JohanMabille · Oct 7, 2026 · Oct 6, 2026 · Oct 7, 2026
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -90,6 +90,8 @@ set(GIT2CPP_SRC
     ${GIT2CPP_SOURCE_DIR}/utils/ansi_code.hpp
     ${GIT2CPP_SOURCE_DIR}/utils/common.cpp
     ${GIT2CPP_SOURCE_DIR}/utils/common.hpp
+    ${GIT2CPP_SOURCE_DIR}/utils/config_overrides.cpp
+    ${GIT2CPP_SOURCE_DIR}/utils/config_overrides.hpp
     ${GIT2CPP_SOURCE_DIR}/utils/credentials.cpp
     ${GIT2CPP_SOURCE_DIR}/utils/credentials.hpp
     ${GIT2CPP_SOURCE_DIR}/utils/git_exception.cpp

diff --git a/src/utils/config_overrides.cpp b/src/utils/config_overrides.cpp
@@ -0,0 +1,51 @@
+#include "config_overrides.hpp"
+
+#ifdef EMSCRIPTEN
+#    include <iterator>
+
+#    include <git2/sys/config.h>
+
+#    include "git_exception.hpp"
+#endif
+
+void apply_config_overrides([[maybe_unused]] git_repository* repo)
+{
+#ifdef EMSCRIPTEN
+    // Config values to override, each in "name=value" form. core.filemode is disabled because
+    // the emscripten filesystem does support executable file permissions but some JupyterLite
+    // drive implementations do not.
+    const char* values[] = {"core.filemode=false"};
+
+    // Create an in-memory config backend holding these values. This backend is read-only, so
+    // any config writes (e.g. `git config` or values set by clone/init) skip it and go to the
+    // highest-priority writable backend instead, which is the repository's own config file.
+    // The overrides are therefore never persisted to disk. backend_type is a label that
+    // identifies where these entries came from when inspecting a config entry's origin.
+    git_config_backend* backend = nullptr;
+    git_config_backend_memory_options opts = GIT_CONFIG_BACKEND_MEMORY_OPTIONS_INIT;
+    opts.backend_type = "git2cpp-overrides";
+    throw_if_error(git_config_backend_from_values(&backend, values, std::size(values), &opts));
+
+    // git_repository_config returns the repository's cached, shared config object rather than a
+    // copy, so adding a backend to it affects all later config lookups through this repository.
+    // GIT_CONFIG_LEVEL_APP is the highest priority level, above the local, global and system
+    // config files, so these values win over any existing setting. The repo is passed so that
+    // conditional includes can be evaluated, and force=0 means fail rather than replace if a
+    // backend already exists at this level.
+    git_config* cfg = nullptr;
+    int error = git_repository_config(&cfg, repo);
+    if (error == 0)
+    {
+        error = git_config_add_backend(cfg, backend, GIT_CONFIG_LEVEL_APP, repo, 0);
+        // Only releases our reference; the repository still holds the config and its backends.
+        git_config_free(cfg);
+    }
+    if (error < 0)
+    {
+        // On success ownership of the backend passes to the config, but on failure it is still
+        // ours to free.
+        backend->free(backend);
+        throw_if_error(error);
+    }
+#endif
+}
diff --git a/src/utils/config_overrides.hpp b/src/utils/config_overrides.hpp
@@ -0,0 +1,8 @@
+#pragma once
+
+#include <git2.h>
+
+// Apply in-memory config overrides to a repository's config. These have a higher priority than
+// the repository's config file but are never written to it. Only used in WebAssembly, where
+// core.filemode=false is set as the filesystem does not always support executable file permissions.
+void apply_config_overrides(git_repository* repo);
diff --git a/src/wrapper/repository_wrapper.cpp b/src/wrapper/repository_wrapper.cpp
@@ -4,6 +4,7 @@
 #include <fstream>
 #include <iostream>
 
+#include "../utils/config_overrides.hpp"
 #include "../utils/git_exception.hpp"
 #include "../wrapper/commit_wrapper.hpp"
 #include "../wrapper/config_wrapper.hpp"
@@ -22,20 +23,23 @@ repository_wrapper repository_wrapper::open(std::string_view directory)
 {
     repository_wrapper rw;
     throw_if_error(git_repository_open(&(rw.p_resource), directory.data()));
+    apply_config_overrides(rw.p_resource);
     return rw;
 }
 
 repository_wrapper repository_wrapper::init(std::string_view directory, bool bare)
 {
     repository_wrapper rw;
     throw_if_error(git_repository_init(&(rw.p_resource), directory.data(), bare));
+    apply_config_overrides(rw.p_resource);
     return rw;
 }
 
 repository_wrapper repository_wrapper::init_ext(std::string_view directory, git_repository_init_options* opts)
 {
     repository_wrapper rw;
     throw_if_error(git_repository_init_ext(&(rw.p_resource), directory.data(), opts));
+    apply_config_overrides(rw.p_resource);
     return rw;
 }
 
@@ -44,6 +48,7 @@ repository_wrapper::clone(std::string_view url, std::string_view path, const git
 {
     repository_wrapper rw;
     throw_if_error(git_clone(&(rw.p_resource), url.data(), path.data(), &opts));
+    apply_config_overrides(rw.p_resource);
     return rw;
 }
 

diff --git a/test/conftest.py b/test/conftest.py
@@ -98,6 +98,21 @@ def private_test_repo():
 # Functions not fixtures below here.
 
 
+def get_filemode_lines(git2cpp_path, cwd):
+    # Return all core.filemode lines from config list.
+    cmd_list = [git2cpp_path, "config", "list"]
+    p_list = subprocess.run(cmd_list, capture_output=True, cwd=cwd, text=True)
+    assert p_list.returncode == 0
+    return [line for line in p_list.stdout.splitlines() if line.startswith("core.filemode")]
+
+
+def set_filemode(git2cpp_path, cwd, value):
+    # Set core.filemode in the repository's config file.
+    cmd_set = [git2cpp_path, "config", "set", "core.filemode", value]
+    p_set = subprocess.run(cmd_set, capture_output=True, cwd=cwd, text=True)
+    assert p_set.returncode == 0
+
+
 def strip_ansi_colours(text):
     # Strip ansi colour code sequences from a string.
     return re.sub(r"\x1b\[[^m]*m", "", text)
diff --git a/test/conftest_wasm.py b/test/conftest_wasm.py
@@ -170,11 +170,11 @@ def subprocess_run(
                 raise RuntimeError(f"Error setting cwd to {cwd}")
 
     def maybe_wrap_arg(s: str | MockPath) -> str:
-        # An argument containing spaces needs to be wrapped in quotes if it is not already, due
-        # to how the command is passed to cockle as a single string.
+        # An argument containing whitespace (including newlines) needs to be wrapped in quotes if
+        # it is not already, due to how the command is passed to cockle as a single string.
         # Could do better here.
         s = str(s)
-        if " " in s and not s.endswith("'"):
+        if re.search(r"\s", s) and not s.endswith("'"):
             return "'" + s + "'"
         return s
 

diff --git a/test/test_clone.py b/test/test_clone.py
@@ -2,7 +2,7 @@
 
 import pytest
 
-from .conftest import GIT2CPP_TEST_WASM
+from .conftest import GIT2CPP_TEST_WASM, get_filemode_lines, set_filemode
 
 xsimd_url = "https://github.com/xtensor-stack/xsimd.git"
 xtl_url = "https://github.com/xtensor-stack/xtl.git"
@@ -229,3 +229,34 @@ def test_clone_large_repo(git2cpp_path, tmp_path, run_in_tmp_path):
     assert (tmp_path / "xsimd").exists()
     assert (tmp_path / "xsimd/include").exists()
     assert (tmp_path / "xsimd/xsimdConfig.cmake.in").exists()
+
+
+def test_clone_filemode(git2cpp_path, tmp_path, run_in_tmp_path):
+    clone_cmd = [git2cpp_path, "clone", xtl_url]
+    p_clone = subprocess.run(clone_cmd, capture_output=True, cwd=tmp_path, text=True)
+    assert p_clone.returncode == 0
+
+    xtl_path = tmp_path / "xtl"
+
+    filemode_lines = get_filemode_lines(git2cpp_path, xtl_path)
+    if GIT2CPP_TEST_WASM:
+        # In WebAssembly core.filemode=false is set by an in-memory config override that has higher
+        # priority than the repository's config file, so is listed after it.
+        assert filemode_lines == ["core.filemode=true", "core.filemode=false"]
+    else:
+        assert filemode_lines == ["core.filemode=true"]
+
+    # Setting writes to the repository's config file, not the in-memory override.
+    set_filemode(git2cpp_path, xtl_path, "true")
+    filemode_lines = get_filemode_lines(git2cpp_path, xtl_path)
+    if GIT2CPP_TEST_WASM:
+        assert filemode_lines == ["core.filemode=true", "core.filemode=false"]
+    else:
+        assert filemode_lines == ["core.filemode=true"]
+
+    set_filemode(git2cpp_path, xtl_path, "false")
+    filemode_lines = get_filemode_lines(git2cpp_path, xtl_path)
+    if GIT2CPP_TEST_WASM:
+        assert filemode_lines == ["core.filemode=false", "core.filemode=false"]
+    else:
+        assert filemode_lines == ["core.filemode=false"]
diff --git a/test/test_init.py b/test/test_init.py
@@ -1,6 +1,8 @@
 import subprocess
 from pathlib import Path
 
+from .conftest import GIT2CPP_TEST_WASM, get_filemode_lines, set_filemode
+
 
 def test_init_in_directory(git2cpp_path, tmp_path):
     # tmp_path exists and is empty.
@@ -155,3 +157,32 @@ def test_init_initial_branch_bare(git2cpp_path, tmp_path):
 
     head = (tmp_path / "HEAD").read_text()
     assert "refs/heads/main" in head
+
+
+def test_init_filemode(git2cpp_path, tmp_path):
+    cmd_init = [git2cpp_path, "init", "."]
+    p_init = subprocess.run(cmd_init, capture_output=True, cwd=tmp_path, text=True)
+    assert p_init.returncode == 0
+
+    filemode_lines = get_filemode_lines(git2cpp_path, tmp_path)
+    if GIT2CPP_TEST_WASM:
+        # In WebAssembly core.filemode=false is set by an in-memory config override that has higher
+        # priority than the repository's config file, so is listed after it.
+        assert filemode_lines == ["core.filemode=true", "core.filemode=false"]
+    else:
+        assert filemode_lines == ["core.filemode=true"]
+
+    # Setting writes to the repository's config file, not the in-memory override.
+    set_filemode(git2cpp_path, tmp_path, "true")
+    filemode_lines = get_filemode_lines(git2cpp_path, tmp_path)
+    if GIT2CPP_TEST_WASM:
+        assert filemode_lines == ["core.filemode=true", "core.filemode=false"]
+    else:
+        assert filemode_lines == ["core.filemode=true"]
+
+    set_filemode(git2cpp_path, tmp_path, "false")
+    filemode_lines = get_filemode_lines(git2cpp_path, tmp_path)
+    if GIT2CPP_TEST_WASM:
+        assert filemode_lines == ["core.filemode=false", "core.filemode=false"]
+    else:
+        assert filemode_lines == ["core.filemode=false"]