Fix repository discovery precedence - #2218

git/repo/base.py:310

• osp.exists follows symlinks, so a dangling .git symlink makes this condition false. Discovery then continues into is_git_dir(curpath) or a parent, allowing a bare-looking worktree/ancestor repository to be selected despite an existing malformed .git entry. Use an existence check that does not follow symlinks (for example, lexists) so broken .git entries stop discovery like other invalid gitfiles.

            if osp.exists(dotgit) and not osp.isdir(dotgit):
                break

git/repo/fun.py:97

• Using or treats an explicitly set empty GIT_OBJECT_DIRECTORY as if the variable were unset. Git's discovery code checks whether this variable is present and then validates that exact path, so with GIT_OBJECT_DIRECTORY="" this implementation can accept a repository that Git rejects and leave later Git commands inconsistent with discovery. Test for presence in os.environ and use the empty value as invalid rather than falling back to <common_dir>/objects.

        object_dir = os.getenv("GIT_OBJECT_DIRECTORY") or osp.join(common_dir, "objects")

git/repo/fun.py:103

• A Git linked-worktree administrative directory contains gitdir, commondir, and HEAD; the .git file is in the working tree, not at d/gitfile. Replacing the HEAD check with gitfile makes this unsupported-worktree detection miss its documented layout when common storage is invalid. Keep checking HEAD here.

            and osp.isfile(osp.join(d, "gitfile"))

Previously missed (2) — in code that hasn't changed since the last review.

git/repo/base.py:309

• Use osp.lexists rather than osp.exists here. exists follows symlinks, so a dangling .git symlink makes this condition false; discovery then proceeds to is_git_dir(curpath) and can classify the directory as a bare repository (or continue to a parent) despite the invalid .git entry. That bypasses the precedence/rejection this guard is meant to enforce.

            if osp.exists(dotgit) and not osp.isdir(dotgit):

git/repo/base.py:300

• The new precedence path recursively follows .git pointers through find_submodule_git_dir before the bare-repository check, but that helper has no cycle detection. A malformed file containing gitdir: .git (or a two-file cycle) recurses until RecursionError instead of being rejected as invalid metadata; bound the resolution or track visited paths and return an invalid-candidate result.

            sm_gitpath = find_submodule_git_dir(dotgit)

git/repo/base.py:385

• When only GIT_DIR is set to a relative path, discovery expands it to an absolute self.git_dir, but this conditional leaves the wrapper's inherited relative GIT_DIR unchanged unless GIT_COMMON_DIR is also set. Git commands run with self.working_dir, so they resolve that value from a different directory and can fail or address the wrong repository. Normalize GIT_DIR whenever it is supplied, independently of GIT_COMMON_DIR.

        if common_dir_env is not None:
            self.git.update_environment(GIT_DIR=os.fspath(self.git_dir), GIT_COMMON_DIR=os.fspath(self.common_dir))

git/repo/base.py:300

• find_submodule_git_dir reads the .git entry with the default text decoder and does not catch UnicodeError. Consequently, a .git file containing invalid UTF-8 raises UnicodeDecodeError from this new discovery path instead of being rejected as an invalid repository; use the same byte-oriented decoding approach as commondir or catch decode errors in the resolver.

            sm_gitpath = find_submodule_git_dir(dotgit)

git/repo/base.py:364

• is_git_dir reads commondir with os.fsdecode, so a valid common-directory path containing non-UTF-8 filesystem bytes can pass discovery. The constructor then re-reads the same file with Path.read_text(), which raises UnicodeDecodeError instead of constructing the repository; use the same filesystem decoding here.

                common_dir = (Path(self.git_dir) / "commondir").read_text().splitlines()[0].strip()

git/repo/fun.py:93

• Treat a dangling commondir symlink as malformed, not as an absent file. read_bytes() raises FileNotFoundError for the dangling link, so this branch assigns d and can accept local HEAD/objects/refs; Repo then opens the candidate as a bare repository instead of rejecting the malformed metadata. Check lexists before taking the missing-file fallback.

            except FileNotFoundError:
                common_dir = os.fspath(d)

Previously missed (1) — in code that hasn't changed since the last review.

git/repo/base.py:310

• osp.exists() returns False for a dangling symlink. Consequently, a worktree containing a broken .git symlink can still fall through to is_git_dir(curpath) and be accepted as a bare repository if it has HEAD, objects, and refs, defeating the malformed-.git guard above. Use osp.lexists(dotgit) so every non-directory .git entry blocks fallback.

            if osp.exists(dotgit) and not osp.isdir(dotgit):

git/repo/base.py:310

• When .git is a dangling symlink, find_submodule_git_dir() returns None and osp.exists(dotgit) is false, so this guard does not stop discovery. With search_parent_directories=True, the loop can then open an unrelated parent repository, contrary to the malformed .git rejection described by this change. Use osp.lexists(dotgit) so a present but unresolved non-directory .git entry blocks fallback.

            if osp.exists(dotgit) and not osp.isdir(dotgit):

git/repo/fun.py:130

• The pre-open st_size check is not sufficient to enforce the 1 MiB Gitfile limit: read_bytes() then reads the entire file without a bound. If a regular file grows or is replaced between stat and the read, repository discovery can allocate unbounded input and defeat the size safeguard. Open the file and read at most (1 << 20) + 1 bytes, rejecting an over-limit read.

    try:
        content = os.fsdecode(Path(dotgit).read_bytes()).rstrip("\r\n")
    except OSError:
        return None
    return content[8:] if len(content) >= 9 and content.startswith("gitdir: ") else None

git/repo/fun.py:110

• This branch now treats a nonempty GIT_OBJECT_DIRECTORY as the repository's object store, but Repo does not carry that value into construction: its ODB is still rooted at common_dir/objects and the Git wrapper only pins GIT_DIR/GIT_COMMON_DIR. A repository whose objects exist only in GIT_OBJECT_DIRECTORY can therefore use a different or nonexistent object database (and a relative value will break when the process cwd changes). Resolve and preserve GIT_OBJECT_DIRECTORY as well, or reject this environment mode consistently.

        object_dir = os.getenv("GIT_OBJECT_DIRECTORY")
        if object_dir is None:
            object_dir = osp.join(common_dir, "objects")
        if valid_head and osp.isdir(object_dir) and osp.isdir(osp.join(common_dir, "refs")):

Previously missed (2) — in code that hasn't changed since the last review.

git/repo/base.py:388

• GIT_OBJECT_DIRECTORY is validated during discovery, but it is not pinned in the Git wrapper's environment. When this value is relative and Repo(path) gives the wrapper a different cwd, discovery checks the path relative to the caller's cwd while later Git commands resolve it relative to the repository's working directory, so object lookups can target a different store. Resolve and propagate this variable along with GIT_DIR and GIT_COMMON_DIR.

        if common_dir_env is not None:
            self.git.update_environment(GIT_DIR=os.fspath(self.git_dir), GIT_COMMON_DIR=os.fspath(self.common_dir))
        elif git_dir_env is not None:
            self.git.update_environment(GIT_DIR=os.fspath(self.git_dir))

git/repo/base.py:310

• osp.exists follows symlinks, so a dangling .git symlink makes this guard false. If the current directory also has bare-repository markers (or parent search is enabled), discovery can then fall through and accept that directory/parent even though an invalid .git entry is present, defeating the precedence check above. Use lexists so dangling metadata is treated as an existing non-directory entry, as is already done for commondir in fun.py.

            if osp.exists(dotgit) and not osp.isdir(dotgit):

git/repo/fun.py:110

• This accepts GIT_OBJECT_DIRECTORY as the repository's object store, but the constructor still creates the object database from self.common_dir/objects (base.py:391). A valid repository whose objects exist only in this environment-provided directory will therefore be opened with an unusable GitDB (and an inaccurate GitCmdObjectDB.root_path()); either use the resolved object-directory environment value when constructing the ODB or reject this configuration consistently.

        object_dir = os.getenv("GIT_OBJECT_DIRECTORY")
        if object_dir is None:
            object_dir = osp.join(common_dir, "objects")
        if valid_head and osp.isdir(object_dir) and osp.isdir(osp.join(common_dir, "refs")):

git/repo/fun.py:129

• The size check applies only to the result of os.stat; Path.read_bytes() reopens the path and reads to EOF. A concurrent replacement or growth can therefore bypass the 1 MiB limit and make repository discovery read an arbitrarily large Gitfile. Read from one descriptor with a bound of statbuf.st_size (and reject a short read), as Git does.

    try:
        content = os.fsdecode(Path(dotgit).read_bytes()).rstrip("\r\n")
    except (OSError, UnicodeError):
        return None

test/test_repo.py:139

• Repo.init(path) leaves a valid path/.git directory in place, so even the bare layout is resolved by find_submodule_git_dir(path/.git) before the new implicit-bare branch at base.py:313 runs. Add a bare-only directory without .git and assert Repo(path) discovers it, otherwise this new discovery path has no positive regression coverage.

                Repo.init(path).close()

git/repo/base.py:391

• The wrapper can run with an absolute cwd while receiving a relative GIT_DIR. For example, GIT_DIR=git with a commondir file makes working_dir the common directory, so Git resolves GIT_DIR=git below that directory instead of the original repository; the same applies when only GIT_COMMON_DIR is set and git_dir came from a relative path. Normalize GIT_DIR before storing it in both branches.

        if common_dir_env is not None:
            self.git.update_environment(GIT_DIR=os.fspath(self.git_dir), GIT_COMMON_DIR=os.fspath(self.common_dir))
        elif git_dir_env is not None:
            self.git.update_environment(GIT_DIR=os.fspath(self.git_dir))

git/repo/base.py:314

• If .git exists as a malformed directory, find_submodule_git_dir(dotgit) returns None, but this condition does not stop discovery because the entry is a directory. A worktree containing repository-looking HEAD, objects, and refs can then be accepted as a bare repository, defeating the new malformed-.git precedence rule; osp.exists also misses dangling .git symlinks. Treat any present but unresolved .git entry as terminal (using lexists) before checking curpath as a bare repository.

            if osp.exists(dotgit) and not osp.isdir(dotgit):
                break

git/repo/base.py:307

• find_submodule_git_dir() has already resolved a relative gitdir: target against dirname(d) (lines 147-149). When Repo is opened with a relative path, sm_gitpath is therefore relative to the process cwd, but joining curpath again prefixes the worktree a second time and selects a nonexistent/wrong admin directory. Use the helper's resolved path directly here so relative Gitfiles work with relative Repo paths.

                git_dir = osp.normpath(osp.join(curpath, os.fspath(sm_gitpath)))

git/repo/base.py:369

• The commondir is normalized with a different rule than Git: trailing spaces/tabs remain in common_dir here even though Git's get_common_dir_noenv() removes them. Once discovery accepts such a file, this leaves self.common_dir pointing at the wrong path and causes config/object access to diverge from Git; use rstrip() here as well.

            try:
                common_dir = os.fsdecode((Path(self.git_dir) / "commondir").read_bytes()).rstrip("\r\n")
                self._common_dir = osp.join(self.git_dir, common_dir)

git/repo/fun.py:130

• Git's read_gitfile_gently() trims trailing whitespace from the gitdir record, not just CR/LF. With this normalization, a valid .git file such as gitdir: /path/to/repo \n is rejected because the target retains the trailing space, so discovery diverges from Git. Strip all trailing whitespace here before extracting the target.

        content = os.fsdecode(Path(dotgit).read_bytes()).rstrip("\r\n")
    except (OSError, UnicodeError):
        return None
    return content[8:] if len(content) >= 9 and content.startswith("gitdir: ") else None

git/repo/fun.py:93

• get_common_dir_noenv() applies Git's trailing-whitespace trimming to the commondir file. Leaving spaces or tabs in common_dir makes this check look in the wrong directory and rejects repositories that Git opens successfully; use the same trimming rule as the later Repo construction path.

            common_dir_file = Path(d) / "commondir"
            try:
                common_dir = os.fsdecode(common_dir_file.read_bytes()).rstrip("\r\n")
            except FileNotFoundError:

test/test_repo.py:252

• These assertions execute while both cwd(tdir) and the patched environment are still active, so relative GIT_DIR/GIT_OBJECT_DIRECTORY values would still resolve correctly even if the wrapper failed to retain absolute paths. Move the repository and GitDB assertions outside both context managers to actually cover the preservation behavior this regression test is intended to protect.

            assert repo.git.cat_file("blob", blob_hexsha) == payload.decode()

test/test_repo.py:223

• This assertion is also inside the cwd(tdir)/environment context, so it does not verify that the relative GIT_DIR remains usable after construction changes the execution context. Place the assertion after the context managers (as in the preceding environment case) to cover the wrapper path normalization.

            assert osp.samefile(repo.git.rev_parse("--absolute-git-dir"), git_dir)

git/repo/base.py:396

• Now that GIT_OBJECT_DIRECTORY is accepted as the active object store and used for rootpath, Repo.alternates still reads and writes common_dir/objects/info/alternates. With objects relocated to the environment-provided directory, that API silently ignores the active alternates file or modifies the wrong repository; derive this path from the resolved object root as well.

        rootpath = object_dir_env if object_dir_env is not None else osp.join(self.common_dir, "objects")

git/repo/base.py:313

• Using osp.exists here misses a dangling .git symlink: find_submodule_git_dir returns None, then this guard is skipped and the loop can still accept curpath as a bare repository if it has HEAD/objects/refs. That bypasses the new malformed-.git no-fallback rule; use osp.lexists (or an equivalent lstat check) for this guard.

            if osp.exists(dotgit) and not osp.isdir(dotgit):

git/repo/base.py:391

• When git_dir_env and common_dir_env are both unset, this code does not pin the resolved self.git_dir into the command wrapper. A valid repository opened from a separate git directory via core.worktree can therefore have self.working_dir set to its worktree while that worktree has no .git entry; subsequent repo.git commands run without GIT_DIR and fail discovery. Preserve the resolved GIT_DIR for path-based discovery too.

        if common_dir_env is not None:
            self.git.update_environment(GIT_DIR=os.fspath(self.git_dir), GIT_COMMON_DIR=os.fspath(self.common_dir))
        elif git_dir_env is not None:
            self.git.update_environment(GIT_DIR=os.fspath(self.git_dir))

git/repo/base.py:313

• A dangling .git symlink is a non-directory entry, but osp.exists() follows symlinks and returns False for it. Since find_submodule_git_dir() has already rejected the dangling target, discovery then reaches is_git_dir(curpath) and can still misclassify a worktree with objects/refs/HEAD as a bare repository. Use a lexists-style check for this guard so any present, invalid .git entry stops fallback.

                    self._working_tree_dir = curpath

git/repo/base.py:391

• When the common directory comes from a commondir file and neither GIT_COMMON_DIR nor GIT_DIR was set, neither branch initializes the wrapper environment. For a split bare repository, working_dir becomes self.common_dir, which may have no HEAD or .git, so later repo.git commands fail repository discovery even though construction succeeded. Pin the resolved GIT_DIR/GIT_COMMON_DIR whenever the resolved common directory differs from the git directory, not only when those variables were inherited.

            self._working_tree_dir = None
        # END working dir handling

        self.working_dir: PathLike = self._working_tree_dir or self.common_dir

git/repo/fun.py:127

• Git's read_gitfile_gently() trims trailing whitespace from the single gitdir: record, so a valid .git file such as gitdir: /path/to/git \n is accepted by Git. This parser only strips CR/LF and returns a target with the trailing space, causing is_git_dir() to reject an otherwise valid worktree; trim the same whitespace set before extracting the target.

        with open(dotgit, "rb") as fp: