templated.git/"));
+
+	cleanup_repository("templated.git");
+}
diff --git a/tests-clar/resources/template/branches/.gitignore b/tests-clar/resources/template/branches/.gitignore
new file mode 100644
index 0000000..16868ce
--- /dev/null
+++ b/tests-clar/resources/template/branches/.gitignore
@@ -0,0 +1,2 @@
+# This file should not be copied, nor should the
+# containing directory, since it is effectively "empty"
diff --git a/tests-clar/resources/template/description b/tests-clar/resources/template/description
new file mode 100644
index 0000000..498b267
--- /dev/null
+++ b/tests-clar/resources/template/description
@@ -0,0 +1 @@
+Unnamed repository; edit this file 'description' to name the repository.
diff --git a/tests-clar/resources/template/hooks/applypatch-msg.sample b/tests-clar/resources/template/hooks/applypatch-msg.sample
new file mode 100755
index 0000000..8b2a2fe
--- /dev/null
+++ b/tests-clar/resources/template/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
+test -x "$GIT_DIR/hooks/commit-msg" &&
+	exec "$GIT_DIR/hooks/commit-msg" ${1+"$@"}
+:
diff --git a/tests-clar/resources/template/hooks/commit-msg.sample b/tests-clar/resources/template/hooks/commit-msg.sample
new file mode 100755
index 0000000..b58d118
--- /dev/null
+++ b/tests-clar/resources/template/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
+}
diff --git a/tests-clar/resources/template/hooks/post-commit.sample b/tests-clar/resources/template/hooks/post-commit.sample
new file mode 100755
index 0000000..2266821
--- /dev/null
+++ b/tests-clar/resources/template/hooks/post-commit.sample
@@ -0,0 +1,8 @@
+#!/bin/sh
+#
+# An example hook script that is called after a successful
+# commit is made.
+#
+# To enable this hook, rename this file to "post-commit".
+
+: Nothing
diff --git a/tests-clar/resources/template/hooks/post-receive.sample b/tests-clar/resources/template/hooks/post-receive.sample
new file mode 100755
index 0000000..7a83e17
--- /dev/null
+++ b/tests-clar/resources/template/hooks/post-receive.sample
@@ -0,0 +1,15 @@
+#!/bin/sh
+#
+# An example hook script for the "post-receive" event.
+#
+# The "post-receive" script is run after receive-pack has accepted a pack
+# and the repository has been updated.  It is passed arguments in through
+# stdin in the form
+#  <oldrev> <newrev> <refname>
+# For example:
+#  aa453216d1b3e49e7f6f98441fa56946ddcd6a20 68f7abf4e6f922807889f52bc043ecd31b79f814 refs/heads/master
+#
+# see contrib/hooks/ for a sample, or uncomment the next line and
+# rename the file to "post-receive".
+
+#. /usr/share/doc/git-core/contrib/hooks/post-receive-email
diff --git a/tests-clar/resources/template/hooks/post-update.sample b/tests-clar/resources/template/hooks/post-update.sample
new file mode 100755
index 0000000..ec17ec1
--- /dev/null
+++ b/tests-clar/resources/template/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
diff --git a/tests-clar/resources/template/hooks/pre-applypatch.sample b/tests-clar/resources/template/hooks/pre-applypatch.sample
new file mode 100755
index 0000000..b1f187c
--- /dev/null
+++ b/tests-clar/resources/template/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
+test -x "$GIT_DIR/hooks/pre-commit" &&
+	exec "$GIT_DIR/hooks/pre-commit" ${1+"$@"}
+:
diff --git a/tests-clar/resources/template/hooks/pre-commit.sample b/tests-clar/resources/template/hooks/pre-commit.sample
new file mode 100755
index 0000000..b187c4b
--- /dev/null
+++ b/tests-clar/resources/template/hooks/pre-commit.sample
@@ -0,0 +1,46 @@
+#!/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=$(git config hooks.allownonascii)
+
+# Cross platform projects tend to avoid non-ascii filenames; prevent
+# them from being added to the repository. We exploit the fact that the
+# printable range starts at the space character and ends with tilde.
+if [ "$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')"
+then
+	echo "Error: Attempt to add a non-ascii file name."
+	echo
+	echo "This can cause problems if you want to work"
+	echo "with people on other platforms."
+	echo
+	echo "To be portable it is advisable to rename the file ..."
+	echo
+	echo "If you know what you are doing you can disable this"
+	echo "check using:"
+	echo
+	echo "  git config hooks.allownonascii true"
+	echo
+	exit 1
+fi
+
+exec git diff-index --check --cached $against --
diff --git a/tests-clar/resources/template/hooks/pre-rebase.sample b/tests-clar/resources/template/hooks/pre-rebase.sample
new file mode 100755
index 0000000..9773ed4
--- /dev/null
+++ b/tests-clar/resources/template/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".
diff --git a/tests-clar/resources/template/hooks/prepare-commit-msg.sample b/tests-clar/resources/template/hooks/prepare-commit-msg.sample
new file mode 100755
index 0000000..f093a02
--- /dev/null
+++ b/tests-clar/resources/template/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"
diff --git a/tests-clar/resources/template/hooks/update.sample b/tests-clar/resources/template/hooks/update.sample
new file mode 100755
index 0000000..71ab04e
--- /dev/null
+++ b/tests-clar/resources/template/hooks/update.sample
@@ -0,0 +1,128 @@
+#!/bin/sh
+#
+# An example hook script to blocks 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
diff --git a/tests-clar/resources/template/info/exclude b/tests-clar/resources/template/info/exclude
new file mode 100644
index 0000000..a5196d1
--- /dev/null
+++ b/tests-clar/resources/template/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]
+# *~
diff --git a/tests-clar/status/status_data.h b/tests-clar/status/status_data.h
index 043b830..85a7cd6 100644
--- a/tests-clar/status/status_data.h
+++ b/tests-clar/status/status_data.h
@@ -44,7 +44,7 @@ static const unsigned int entry_statuses0[] = {
 	GIT_STATUS_WT_NEW,
 };
 
-static const size_t entry_count0 = 16;
+static const int entry_count0 = 16;
 
 /* entries for a copy of tests/resources/status with all content
  * deleted from the working directory
@@ -86,7 +86,7 @@ static const unsigned int entry_statuses2[] = {
 	GIT_STATUS_WT_DELETED,
 };
 
-static const size_t entry_count2 = 15;
+static const int entry_count2 = 15;
 
 /* entries for a copy of tests/resources/status with some mods */
 
@@ -140,7 +140,7 @@ static const unsigned int entry_statuses3[] = {
 	GIT_STATUS_WT_NEW,
 };
 
-static const size_t entry_count3 = 22;
+static const int entry_count3 = 22;
 
 
 /* entries for a copy of tests/resources/status with some mods
@@ -199,4 +199,4 @@ static const unsigned int entry_statuses4[] = {
 	GIT_STATUS_WT_NEW,
 };
 
-static const size_t entry_count4 = 23;
+static const int entry_count4 = 23;
diff --git a/tests-clar/status/status_helpers.h b/tests-clar/status/status_helpers.h
index cffca66..3f9c1f5 100644
--- a/tests-clar/status/status_helpers.h
+++ b/tests-clar/status/status_helpers.h
@@ -2,12 +2,12 @@
 #define INCLUDE_cl_status_helpers_h__
 
 typedef struct {
-	size_t wrong_status_flags_count;
-	size_t wrong_sorted_path;
-	size_t entry_count;
+	int wrong_status_flags_count;
+	int wrong_sorted_path;
+	int entry_count;
 	const unsigned int* expected_statuses;
 	const char** expected_paths;
-	size_t expected_entry_count;
+	int expected_entry_count;
 } status_entry_counts;
 
 /* cb_status__normal takes payload of "status_entry_counts *" */
diff --git a/tests-clar/status/worktree.c b/tests-clar/status/worktree.c
index 2abf368..75975c9 100644
--- a/tests-clar/status/worktree.c
+++ b/tests-clar/status/worktree.c
@@ -683,7 +683,7 @@ static unsigned int filemode_statuses[] = {
 	GIT_STATUS_WT_NEW
 };
 
-static const size_t filemode_count = 8;
+static const int filemode_count = 8;
 
 void test_status_worktree__filemode_changes(void)
 {
@@ -697,7 +697,7 @@ void test_status_worktree__filemode_changes(void)
 	if (cl_is_chmod_supported())
 		cl_git_pass(git_config_set_bool(cfg, "core.filemode", true));
 	else {
-		unsigned int i;
+		int i;
 		cl_git_pass(git_config_set_bool(cfg, "core.filemode", false));
 
 		/* won't trust filesystem mode diffs, so these will appear unchanged */