diff --git a/.github/workflows/alpine-test.yml b/.github/workflows/alpine-test.yml
index 2c1eed391..b7de7482e 100644
--- a/.github/workflows/alpine-test.yml
+++ b/.github/workflows/alpine-test.yml
@@ -2,8 +2,11 @@ name: test-alpine
 
 on: [push, pull_request, workflow_dispatch]
 
+permissions:
+  contents: read
+
 jobs:
-  build:
+  test:
     runs-on: ubuntu-latest
 
     container:
@@ -16,14 +19,14 @@ jobs:
     steps:
     - name: Prepare Alpine Linux
       run: |
-        apk add sudo git git-daemon python3 py3-pip
+        apk add sudo git git-daemon python3 py3-pip py3-virtualenv
         echo 'Defaults env_keep += "CI GITHUB_* RUNNER_*"' >/etc/sudoers.d/ci_env
         addgroup -g 127 docker
-        adduser -D -u 1001 runner
+        adduser -D -u 1001 runner  # TODO: Check if this still works on GHA as intended.
         adduser runner docker
       shell: sh -exo pipefail {0}  # Run this as root, not the "runner" user.
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
 
@@ -44,23 +47,23 @@ jobs:
         # and cause subsequent tests to fail
         cat test/fixtures/.gitconfig >> ~/.gitconfig
 
-    - name: Set up virtualenv
+    - name: Set up virtual environment
       run: |
         python -m venv .venv
-        . .venv/bin/activate
-        printf '%s=%s\n' 'PATH' "$PATH" 'VIRTUAL_ENV' "$VIRTUAL_ENV" >>"$GITHUB_ENV"
 
     - name: Update PyPA packages
       run: |
-        # Get the latest pip, wheel, and prior to Python 3.12, setuptools.
-        python -m pip install -U pip $(pip freeze --all | grep -ow ^setuptools) wheel
+        . .venv/bin/activate
+        python -m pip install -U pip 'setuptools; python_version<"3.12"' wheel
 
     - name: Install project and test dependencies
       run: |
-        pip install ".[test]"
+        . .venv/bin/activate
+        pip install '.[test]'
 
     - name: Show version and platform information
       run: |
+        . .venv/bin/activate
         uname -a
         command -v git python
         git version
@@ -69,4 +72,5 @@ jobs:
 
     - name: Test with pytest
       run: |
+        . .venv/bin/activate
         pytest --color=yes -p no:sugar --instafail -vv
diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
index ae5241898..e243416a8 100644
--- a/.github/workflows/codeql.yml
+++ b/.github/workflows/codeql.yml
@@ -19,38 +19,48 @@ on:
 
 jobs:
   analyze:
-    name: Analyze
+    name: Analyze (${{ matrix.language }})
     # Runner size impacts CodeQL analysis time. To learn more, please see:
     #   - https://gh.io/recommended-hardware-resources-for-running-codeql
     #   - https://gh.io/supported-runners-and-hardware-resources
-    #   - https://gh.io/using-larger-runners
-    # Consider using larger runners for possible analysis time improvements.
+    #   - https://gh.io/using-larger-runners (GitHub.com only)
+    # Consider using larger runners or machines with greater resources for possible analysis time improvements.
     runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
-    timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }}
     permissions:
-      actions: read
-      contents: read
       security-events: write
 
     strategy:
       fail-fast: false
       matrix:
-        language: [ 'python' ]
-        # CodeQL supports [ 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift' ]
-        # Use only 'java-kotlin' to analyze code written in Java, Kotlin or both
-        # Use only 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
-        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
-
+        include:
+        - language: actions
+          build-mode: none
+        - language: python
+          build-mode: none
+        # CodeQL supports the following values keywords for 'language': 'actions', 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift'
+        # Use `c-cpp` to analyze code written in C, C++ or both
+        # Use 'java-kotlin' to analyze code written in Java, Kotlin or both
+        # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+        # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
+        # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
+        # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
+        # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v6
+
+    # Add any setup steps before running the `github/codeql-action/init` action.
+    # This includes steps like installing compilers or runtimes (`actions/setup-node`
+    # or others). This is typically only required for manual builds.
+    # - name: Setup runtime (example)
+    #   uses: actions/setup-example@v1
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v3
+      uses: github/codeql-action/init@v4
       with:
         languages: ${{ matrix.language }}
-        setup-python-dependencies: false
+        build-mode: ${{ matrix.build-mode }}
         # If you wish to specify custom queries, you can do so here or in a config file.
         # By default, queries listed here will override any specified in a config file.
         # Prefix the list here with "+" to use these queries and those in the config file.
@@ -58,23 +68,23 @@ jobs:
         # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
         # queries: security-extended,security-and-quality
 
-
-    # Autobuild attempts to build any compiled languages (C/C++, C#, Go, Java, or Swift).
-    # If this step fails, then you should remove it and run the build manually (see below)
-    - name: Autobuild
-      uses: github/codeql-action/autobuild@v3
-
+    # If the analyze step fails for one of the languages you are analyzing with
+    # "We were unable to automatically build your code", modify the matrix above
+    # to set the build mode to "manual" for that language. Then modify this step
+    # to build your code.
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
-
-    #   If the Autobuild fails above, remove it and uncomment the following three lines.
-    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
-
-    # - run: |
-    #     echo "Run, Build Application using script"
-    #     ./location_of_script_within_repo/buildscript.sh
+    - if: matrix.build-mode == 'manual'
+      shell: bash
+      run: |
+        echo 'If you are using a "manual" build mode for one or more of the' \
+          'languages you are analyzing, replace this with the commands to build' \
+          'your code, for example:'
+        echo '  make bootstrap'
+        echo '  make release'
+        exit 1
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v3
+      uses: github/codeql-action/analyze@v4
       with:
         category: "/language:${{matrix.language}}"
diff --git a/.github/workflows/cygwin-test.yml b/.github/workflows/cygwin-test.yml
index bde4ea659..327e1f10c 100644
--- a/.github/workflows/cygwin-test.yml
+++ b/.github/workflows/cygwin-test.yml
@@ -2,35 +2,47 @@ name: test-cygwin
 
 on: [push, pull_request, workflow_dispatch]
 
-jobs:
-  build:
-    runs-on: windows-latest
+permissions:
+  contents: read
 
+jobs:
+  test:
     strategy:
+      matrix:
+        selection: [fast, perf]
+        include:
+        - selection: fast
+          additional-pytest-args: --ignore=test/performance
+        - selection: perf
+          additional-pytest-args: test/performance
+
       fail-fast: false
 
+    runs-on: windows-latest
+
     env:
       CHERE_INVOKING: "1"
       CYGWIN_NOWINPATH: "1"
 
     defaults:
       run:
-        shell: C:\tools\cygwin\bin\bash.exe --login --norc -eo pipefail -o igncr "{0}"
+        shell: C:\cygwin\bin\bash.exe --login --norc -eo pipefail -o igncr "{0}"
 
     steps:
     - name: Force LF line endings
       run: |
         git config --global core.autocrlf false  # Affects the non-Cygwin git.
-      shell: bash  # Use Git Bash instead of Cygwin Bash for this step.
+      shell: pwsh  # Do this outside Cygwin, to affect actions/checkout.
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
 
-    - name: Set up Cygwin
-      uses: egor-tensin/setup-cygwin@v4
+    - name: Install Cygwin
+      uses: cygwin/cygwin-install-action@v6
       with:
-        packages: python39=3.9.16-1 python39-pip python39-virtualenv git
+        packages: git python39 python-pip-wheel python-setuptools-wheel python-wheel-wheel
+        add-to-path: false  # No need to change $PATH outside the Cygwin environment.
 
     - name: Arrange for verbose output
       run: |
@@ -55,19 +67,18 @@ jobs:
         # and cause subsequent tests to fail
         cat test/fixtures/.gitconfig >> ~/.gitconfig
 
-    - name: Ensure the "pip" command is available
+    - name: Set up virtual environment
       run: |
-        # This is used unless, and before, an updated pip is installed.
-        ln -s pip3 /usr/bin/pip
+        python3.9 -m venv .venv
+        echo 'BASH_ENV=.venv/bin/activate' >>"$GITHUB_ENV"
 
     - name: Update PyPA packages
       run: |
-        # Get the latest pip, wheel, and prior to Python 3.12, setuptools.
-        python -m pip install -U pip $(pip freeze --all | grep -ow ^setuptools) wheel
+        python -m pip install -U pip 'setuptools; python_version<"3.12"' wheel
 
     - name: Install project and test dependencies
       run: |
-        pip install ".[test]"
+        pip install '.[test]'
 
     - name: Show version and platform information
       run: |
@@ -77,6 +88,6 @@ jobs:
         python --version
         python -c 'import os, sys; print(f"sys.platform={sys.platform!r}, os.name={os.name!r}")'
 
-    - name: Test with pytest
+    - name: Test with pytest (${{ matrix.additional-pytest-args }})
       run: |
-        pytest --color=yes -p no:sugar --instafail -vv
+        pytest --color=yes -p no:sugar --instafail -vv ${{ matrix.additional-pytest-args }}
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index a0e81a993..956b38963 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -2,14 +2,17 @@ name: Lint
 
 on: [push, pull_request, workflow_dispatch]
 
+permissions:
+  contents: read
+
 jobs:
   lint:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
-    - uses: actions/setup-python@v5
+    - uses: actions/setup-python@v6
       with:
         python-version: "3.x"
 
diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index 031b0e6b2..ac764d9a7 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -9,44 +9,53 @@ permissions:
   contents: read
 
 jobs:
-  build:
+  test:
     strategy:
-      fail-fast: false
       matrix:
-        os: ["ubuntu-latest", "macos-13", "macos-14", "windows-latest"]
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+        os-type: [ubuntu, macos, windows]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12", "3.13", "3.13t"]
         exclude:
-        - os: "macos-14"
-          python-version: "3.7"
-        - os: "macos-14"
-          python-version: "3.8"
-        - os: "macos-14"
-          python-version: "3.9"
+        - os-type: macos
+          python-version: "3.7"  # Not available for the ARM-based macOS runners.
+        - os-type: macos
+          python-version: "3.13t"
+        - os-type: windows
+          python-version: "3.13"  # FIXME: Fix and enable Python 3.13 on Windows (#1955).
+        - os-type: windows
+          python-version: "3.13t"
         include:
+        - os-ver: latest
+        - os-type: ubuntu
+          python-version: "3.7"
+          os-ver: "22.04"
         - experimental: false
 
-    runs-on: ${{ matrix.os }}
+      fail-fast: false
+
+    runs-on: ${{ matrix.os-type }}-${{ matrix.os-ver }}
 
     defaults:
       run:
         shell: bash --noprofile --norc -exo pipefail {0}
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
         allow-prereleases: ${{ matrix.experimental }}
 
     - name: Set up WSL (Windows)
-      if: startsWith(matrix.os, 'windows')
-      uses: Vampire/setup-wsl@v3.1.1
+      if: matrix.os-type == 'windows'
+      uses: Vampire/setup-wsl@v6.0.0
       with:
-        distribution: Debian
+        wsl-version: 1
+        distribution: Alpine
+        additional-packages: bash
 
     - name: Prepare this repo for tests
       run: |
@@ -62,12 +71,11 @@ jobs:
 
     - name: Update PyPA packages
       run: |
-        # Get the latest pip, wheel, and prior to Python 3.12, setuptools.
-        python -m pip install -U pip $(pip freeze --all | grep -ow ^setuptools) wheel
+        python -m pip install -U pip 'setuptools; python_version<"3.12"' wheel
 
     - name: Install project and test dependencies
       run: |
-        pip install ".[test]"
+        pip install '.[test]'
 
     - name: Show version and platform information
       run: |
@@ -79,7 +87,7 @@ jobs:
 
     # For debugging hook tests on native Windows systems that may have WSL.
     - name: Show bash.exe candidates (Windows)
-      if: startsWith(matrix.os, 'windows')
+      if: matrix.os-type == 'windows'
       run: |
         set +e
         bash.exe -c 'printenv WSL_DISTRO_NAME; uname -a'
@@ -87,14 +95,13 @@ jobs:
       continue-on-error: true
 
     - name: Check types with mypy
+      if: matrix.python-version != '3.7' && matrix.python-version != '3.8'
       run: |
-        mypy --python-version=${{ matrix.python-version }}
+        mypy --python-version="${PYTHON_VERSION%t}"  # Version only, with no "t" for free-threaded.
       env:
         MYPY_FORCE_COLOR: "1"
         TERM: "xterm-256color"  # For color: https://github.com/python/mypy/issues/13817
-      # With new versions of mypy new issues might arise. This is a problem if there is
-      # nobody able to fix them, so we have to ignore errors until that changes.
-      continue-on-error: true
+        PYTHON_VERSION: ${{ matrix.python-version }}
 
     - name: Test with pytest
       run: |
@@ -102,6 +109,7 @@ jobs:
       continue-on-error: false
 
     - name: Documentation
+      if: matrix.python-version != '3.7'
       run: |
-        pip install ".[doc]"
+        pip install '.[doc]'
         make -C doc html
diff --git a/.gitignore b/.gitignore
index d85569405..eab294a65 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,6 +10,8 @@ __pycache__/
 # Transient editor files
 *.swp
 *~
+\#*#
+.#*#
 
 # Editor configuration
 nbproject
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 686d5fa1e..737b56d45 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,28 +1,38 @@
 repos:
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.4.1
+  hooks:
+  - id: codespell
+    additional_dependencies: [tomli]
+    exclude: ^test/fixtures/
+
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.4.3
+  rev: v0.11.12
   hooks:
-  - id: ruff
+  - id: ruff-check
     args: ["--fix"]
     exclude: ^git/ext/
   - id: ruff-format
     exclude: ^git/ext/
 
 - repo: https://github.com/shellcheck-py/shellcheck-py
-  rev: v0.9.0.6
+  rev: v0.10.0.1
   hooks:
   - id: shellcheck
     args: [--color]
     exclude: ^test/fixtures/polyglot$|^git/ext/
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v5.0.0
   hooks:
+  - id: end-of-file-fixer
+    exclude: ^test/fixtures/|COPYING|LICENSE
+  - id: check-symlinks
   - id: check-toml
   - id: check-yaml
   - id: check-merge-conflict
 
 - repo: https://github.com/abravalheri/validate-pyproject
-  rev: v0.16
+  rev: v0.24.1
   hooks:
-    - id: validate-pyproject
+  - id: validate-pyproject
diff --git a/AUTHORS b/AUTHORS
index 9311b3962..b57113edd 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -54,5 +54,7 @@ Contributors are:
 -Wenhan Zhu <wzhu.cosmos _at_ gmail.com>
 -Eliah Kagan <eliah.kagan _at_ gmail.com>
 -Ethan Lin <et.repositories _at_ gmail.com>
+-Jonas Scharpf <jonas.scharpf _at_ checkmk.com>
+-Gordon Marx
 
 Portions derived from other open source works and are clearly marked.
diff --git a/README.md b/README.md
index d365a6584..59c6f995b 100644
--- a/README.md
+++ b/README.md
@@ -101,7 +101,7 @@ In the less common case that you do not want to install test dependencies, `pip
 
 #### With editable *dependencies* (not preferred, and rarely needed)
 
-In rare cases, you may want to work on GitPython and one or both of its [gitdb](https://github.com/gitpython-developers/gitdb) and [smmap](https://github.com/gitpython-developers/smmap) dependencies at the same time, with changes in your local working copy of gitdb or smmap immediatley reflected in the behavior of your local working copy of GitPython. This can be done by making editable installations of those dependencies in the same virtual environment where you install GitPython.
+In rare cases, you may want to work on GitPython and one or both of its [gitdb](https://github.com/gitpython-developers/gitdb) and [smmap](https://github.com/gitpython-developers/smmap) dependencies at the same time, with changes in your local working copy of gitdb or smmap immediately reflected in the behavior of your local working copy of GitPython. This can be done by making editable installations of those dependencies in the same virtual environment where you install GitPython.
 
 If you want to do that *and* you want the versions in GitPython's git submodules to be used, then pass `-e git/ext/gitdb` and/or `-e git/ext/gitdb/gitdb/ext/smmap` to `pip install`. This can be done in any order, and in separate `pip install` commands or the same one, so long as `-e` appears before *each* path. For example, you can install GitPython, gitdb, and smmap editably in the currently active virtual environment this way:
 
diff --git a/SECURITY.md b/SECURITY.md
index d39425b70..0aea34845 100644
--- a/SECURITY.md
+++ b/SECURITY.md
@@ -11,4 +11,6 @@ Only the latest version of GitPython can receive security updates. If a vulnerab
 
 ## Reporting a Vulnerability
 
-Please report private portions of a vulnerability to <https://github.com/gitpython-developers/GitPython/security/advisories/new>. Doing so helps to receive updates and collaborate on the matter, without disclosing it publicliy right away.
+Please report private portions of a vulnerability to <https://github.com/gitpython-developers/GitPython/security/advisories/new>. Doing so helps to receive updates and collaborate on the matter, without disclosing it publicly right away.
+
+Vulnerabilities in GitPython's dependencies [gitdb](https://github.com/gitpython-developers/gitdb/blob/master/SECURITY.md) or [smmap](https://github.com/gitpython-developers/smmap/blob/master/SECURITY.md), which primarily exist to support GitPython, can be reported here as well, at that same link. The affected package (`GitPython`, `gitdb`, or `smmap`) can be included in the report, if known.
diff --git a/VERSION b/VERSION
index d1bf6638d..3c91929a4 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-3.1.43
+3.1.45
diff --git a/doc/Makefile b/doc/Makefile
index ddeadbd7e..7e0d325fe 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -3,7 +3,7 @@
 
 # You can set these variables from the command line.
 BUILDDIR      = build
-SPHINXOPTS    = -W
+SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
 PAPER         =
 
diff --git a/doc/requirements.txt b/doc/requirements.txt
index 7769af5ae..81140d898 100644
--- a/doc/requirements.txt
+++ b/doc/requirements.txt
@@ -1,8 +1,3 @@
-sphinx == 4.3.2
+sphinx >= 7.1.2, < 7.2
 sphinx_rtd_theme
-sphinxcontrib-applehelp >= 1.0.2, <= 1.0.4
-sphinxcontrib-devhelp == 1.0.2
-sphinxcontrib-htmlhelp >= 2.0.0, <= 2.0.1
-sphinxcontrib-qthelp == 1.0.3
-sphinxcontrib-serializinghtml == 1.1.5
 sphinx-autodoc-typehints
diff --git a/doc/source/changes.rst b/doc/source/changes.rst
index 0bc757134..151059ed2 100644
--- a/doc/source/changes.rst
+++ b/doc/source/changes.rst
@@ -2,6 +2,18 @@
 Changelog
 =========
 
+3.1.45
+======
+
+See the following for all changes.
+https://github.com/gitpython-developers/GitPython/releases/tag/3.1.45
+
+3.1.44
+======
+
+See the following for all changes.
+https://github.com/gitpython-developers/GitPython/releases/tag/3.1.44
+
 3.1.43
 ======
 
@@ -20,7 +32,7 @@ https://github.com/gitpython-developers/GitPython/releases/tag/3.1.42
 3.1.41
 ======
 
-This release is relevant for security as it fixes a possible arbitary
+This release is relevant for security as it fixes a possible arbitrary
 code execution on Windows.
 
 See this PR for details: https://github.com/gitpython-developers/GitPython/pull/1792
diff --git a/doc/source/index.rst b/doc/source/index.rst
index 72db8ee5a..ca5229ac3 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -21,4 +21,3 @@ Indices and tables
 * :ref:`genindex`
 * :ref:`modindex`
 * :ref:`search`
-
diff --git a/doc/source/intro.rst b/doc/source/intro.rst
index 4f22a0942..d053bd117 100644
--- a/doc/source/intro.rst
+++ b/doc/source/intro.rst
@@ -122,4 +122,3 @@ License Information
 ===================
 GitPython is licensed under the New BSD License.  See the LICENSE file for
 more information.
-
diff --git a/doc/source/roadmap.rst b/doc/source/roadmap.rst
index a573df33a..34c953626 100644
--- a/doc/source/roadmap.rst
+++ b/doc/source/roadmap.rst
@@ -6,4 +6,3 @@ The full list of milestones including associated tasks can be found on GitHub:
 https://github.com/gitpython-developers/GitPython/issues
 
 Select the respective milestone to filter the list of issues accordingly.
-
diff --git a/fuzzing/fuzz-targets/fuzz_submodule.py b/fuzzing/fuzz-targets/fuzz_submodule.py
index ca47690ea..afa653d0d 100644
--- a/fuzzing/fuzz-targets/fuzz_submodule.py
+++ b/fuzzing/fuzz-targets/fuzz_submodule.py
@@ -3,24 +3,21 @@
 import os
 import tempfile
 from configparser import ParsingError
-from utils import is_expected_exception_message, get_max_filename_length
-
-if getattr(sys, "frozen", False) and hasattr(sys, "_MEIPASS"):  # pragma: no cover
-    path_to_bundled_git_binary = os.path.abspath(os.path.join(os.path.dirname(__file__), "git"))
-    os.environ["GIT_PYTHON_GIT_EXECUTABLE"] = path_to_bundled_git_binary
-
+from utils import (
+    setup_git_environment,
+    handle_exception,
+    get_max_filename_length,
+)
+
+# Setup the Git environment
+setup_git_environment()
 from git import Repo, GitCommandError, InvalidGitRepositoryError
 
-if not sys.warnoptions:  # pragma: no cover
-    # The warnings filter below can be overridden by passing the -W option
-    # to the Python interpreter command line or setting the `PYTHONWARNINGS` environment variable.
-    import warnings
-    import logging
 
-    # Fuzzing data causes some modules to generate a large number of warnings
-    # which are not usually interesting and make the test output hard to read, so we ignore them.
-    warnings.simplefilter("ignore")
-    logging.getLogger().setLevel(logging.ERROR)
+def sanitize_input(input_str, max_length=255):
+    """Sanitize and truncate inputs to avoid invalid Git operations."""
+    sanitized = "".join(ch for ch in input_str if ch.isalnum() or ch in ("-", "_", "."))
+    return sanitized[:max_length]
 
 
 def TestOneInput(data):
@@ -33,39 +30,64 @@ def TestOneInput(data):
         try:
             with tempfile.TemporaryDirectory() as submodule_temp_dir:
                 sub_repo = Repo.init(submodule_temp_dir, bare=fdp.ConsumeBool())
-                sub_repo.index.commit(fdp.ConsumeUnicodeNoSurrogates(fdp.ConsumeIntInRange(1, 512)))
+                commit_message = sanitize_input(fdp.ConsumeUnicodeNoSurrogates(fdp.ConsumeIntInRange(1, 512)))
+                sub_repo.index.commit(commit_message)
+
+                submodule_name = sanitize_input(
+                    fdp.ConsumeUnicodeNoSurrogates(
+                        fdp.ConsumeIntInRange(1, get_max_filename_length(repo.working_tree_dir))
+                    )
+                )
+
+                submodule_path = os.path.relpath(
+                    os.path.join(repo.working_tree_dir, submodule_name),
+                    start=repo.working_tree_dir,
+                )
 
-                submodule_name = f"submodule_{fdp.ConsumeUnicodeNoSurrogates(fdp.ConsumeIntInRange(1, 512))}"
-                submodule_path = os.path.join(repo.working_tree_dir, submodule_name)
-                submodule_url = sub_repo.git_dir
+                # Ensure submodule_path is valid
+                if not submodule_name or submodule_name.startswith("/") or ".." in submodule_name:
+                    return -1  # Reject invalid input so they are not added to the corpus
 
-                submodule = repo.create_submodule(submodule_name, submodule_path, url=submodule_url)
-                repo.index.commit(f"Added submodule {submodule_name}")
+                submodule = repo.create_submodule(submodule_name, submodule_path, url=sub_repo.git_dir)
+                repo.index.commit("Added submodule")
 
                 with submodule.config_writer() as writer:
                     key_length = fdp.ConsumeIntInRange(1, max(1, fdp.remaining_bytes()))
                     value_length = fdp.ConsumeIntInRange(1, max(1, fdp.remaining_bytes()))
 
                     writer.set_value(
-                        fdp.ConsumeUnicodeNoSurrogates(key_length), fdp.ConsumeUnicodeNoSurrogates(value_length)
+                        sanitize_input(fdp.ConsumeUnicodeNoSurrogates(key_length)),
+                        sanitize_input(fdp.ConsumeUnicodeNoSurrogates(value_length)),
                     )
                     writer.release()
 
-                submodule.update(init=fdp.ConsumeBool(), dry_run=fdp.ConsumeBool(), force=fdp.ConsumeBool())
+                submodule.update(
+                    init=fdp.ConsumeBool(),
+                    dry_run=fdp.ConsumeBool(),
+                    force=fdp.ConsumeBool(),
+                )
+
                 submodule_repo = submodule.module()
 
-                new_file_name = fdp.ConsumeUnicodeNoSurrogates(
-                    fdp.ConsumeIntInRange(1, max(1, get_max_filename_length(submodule_repo.working_tree_dir)))
+                new_file_name = sanitize_input(
+                    fdp.ConsumeUnicodeNoSurrogates(
+                        fdp.ConsumeIntInRange(1, get_max_filename_length(submodule_repo.working_tree_dir))
+                    )
                 )
                 new_file_path = os.path.join(submodule_repo.working_tree_dir, new_file_name)
                 with open(new_file_path, "wb") as new_file:
                     new_file.write(fdp.ConsumeBytes(fdp.ConsumeIntInRange(1, 512)))
+
                 submodule_repo.index.add([new_file_path])
                 submodule_repo.index.commit("Added new file to submodule")
 
                 repo.submodule_update(recursive=fdp.ConsumeBool())
-                submodule_repo.head.reset(commit="HEAD~1", working_tree=fdp.ConsumeBool(), head=fdp.ConsumeBool())
-                # Use fdp.PickValueInList to ensure at least one of 'module' or 'configuration' is True
+                submodule_repo.head.reset(
+                    commit="HEAD~1",
+                    working_tree=fdp.ConsumeBool(),
+                    head=fdp.ConsumeBool(),
+                )
+
                 module_option_value, configuration_option_value = fdp.PickValueInList(
                     [(True, False), (False, True), (True, True)]
                 )
@@ -86,20 +108,11 @@ def TestOneInput(data):
             IsADirectoryError,
             NotADirectoryError,
             BrokenPipeError,
+            PermissionError,
         ):
             return -1
-        except ValueError as e:
-            expected_messages = [
-                "SHA is empty",
-                "Reference at",
-                "embedded null byte",
-                "This submodule instance does not exist anymore",
-                "cmd stdin was empty",
-            ]
-            if is_expected_exception_message(e, expected_messages):
-                return -1
-            else:
-                raise e
+        except Exception as e:
+            return handle_exception(e)
 
 
 def main():
diff --git a/fuzzing/fuzz-targets/utils.py b/fuzzing/fuzz-targets/utils.py
index f522d2959..97e6eab98 100644
--- a/fuzzing/fuzz-targets/utils.py
+++ b/fuzzing/fuzz-targets/utils.py
@@ -1,6 +1,9 @@
 import atheris  # pragma: no cover
 import os  # pragma: no cover
-from typing import List  # pragma: no cover
+import re  # pragma: no cover
+import traceback  # pragma: no cover
+import sys  # pragma: no cover
+from typing import Set, Tuple, List  # pragma: no cover
 
 
 @atheris.instrument_func
@@ -35,3 +38,85 @@ def get_max_filename_length(path: str) -> int:  # pragma: no cover
         int: The maximum filename length.
     """
     return os.pathconf(path, "PC_NAME_MAX")
+
+
+@atheris.instrument_func
+def read_lines_from_file(file_path: str) -> list:
+    """Read lines from a file and return them as a list."""
+    try:
+        with open(file_path, "r") as f:
+            return [line.strip() for line in f if line.strip()]
+    except FileNotFoundError:
+        print(f"File not found: {file_path}")
+        return []
+    except IOError as e:
+        print(f"Error reading file {file_path}: {e}")
+        return []
+
+
+@atheris.instrument_func
+def load_exception_list(file_path: str = "explicit-exceptions-list.txt") -> Set[Tuple[str, str]]:
+    """Load and parse the exception list from a default or specified file."""
+    try:
+        bundle_dir = os.path.dirname(os.path.abspath(__file__))
+        full_path = os.path.join(bundle_dir, file_path)
+        lines = read_lines_from_file(full_path)
+        exception_list: Set[Tuple[str, str]] = set()
+        for line in lines:
+            match = re.match(r"(.+):(\d+):", line)
+            if match:
+                file_path: str = match.group(1).strip()
+                line_number: str = str(match.group(2).strip())
+                exception_list.add((file_path, line_number))
+        return exception_list
+    except Exception as e:
+        print(f"Error loading exception list: {e}")
+        return set()
+
+
+@atheris.instrument_func
+def match_exception_with_traceback(exception_list: Set[Tuple[str, str]], exc_traceback) -> bool:
+    """Match exception traceback with the entries in the exception list."""
+    for filename, lineno, _, _ in traceback.extract_tb(exc_traceback):
+        for file_pattern, line_pattern in exception_list:
+            # Ensure filename and line_number are strings for regex matching
+            if re.fullmatch(file_pattern, filename) and re.fullmatch(line_pattern, str(lineno)):
+                return True
+    return False
+
+
+@atheris.instrument_func
+def check_exception_against_list(exc_traceback, exception_file: str = "explicit-exceptions-list.txt") -> bool:
+    """Check if the exception traceback matches any entry in the exception list."""
+    exception_list = load_exception_list(exception_file)
+    return match_exception_with_traceback(exception_list, exc_traceback)
+
+
+@atheris.instrument_func
+def handle_exception(e: Exception) -> int:
+    """Encapsulate exception handling logic for reusability."""
+    exc_traceback = e.__traceback__
+    if check_exception_against_list(exc_traceback):
+        return -1
+    else:
+        raise e
+
+
+@atheris.instrument_func
+def setup_git_environment() -> None:
+    """Set up the environment variables for Git."""
+    bundle_dir = os.path.dirname(os.path.abspath(__file__))
+    if getattr(sys, "frozen", False) and hasattr(sys, "_MEIPASS"):  # pragma: no cover
+        bundled_git_binary_path = os.path.join(bundle_dir, "git")
+        os.environ["GIT_PYTHON_GIT_EXECUTABLE"] = bundled_git_binary_path
+
+    if not sys.warnoptions:  # pragma: no cover
+        # The warnings filter below can be overridden by passing the -W option
+        # to the Python interpreter command line or setting the `PYTHONWARNINGS` environment variable.
+        import warnings
+        import logging
+
+        # Fuzzing data causes some modules to generate a large number of warnings
+        # which are not usually interesting and make the test output hard to read, so we ignore them.
+        warnings.simplefilter("ignore")
+        logging.getLogger().setLevel(logging.ERROR)
diff --git a/fuzzing/oss-fuzz-scripts/build.sh b/fuzzing/oss-fuzz-scripts/build.sh
index e0b3a50ab..c156e872d 100644
--- a/fuzzing/oss-fuzz-scripts/build.sh
+++ b/fuzzing/oss-fuzz-scripts/build.sh
@@ -15,5 +15,5 @@ find "$SRC" -maxdepth 1 \
 
 # Build fuzzers in $OUT.
 find "$SRC/gitpython/fuzzing" -name 'fuzz_*.py' -print0 | while IFS= read -r -d '' fuzz_harness; do
-  compile_python_fuzzer "$fuzz_harness" --add-binary="$(command -v git):."
+  compile_python_fuzzer "$fuzz_harness" --add-binary="$(command -v git):." --add-data="$SRC/explicit-exceptions-list.txt:."
 done
diff --git a/fuzzing/oss-fuzz-scripts/container-environment-bootstrap.sh b/fuzzing/oss-fuzz-scripts/container-environment-bootstrap.sh
index bbdcf5357..924a3cbf3 100755
--- a/fuzzing/oss-fuzz-scripts/container-environment-bootstrap.sh
+++ b/fuzzing/oss-fuzz-scripts/container-environment-bootstrap.sh
@@ -91,6 +91,17 @@ create_seed_corpora_zips "$WORK/qa-assets/gitpython/corpora"
 
 prepare_dictionaries_for_fuzz_targets "$WORK/qa-assets/gitpython/dictionaries" "$SRC/gitpython/fuzzing"
 
+pushd "$SRC/gitpython/"
+# Search for 'raise' and 'assert' statements in Python files within GitPython's source code and submodules, saving the
+# matched file path, line number, and line content to a file named 'explicit-exceptions-list.txt'.
+# This file can then be used by fuzz harnesses to check exception tracebacks and filter out explicitly raised or otherwise
+# anticipated exceptions to reduce false positive test failures.
+
+git grep -n --recurse-submodules -e '\braise\b' -e '\bassert\b' -- '*.py' -- ':!setup.py' -- ':!test/**' -- ':!fuzzing/**' > "$SRC/explicit-exceptions-list.txt"
+
+popd
+
+
 # The OSS-Fuzz base image has outdated dependencies by default so we upgrade them below.
 python3 -m pip install --upgrade pip
 # Upgrade to the latest versions known to work at the time the below changes were introduced:
diff --git a/git/cmd.py b/git/cmd.py
index 90fc39cd6..15d7820df 100644
--- a/git/cmd.py
+++ b/git/cmd.py
@@ -60,6 +60,11 @@
     overload,
 )
 
+if sys.version_info >= (3, 10):
+    from typing import TypeAlias
+else:
+    from typing_extensions import TypeAlias
+
 from git.types import Literal, PathLike, TBD
 
 if TYPE_CHECKING:
@@ -207,7 +212,7 @@ def pump_stream(
                 )
             if stderr_handler:
                 error_str: Union[str, bytes] = (
-                    "error: process killed because it timed out." f" kill_after_timeout={kill_after_timeout} seconds"
+                    f"error: process killed because it timed out. kill_after_timeout={kill_after_timeout} seconds"
                 )
                 if not decode_streams and isinstance(p_stderr, BinaryIO):
                     # Assume stderr_handler needs binary input.
@@ -268,12 +273,12 @@ def _safer_popen_windows(
         if shell:
             # The original may be immutable, or the caller may reuse it. Mutate a copy.
             env = {} if env is None else dict(env)
-            env["NoDefaultCurrentDirectoryInExePath"] = "1"  # The "1" can be an value.
+            env["NoDefaultCurrentDirectoryInExePath"] = "1"  # The "1" can be any value.
 
         # When not using a shell, the current process does the search in a
         # CreateProcessW API call, so the variable must be set in our environment. With
         # a shell, that's unnecessary if https://github.com/python/cpython/issues/101283
-        # is patched. In Python versions where it is unpatched, and in the rare case the
+        # is patched. In Python versions where it is unpatched, in the rare case the
         # ComSpec environment variable is unset, the search for the shell itself is
         # unsafe. Setting NoDefaultCurrentDirectoryInExePath in all cases, as done here,
         # is simpler and protects against that. (As above, the "1" can be any value.)
@@ -308,6 +313,230 @@ def dict_to_slots_and__excluded_are_none(self: object, d: Mapping[str, Any], exc
 
 ## -- End Utilities -- @}
 
+
+class _AutoInterrupt:
+    """Process wrapper that terminates the wrapped process on finalization.
+
+    This kills/interrupts the stored process instance once this instance goes out of
+    scope. It is used to prevent processes piling up in case iterators stop reading.
+
+    All attributes are wired through to the contained process object.
+
+    The wait method is overridden to perform automatic status code checking and possibly
+    raise.
+    """
+
+    __slots__ = ("proc", "args", "status")
+
+    # If this is non-zero it will override any status code during _terminate, used
+    # to prevent race conditions in testing.
+    _status_code_if_terminate: int = 0
+
+    def __init__(self, proc: Union[None, subprocess.Popen], args: Any) -> None:
+        self.proc = proc
+        self.args = args
+        self.status: Union[int, None] = None
+
+    def _terminate(self) -> None:
+        """Terminate the underlying process."""
+        if self.proc is None:
+            return
+
+        proc = self.proc
+        self.proc = None
+        if proc.stdin:
+            proc.stdin.close()
+        if proc.stdout:
+            proc.stdout.close()
+        if proc.stderr:
+            proc.stderr.close()
+        # Did the process finish already so we have a return code?
+        try:
+            if proc.poll() is not None:
+                self.status = self._status_code_if_terminate or proc.poll()
+                return
+        except OSError as ex:
+            _logger.info("Ignored error after process had died: %r", ex)
+
+        # It can be that nothing really exists anymore...
+        if os is None or getattr(os, "kill", None) is None:
+            return
+
+        # Try to kill it.
+        try:
+            proc.terminate()
+            status = proc.wait()  # Ensure the process goes away.
+
+            self.status = self._status_code_if_terminate or status
+        except OSError as ex:
+            _logger.info("Ignored error after process had died: %r", ex)
+        # END exception handling
+
+    def __del__(self) -> None:
+        self._terminate()
+
+    def __getattr__(self, attr: str) -> Any:
+        return getattr(self.proc, attr)
+
+    # TODO: Bad choice to mimic `proc.wait()` but with different args.
+    def wait(self, stderr: Union[None, str, bytes] = b"") -> int:
+        """Wait for the process and return its status code.
+
+        :param stderr:
+            Previously read value of stderr, in case stderr is already closed.
+
+        :warn:
+            May deadlock if output or error pipes are used and not handled separately.
+
+        :raise git.exc.GitCommandError:
+            If the return status is not 0.
+        """
+        if stderr is None:
+            stderr_b = b""
+        stderr_b = force_bytes(data=stderr, encoding="utf-8")
+        status: Union[int, None]
+        if self.proc is not None:
+            status = self.proc.wait()
+            p_stderr = self.proc.stderr
+        else:  # Assume the underlying proc was killed earlier or never existed.
+            status = self.status
+            p_stderr = None
+
+        def read_all_from_possibly_closed_stream(stream: Union[IO[bytes], None]) -> bytes:
+            if stream:
+                try:
+                    return stderr_b + force_bytes(stream.read())
+                except (OSError, ValueError):
+                    return stderr_b or b""
+            else:
+                return stderr_b or b""
+
+        # END status handling
+
+        if status != 0:
+            errstr = read_all_from_possibly_closed_stream(p_stderr)
+            _logger.debug("AutoInterrupt wait stderr: %r" % (errstr,))
+            raise GitCommandError(remove_password_if_present(self.args), status, errstr)
+        return status
+
+
+_AutoInterrupt.__name__ = "AutoInterrupt"
+_AutoInterrupt.__qualname__ = "Git.AutoInterrupt"
+
+
+class _CatFileContentStream:
+    """Object representing a sized read-only stream returning the contents of
+    an object.
+
+    This behaves like a stream, but counts the data read and simulates an empty stream
+    once our sized content region is empty.
+
+    If not all data are read to the end of the object's lifetime, we read the rest to
+    ensure the underlying stream continues to work.
+    """
+
+    __slots__ = ("_stream", "_nbr", "_size")
+
+    def __init__(self, size: int, stream: IO[bytes]) -> None:
+        self._stream = stream
+        self._size = size
+        self._nbr = 0  # Number of bytes read.
+
+        # Special case: If the object is empty, has null bytes, get the final
+        # newline right away.
+        if size == 0:
+            stream.read(1)
+        # END handle empty streams
+
+    def read(self, size: int = -1) -> bytes:
+        bytes_left = self._size - self._nbr
+        if bytes_left == 0:
+            return b""
+        if size > -1:
+            # Ensure we don't try to read past our limit.
+            size = min(bytes_left, size)
+        else:
+            # They try to read all, make sure it's not more than what remains.
+            size = bytes_left
+        # END check early depletion
+        data = self._stream.read(size)
+        self._nbr += len(data)
+
+        # Check for depletion, read our final byte to make the stream usable by
+        # others.
+        if self._size - self._nbr == 0:
+            self._stream.read(1)  # final newline
+        # END finish reading
+        return data
+
+    def readline(self, size: int = -1) -> bytes:
+        if self._nbr == self._size:
+            return b""
+
+        # Clamp size to lowest allowed value.
+        bytes_left = self._size - self._nbr
+        if size > -1:
+            size = min(bytes_left, size)
+        else:
+            size = bytes_left
+        # END handle size
+
+        data = self._stream.readline(size)
+        self._nbr += len(data)
+
+        # Handle final byte.
+        if self._size - self._nbr == 0:
+            self._stream.read(1)
+        # END finish reading
+
+        return data
+
+    def readlines(self, size: int = -1) -> List[bytes]:
+        if self._nbr == self._size:
+            return []
+
+        # Leave all additional logic to our readline method, we just check the size.
+        out = []
+        nbr = 0
+        while True:
+            line = self.readline()
+            if not line:
+                break
+            out.append(line)
+            if size > -1:
+                nbr += len(line)
+                if nbr > size:
+                    break
+            # END handle size constraint
+        # END readline loop
+        return out
+
+    # skipcq: PYL-E0301
+    def __iter__(self) -> "Git.CatFileContentStream":
+        return self
+
+    def __next__(self) -> bytes:
+        line = self.readline()
+        if not line:
+            raise StopIteration
+
+        return line
+
+    next = __next__
+
+    def __del__(self) -> None:
+        bytes_left = self._size - self._nbr
+        if bytes_left:
+            # Read and discard - seeking is impossible within a stream.
+            # This includes any terminating newline.
+            self._stream.read(bytes_left + 1)
+        # END handle incomplete read
+
+
+_CatFileContentStream.__name__ = "CatFileContentStream"
+_CatFileContentStream.__qualname__ = "Git.CatFileContentStream"
+
+
 _USE_SHELL_DEFAULT_MESSAGE = (
     "Git.USE_SHELL is deprecated, because only its default value of False is safe. "
     "It will be removed in a future release."
@@ -321,7 +550,7 @@ def dict_to_slots_and__excluded_are_none(self: object, d: Mapping[str, Any], exc
 )
 
 
-def _warn_use_shell(extra_danger: bool) -> None:
+def _warn_use_shell(*, extra_danger: bool) -> None:
     warnings.warn(
         _USE_SHELL_DANGER_MESSAGE if extra_danger else _USE_SHELL_DEFAULT_MESSAGE,
         DeprecationWarning,
@@ -337,12 +566,12 @@ class _GitMeta(type):
 
     def __getattribute(cls, name: str) -> Any:
         if name == "USE_SHELL":
-            _warn_use_shell(False)
+            _warn_use_shell(extra_danger=False)
         return super().__getattribute__(name)
 
     def __setattr(cls, name: str, value: Any) -> Any:
         if name == "USE_SHELL":
-            _warn_use_shell(value)
+            _warn_use_shell(extra_danger=value)
         super().__setattr__(name, value)
 
     if not TYPE_CHECKING:
@@ -728,221 +957,9 @@ def check_unsafe_options(cls, options: List[str], unsafe_options: List[str]) ->
                         f"{unsafe_option} is not allowed, use `allow_unsafe_options=True` to allow it."
                     )
 
-    class AutoInterrupt:
-        """Process wrapper that terminates the wrapped process on finalization.
-
-        This kills/interrupts the stored process instance once this instance goes out of
-        scope. It is used to prevent processes piling up in case iterators stop reading.
-
-        All attributes are wired through to the contained process object.
-
-        The wait method is overridden to perform automatic status code checking and
-        possibly raise.
-        """
-
-        __slots__ = ("proc", "args", "status")
-
-        # If this is non-zero it will override any status code during _terminate, used
-        # to prevent race conditions in testing.
-        _status_code_if_terminate: int = 0
-
-        def __init__(self, proc: Union[None, subprocess.Popen], args: Any) -> None:
-            self.proc = proc
-            self.args = args
-            self.status: Union[int, None] = None
-
-        def _terminate(self) -> None:
-            """Terminate the underlying process."""
-            if self.proc is None:
-                return
-
-            proc = self.proc
-            self.proc = None
-            if proc.stdin:
-                proc.stdin.close()
-            if proc.stdout:
-                proc.stdout.close()
-            if proc.stderr:
-                proc.stderr.close()
-            # Did the process finish already so we have a return code?
-            try:
-                if proc.poll() is not None:
-                    self.status = self._status_code_if_terminate or proc.poll()
-                    return
-            except OSError as ex:
-                _logger.info("Ignored error after process had died: %r", ex)
-
-            # It can be that nothing really exists anymore...
-            if os is None or getattr(os, "kill", None) is None:
-                return
-
-            # Try to kill it.
-            try:
-                proc.terminate()
-                status = proc.wait()  # Ensure the process goes away.
-
-                self.status = self._status_code_if_terminate or status
-            except OSError as ex:
-                _logger.info("Ignored error after process had died: %r", ex)
-            # END exception handling
-
-        def __del__(self) -> None:
-            self._terminate()
-
-        def __getattr__(self, attr: str) -> Any:
-            return getattr(self.proc, attr)
-
-        # TODO: Bad choice to mimic `proc.wait()` but with different args.
-        def wait(self, stderr: Union[None, str, bytes] = b"") -> int:
-            """Wait for the process and return its status code.
-
-            :param stderr:
-                Previously read value of stderr, in case stderr is already closed.
-
-            :warn:
-                May deadlock if output or error pipes are used and not handled
-                separately.
-
-            :raise git.exc.GitCommandError:
-                If the return status is not 0.
-            """
-            if stderr is None:
-                stderr_b = b""
-            stderr_b = force_bytes(data=stderr, encoding="utf-8")
-            status: Union[int, None]
-            if self.proc is not None:
-                status = self.proc.wait()
-                p_stderr = self.proc.stderr
-            else:  # Assume the underlying proc was killed earlier or never existed.
-                status = self.status
-                p_stderr = None
-
-            def read_all_from_possibly_closed_stream(stream: Union[IO[bytes], None]) -> bytes:
-                if stream:
-                    try:
-                        return stderr_b + force_bytes(stream.read())
-                    except (OSError, ValueError):
-                        return stderr_b or b""
-                else:
-                    return stderr_b or b""
-
-            # END status handling
-
-            if status != 0:
-                errstr = read_all_from_possibly_closed_stream(p_stderr)
-                _logger.debug("AutoInterrupt wait stderr: %r" % (errstr,))
-                raise GitCommandError(remove_password_if_present(self.args), status, errstr)
-            return status
-
-    # END auto interrupt
-
-    class CatFileContentStream:
-        """Object representing a sized read-only stream returning the contents of
-        an object.
-
-        This behaves like a stream, but counts the data read and simulates an empty
-        stream once our sized content region is empty.
-
-        If not all data are read to the end of the object's lifetime, we read the
-        rest to ensure the underlying stream continues to work.
-        """
-
-        __slots__ = ("_stream", "_nbr", "_size")
-
-        def __init__(self, size: int, stream: IO[bytes]) -> None:
-            self._stream = stream
-            self._size = size
-            self._nbr = 0  # Number of bytes read.
-
-            # Special case: If the object is empty, has null bytes, get the final
-            # newline right away.
-            if size == 0:
-                stream.read(1)
-            # END handle empty streams
-
-        def read(self, size: int = -1) -> bytes:
-            bytes_left = self._size - self._nbr
-            if bytes_left == 0:
-                return b""
-            if size > -1:
-                # Ensure we don't try to read past our limit.
-                size = min(bytes_left, size)
-            else:
-                # They try to read all, make sure it's not more than what remains.
-                size = bytes_left
-            # END check early depletion
-            data = self._stream.read(size)
-            self._nbr += len(data)
-
-            # Check for depletion, read our final byte to make the stream usable by
-            # others.
-            if self._size - self._nbr == 0:
-                self._stream.read(1)  # final newline
-            # END finish reading
-            return data
-
-        def readline(self, size: int = -1) -> bytes:
-            if self._nbr == self._size:
-                return b""
-
-            # Clamp size to lowest allowed value.
-            bytes_left = self._size - self._nbr
-            if size > -1:
-                size = min(bytes_left, size)
-            else:
-                size = bytes_left
-            # END handle size
-
-            data = self._stream.readline(size)
-            self._nbr += len(data)
-
-            # Handle final byte.
-            if self._size - self._nbr == 0:
-                self._stream.read(1)
-            # END finish reading
-
-            return data
-
-        def readlines(self, size: int = -1) -> List[bytes]:
-            if self._nbr == self._size:
-                return []
-
-            # Leave all additional logic to our readline method, we just check the size.
-            out = []
-            nbr = 0
-            while True:
-                line = self.readline()
-                if not line:
-                    break
-                out.append(line)
-                if size > -1:
-                    nbr += len(line)
-                    if nbr > size:
-                        break
-                # END handle size constraint
-            # END readline loop
-            return out
-
-        # skipcq: PYL-E0301
-        def __iter__(self) -> "Git.CatFileContentStream":
-            return self
-
-        def __next__(self) -> bytes:
-            line = self.readline()
-            if not line:
-                raise StopIteration
-
-            return line
-
-        next = __next__
+    AutoInterrupt: TypeAlias = _AutoInterrupt
 
-        def __del__(self) -> None:
-            bytes_left = self._size - self._nbr
-            if bytes_left:
-                # Read and discard - seeking is impossible within a stream.
-                # This includes any terminating newline.
-                self._stream.read(bytes_left + 1)
-            # END handle incomplete read
+    CatFileContentStream: TypeAlias = _CatFileContentStream
 
     def __init__(self, working_dir: Union[None, PathLike] = None) -> None:
         """Initialize this instance with:
@@ -971,7 +988,7 @@ def __init__(self, working_dir: Union[None, PathLike] = None) -> None:
 
     def __getattribute__(self, name: str) -> Any:
         if name == "USE_SHELL":
-            _warn_use_shell(False)
+            _warn_use_shell(extra_danger=False)
         return super().__getattribute__(name)
 
     def __getattr__(self, name: str) -> Any:
@@ -1269,6 +1286,7 @@ def execute(
                 stdout=stdout_sink,
                 shell=shell,
                 universal_newlines=universal_newlines,
+                encoding=defenc if universal_newlines else None,
                 **subprocess_kwargs,
             )
         except cmd_not_found_exception as err:
@@ -1318,7 +1336,7 @@ def communicate() -> Tuple[AnyStr, AnyStr]:
                 out, err = proc.communicate()
                 watchdog.cancel()
                 if kill_check.is_set():
-                    err = 'Timeout: the command "%s" did not complete in %d ' "secs." % (
+                    err = 'Timeout: the command "%s" did not complete in %d secs.' % (
                         " ".join(redacted_command),
                         timeout,
                     )
diff --git a/git/config.py b/git/config.py
index de3508360..769929441 100644
--- a/git/config.py
+++ b/git/config.py
@@ -66,7 +66,7 @@
 CONFIG_LEVELS: ConfigLevels_Tup = ("system", "user", "global", "repository")
 """The configuration level of a configuration file."""
 
-CONDITIONAL_INCLUDE_REGEXP = re.compile(r"(?<=includeIf )\"(gitdir|gitdir/i|onbranch):(.+)\"")
+CONDITIONAL_INCLUDE_REGEXP = re.compile(r"(?<=includeIf )\"(gitdir|gitdir/i|onbranch|hasconfig:remote\.\*\.url):(.+)\"")
 """Section pattern to detect conditional includes.
 
 See: https://git-scm.com/docs/git-config#_conditional_includes
@@ -87,15 +87,15 @@ def __new__(cls, name: str, bases: Tuple, clsdict: Dict[str, Any]) -> "MetaParse
             mutating_methods = clsdict[kmm]
             for base in bases:
                 methods = (t for t in inspect.getmembers(base, inspect.isroutine) if not t[0].startswith("_"))
-                for name, method in methods:
-                    if name in clsdict:
+                for method_name, method in methods:
+                    if method_name in clsdict:
                         continue
                     method_with_values = needs_values(method)
-                    if name in mutating_methods:
+                    if method_name in mutating_methods:
                         method_with_values = set_dirty_and_flush_changes(method_with_values)
                     # END mutating methods handling
 
-                    clsdict[name] = method_with_values
+                    clsdict[method_name] = method_with_values
                 # END for each name/method pair
             # END for each base
         # END if mutating methods configuration is set
@@ -496,19 +496,26 @@ def string_decode(v: str) -> str:
                 if mo:
                     # We might just have handled the last line, which could contain a quotation we want to remove.
                     optname, vi, optval = mo.group("option", "vi", "value")
+                    optname = self.optionxform(optname.rstrip())
+
                     if vi in ("=", ":") and ";" in optval and not optval.strip().startswith('"'):
                         pos = optval.find(";")
                         if pos != -1 and optval[pos - 1].isspace():
                             optval = optval[:pos]
                     optval = optval.strip()
-                    if optval == '""':
-                        optval = ""
-                    # END handle empty string
-                    optname = self.optionxform(optname.rstrip())
-                    if len(optval) > 1 and optval[0] == '"' and optval[-1] != '"':
+
+                    if len(optval) < 2 or optval[0] != '"':
+                        # Does not open quoting.
+                        pass
+                    elif optval[-1] != '"':
+                        # Opens quoting and does not close: appears to start multi-line quoting.
                         is_multi_line = True
                         optval = string_decode(optval[1:])
-                    # END handle multi-line
+                    elif optval.find("\\", 1, -1) == -1 and optval.find('"', 1, -1) == -1:
+                        # Opens and closes quoting. Single line, and all we need is quote removal.
+                        optval = optval[1:-1]
+                    # TODO: Handle other quoted content, especially well-formed backslash escapes.
+
                     # Preserves multiple values for duplicate optnames.
                     cursect.add(optname, optval)
                 else:
@@ -567,11 +574,11 @@ def _included_paths(self) -> List[Tuple[str, str]]:
                 if keyword.endswith("/i"):
                     value = re.sub(
                         r"[a-zA-Z]",
-                        lambda m: "[{}{}]".format(m.group().lower(), m.group().upper()),
+                        lambda m: f"[{m.group().lower()!r}{m.group().upper()!r}]",
                         value,
                     )
                 if self._repo.git_dir:
-                    if fnmatch.fnmatchcase(str(self._repo.git_dir), value):
+                    if fnmatch.fnmatchcase(os.fspath(self._repo.git_dir), value):
                         paths += self.items(section)
 
             elif keyword == "onbranch":
@@ -583,7 +590,11 @@ def _included_paths(self) -> List[Tuple[str, str]]:
 
                 if fnmatch.fnmatchcase(branch_name, value):
                     paths += self.items(section)
-
+            elif keyword == "hasconfig:remote.*.url":
+                for remote in self._repo.remotes:
+                    if fnmatch.fnmatchcase(remote.url, value):
+                        paths += self.items(section)
+                        break
         return paths
 
     def read(self) -> None:  # type: ignore[override]
@@ -622,8 +633,6 @@ def read(self) -> None:  # type: ignore[override]
                 file_path = cast(IO[bytes], file_path)
                 self._read(file_path, file_path.name)
             else:
-                # Assume a path if it is not a file-object.
-                file_path = cast(PathLike, file_path)
                 try:
                     with open(file_path, "rb") as fp:
                         file_ok = True
@@ -757,7 +766,7 @@ def _assure_writable(self, method_name: str) -> None:
         if self.read_only:
             raise IOError("Cannot execute non-constant method %s.%s" % (self, method_name))
 
-    def add_section(self, section: str) -> None:
+    def add_section(self, section: "cp._SectionName") -> None:
         """Assures added options will stay in order."""
         return super().add_section(section)
 
diff --git a/git/diff.py b/git/diff.py
index 8d2646f99..23cb5675e 100644
--- a/git/diff.py
+++ b/git/diff.py
@@ -23,13 +23,14 @@
     List,
     Match,
     Optional,
+    Sequence,
     Tuple,
     TYPE_CHECKING,
     TypeVar,
     Union,
     cast,
 )
-from git.types import Literal, PathLike
+from git.types import PathLike, Literal
 
 if TYPE_CHECKING:
     from subprocess import Popen
@@ -289,7 +290,7 @@ class DiffIndex(List[T_Diff]):
     The class improves the diff handling convenience.
     """
 
-    change_type = ("A", "C", "D", "R", "M", "T")
+    change_type: Sequence[Literal["A", "C", "D", "R", "M", "T"]] = ("A", "C", "D", "R", "M", "T")  # noqa: F821
     """Change type invariant identifying possible ways a blob can have changed:
 
     * ``A`` = Added
@@ -695,7 +696,7 @@ def _handle_diff_line(lines_bytes: bytes, repo: "Repo", index: DiffIndex["Diff"]
             change_type: Lit_change_type = cast(Lit_change_type, _change_type[0])
             score_str = "".join(_change_type[1:])
             score = int(score_str) if score_str.isdigit() else None
-            path = path.strip()
+            path = path.strip("\n")
             a_path = path.encode(defenc)
             b_path = path.encode(defenc)
             deleted_file = False
diff --git a/git/ext/gitdb b/git/ext/gitdb
index 3d3e9572d..65321a28b 160000
--- a/git/ext/gitdb
+++ b/git/ext/gitdb
@@ -1 +1 @@
-Subproject commit 3d3e9572dc452fea53d328c101b3d1440bbefe40
+Subproject commit 65321a28b586df60b9d1508228e2f53a35f938eb
diff --git a/git/index/base.py b/git/index/base.py
index 28b60a880..93de7933c 100644
--- a/git/index/base.py
+++ b/git/index/base.py
@@ -28,6 +28,7 @@
 from git.objects import Blob, Commit, Object, Submodule, Tree
 from git.objects.util import Serializable
 from git.util import (
+    Actor,
     LazyMixin,
     LockedFD,
     join_path_native,
@@ -76,7 +77,6 @@
 
     from git.refs.reference import Reference
     from git.repo import Repo
-    from git.util import Actor
 
 
 Treeish = Union[Tree, Commit, str, bytes]
@@ -407,7 +407,7 @@ def raise_exc(e: Exception) -> NoReturn:
         r = str(self.repo.working_tree_dir)
         rs = r + os.sep
         for path in paths:
-            abs_path = str(path)
+            abs_path = os.fspath(path)
             if not osp.isabs(abs_path):
                 abs_path = osp.join(r, path)
             # END make absolute path
@@ -508,7 +508,7 @@ def iter_blobs(
 
         :param predicate:
             Function(t) returning ``True`` if tuple(stage, Blob) should be yielded by
-            the iterator. A default filter, the `~git.index.typ.BlobFilter`, allows you
+            the iterator. A default filter, the :class:`~git.index.typ.BlobFilter`, allows you
             to yield blobs only if they match a given list of paths.
         """
         for entry in self.entries.values():
@@ -530,7 +530,10 @@ def unmerged_blobs(self) -> Dict[PathLike, List[Tuple[StageType, Blob]]]:
             stage. That is, a file removed on the 'other' branch whose entries are at
             stage 3 will not have a stage 3 entry.
         """
-        is_unmerged_blob = lambda t: t[0] != 0
+
+        def is_unmerged_blob(t: Tuple[StageType, Blob]) -> bool:
+            return t[0] != 0
+
         path_map: Dict[PathLike, List[Tuple[StageType, Blob]]] = {}
         for stage, blob in self.iter_blobs(is_unmerged_blob):
             path_map.setdefault(blob.path, []).append((stage, blob))
@@ -653,9 +656,12 @@ def _to_relative_path(self, path: PathLike) -> PathLike:
             return path
         if self.repo.bare:
             raise InvalidGitRepositoryError("require non-bare repository")
-        if not str(path).startswith(str(self.repo.working_tree_dir)):
+        if not osp.normpath(path).startswith(str(self.repo.working_tree_dir)):
             raise ValueError("Absolute path %r is not in git repository at %r" % (path, self.repo.working_tree_dir))
-        return os.path.relpath(path, self.repo.working_tree_dir)
+        result = os.path.relpath(path, self.repo.working_tree_dir)
+        if os.fspath(path).endswith(os.sep) and not result.endswith(os.sep):
+            result += os.sep
+        return result
 
     def _preprocess_add_items(
         self, items: Union[PathLike, Sequence[Union[PathLike, Blob, BaseIndexEntry, "Submodule"]]]
@@ -687,12 +693,17 @@ def _store_path(self, filepath: PathLike, fprogress: Callable) -> BaseIndexEntry
             This must be ensured in the calling code.
         """
         st = os.lstat(filepath)  # Handles non-symlinks as well.
+
         if S_ISLNK(st.st_mode):
             # In PY3, readlink is a string, but we need bytes.
             # In PY2, it was just OS encoded bytes, we assumed UTF-8.
-            open_stream: Callable[[], BinaryIO] = lambda: BytesIO(force_bytes(os.readlink(filepath), encoding=defenc))
+            def open_stream() -> BinaryIO:
+                return BytesIO(force_bytes(os.readlink(filepath), encoding=defenc))
         else:
-            open_stream = lambda: open(filepath, "rb")
+
+            def open_stream() -> BinaryIO:
+                return open(filepath, "rb")
+
         with open_stream() as stream:
             fprogress(filepath, False, filepath)
             istream = self.repo.odb.store(IStream(Blob.type, st.st_size, stream))
@@ -767,7 +778,7 @@ def add(
             - path string
 
                 Strings denote a relative or absolute path into the repository pointing
-                to an existing file, e.g., ``CHANGES``, `lib/myfile.ext``,
+                to an existing file, e.g., ``CHANGES``, ``lib/myfile.ext``,
                 ``/home/gitrepo/lib/myfile.ext``.
 
                 Absolute paths must start with working tree directory of this index's
@@ -786,7 +797,7 @@ def add(
 
                 They are added at stage 0.
 
-            - :class:~`git.objects.blob.Blob` or
+            - :class:`~git.objects.blob.Blob` or
               :class:`~git.objects.submodule.base.Submodule` object
 
                 Blobs are added as they are assuming a valid mode is set.
@@ -812,7 +823,7 @@ def add(
 
             - :class:`~git.index.typ.BaseIndexEntry` or type
 
-                Handling equals the one of :class:~`git.objects.blob.Blob` objects, but
+                Handling equals the one of :class:`~git.objects.blob.Blob` objects, but
                 the stage may be explicitly set. Please note that Index Entries require
                 binary sha's.
 
@@ -995,7 +1006,7 @@ def remove(
 
                 The path string may include globs, such as ``*.c``.
 
-            - :class:~`git.objects.blob.Blob` object
+            - :class:`~git.objects.blob.Blob` object
 
                 Only the path portion is used in this case.
 
@@ -1025,7 +1036,7 @@ def remove(
         args.append("--")
 
         # Preprocess paths.
-        paths = self._items_to_rela_paths(items)
+        paths = list(map(os.fspath, self._items_to_rela_paths(items)))  # type: ignore[arg-type]
         removed_paths = self.repo.git.rm(args, paths, **kwargs).splitlines()
 
         # Process output to gain proper paths.
@@ -1117,8 +1128,8 @@ def commit(
         message: str,
         parent_commits: Union[List[Commit], None] = None,
         head: bool = True,
-        author: Union[None, "Actor"] = None,
-        committer: Union[None, "Actor"] = None,
+        author: Union[None, Actor] = None,
+        committer: Union[None, Actor] = None,
         author_date: Union[datetime.datetime, str, None] = None,
         commit_date: Union[datetime.datetime, str, None] = None,
         skip_hooks: bool = False,
@@ -1333,8 +1344,11 @@ def handle_stderr(proc: "Popen[bytes]", iter_checked_out_files: Iterable[PathLik
             kwargs["as_process"] = True
             kwargs["istream"] = subprocess.PIPE
             proc = self.repo.git.checkout_index(args, **kwargs)
+
             # FIXME: Reading from GIL!
-            make_exc = lambda: GitCommandError(("git-checkout-index",) + tuple(args), 128, proc.stderr.read())
+            def make_exc() -> GitCommandError:
+                return GitCommandError(("git-checkout-index", *args), 128, proc.stderr.read())
+
             checked_out_files: List[PathLike] = []
 
             for path in paths:
@@ -1345,11 +1359,11 @@ def handle_stderr(proc: "Popen[bytes]", iter_checked_out_files: Iterable[PathLik
                 try:
                     self.entries[(co_path, 0)]
                 except KeyError:
-                    folder = str(co_path)
+                    folder = co_path
                     if not folder.endswith("/"):
                         folder += "/"
                     for entry in self.entries.values():
-                        if str(entry.path).startswith(folder):
+                        if os.fspath(entry.path).startswith(folder):
                             p = entry.path
                             self._write_path_to_stdin(proc, p, p, make_exc, fprogress, read_from_stdout=False)
                             checked_out_files.append(p)
@@ -1443,7 +1457,7 @@ def reset(
                     key = entry_key(path, 0)
                     self.entries[key] = nie[key]
                 except KeyError:
-                    # If key is not in theirs, it musn't be in ours.
+                    # If key is not in theirs, it mustn't be in ours.
                     try:
                         del self.entries[key]
                     except KeyError:
diff --git a/git/index/fun.py b/git/index/fun.py
index 59cce6ae6..629c19b1e 100644
--- a/git/index/fun.py
+++ b/git/index/fun.py
@@ -36,7 +36,7 @@
 )
 from git.util import IndexFileSHA1Writer, finalize_process
 
-from .typ import BaseIndexEntry, IndexEntry, CE_NAMEMASK, CE_STAGESHIFT
+from .typ import CE_EXTENDED, BaseIndexEntry, IndexEntry, CE_NAMEMASK, CE_STAGESHIFT
 from .util import pack, unpack
 
 # typing -----------------------------------------------------------------------------
@@ -87,7 +87,7 @@ def run_commit_hook(name: str, index: "IndexFile", *args: str) -> None:
         return
 
     env = os.environ.copy()
-    env["GIT_INDEX_FILE"] = safe_decode(str(index.path))
+    env["GIT_INDEX_FILE"] = safe_decode(os.fspath(index.path))
     env["GIT_EDITOR"] = ":"
     cmd = [hp]
     try:
@@ -158,7 +158,7 @@ def write_cache(
     write = stream_sha.write
 
     # Header
-    version = 2
+    version = 3 if any(entry.extended_flags for entry in entries) else 2
     write(b"DIRC")
     write(pack(">LL", version, len(entries)))
 
@@ -172,6 +172,8 @@ def write_cache(
         plen = len(path) & CE_NAMEMASK  # Path length
         assert plen == len(path), "Path %s too long to fit into index" % entry.path
         flags = plen | (entry.flags & CE_NAMEMASK_INV)  # Clear possible previous values.
+        if entry.extended_flags:
+            flags |= CE_EXTENDED
         write(
             pack(
                 ">LLLLLL20sH",
@@ -185,6 +187,8 @@ def write_cache(
                 flags,
             )
         )
+        if entry.extended_flags:
+            write(pack(">H", entry.extended_flags))
         write(path)
         real_size = (tell() - beginoffset + 8) & ~7
         write(b"\0" * ((beginoffset + real_size) - tell()))
@@ -206,8 +210,7 @@ def read_header(stream: IO[bytes]) -> Tuple[int, int]:
     unpacked = cast(Tuple[int, int], unpack(">LL", stream.read(4 * 2)))
     version, num_entries = unpacked
 
-    # TODO: Handle version 3: extended data, see read-cache.c.
-    assert version in (1, 2)
+    assert version in (1, 2, 3), "Unsupported git index version %i, only 1, 2, and 3 are supported" % version
     return version, num_entries
 
 
@@ -260,12 +263,15 @@ def read_cache(
         ctime = unpack(">8s", read(8))[0]
         mtime = unpack(">8s", read(8))[0]
         (dev, ino, mode, uid, gid, size, sha, flags) = unpack(">LLLLLL20sH", read(20 + 4 * 6 + 2))
+        extended_flags = 0
+        if flags & CE_EXTENDED:
+            extended_flags = unpack(">H", read(2))[0]
         path_size = flags & CE_NAMEMASK
         path = read(path_size).decode(defenc)
 
         real_size = (tell() - beginoffset + 8) & ~7
         read((beginoffset + real_size) - tell())
-        entry = IndexEntry((mode, sha, flags, path, ctime, mtime, dev, ino, uid, gid, size))
+        entry = IndexEntry((mode, sha, flags, path, ctime, mtime, dev, ino, uid, gid, size, extended_flags))
         # entry_key would be the method to use, but we save the effort.
         entries[(path, entry.stage)] = entry
         count += 1
diff --git a/git/index/typ.py b/git/index/typ.py
index 974252528..927633a9f 100644
--- a/git/index/typ.py
+++ b/git/index/typ.py
@@ -32,6 +32,9 @@
 CE_VALID = 0x8000
 CE_STAGESHIFT = 12
 
+CE_EXT_SKIP_WORKTREE = 0x4000
+CE_EXT_INTENT_TO_ADD = 0x2000
+
 # } END invariants
 
 
@@ -87,6 +90,8 @@ class BaseIndexEntryHelper(NamedTuple):
     uid: int = 0
     gid: int = 0
     size: int = 0
+    # version 3 extended flags, only when (flags & CE_EXTENDED) is set
+    extended_flags: int = 0
 
 
 class BaseIndexEntry(BaseIndexEntryHelper):
@@ -102,7 +107,7 @@ def __new__(
         cls,
         inp_tuple: Union[
             Tuple[int, bytes, int, PathLike],
-            Tuple[int, bytes, int, PathLike, bytes, bytes, int, int, int, int, int],
+            Tuple[int, bytes, int, PathLike, bytes, bytes, int, int, int, int, int, int],
         ],
     ) -> "BaseIndexEntry":
         """Override ``__new__`` to allow construction from a tuple for backwards
@@ -134,6 +139,14 @@ def stage(self) -> int:
         """
         return (self.flags & CE_STAGEMASK) >> CE_STAGESHIFT
 
+    @property
+    def skip_worktree(self) -> bool:
+        return (self.extended_flags & CE_EXT_SKIP_WORKTREE) > 0
+
+    @property
+    def intent_to_add(self) -> bool:
+        return (self.extended_flags & CE_EXT_INTENT_TO_ADD) > 0
+
     @classmethod
     def from_blob(cls, blob: Blob, stage: int = 0) -> "BaseIndexEntry":
         """:return: Fully equipped BaseIndexEntry at the given stage"""
@@ -179,7 +192,7 @@ def from_base(cls, base: "BaseIndexEntry") -> "IndexEntry":
             Instance of type :class:`BaseIndexEntry`.
         """
         time = pack(">LL", 0, 0)
-        return IndexEntry((base.mode, base.binsha, base.flags, base.path, time, time, 0, 0, 0, 0, 0))
+        return IndexEntry((base.mode, base.binsha, base.flags, base.path, time, time, 0, 0, 0, 0, 0))  # type: ignore[arg-type]
 
     @classmethod
     def from_blob(cls, blob: Blob, stage: int = 0) -> "IndexEntry":
@@ -198,5 +211,5 @@ def from_blob(cls, blob: Blob, stage: int = 0) -> "IndexEntry":
                 0,
                 0,
                 blob.size,
-            )
+            )  # type: ignore[arg-type]
         )
diff --git a/git/index/util.py b/git/index/util.py
index e59cb609f..982a5afb7 100644
--- a/git/index/util.py
+++ b/git/index/util.py
@@ -15,7 +15,7 @@
 
 # typing ----------------------------------------------------------------------
 
-from typing import Any, Callable, TYPE_CHECKING, Optional, Type
+from typing import Any, Callable, TYPE_CHECKING, Optional, Type, cast
 
 from git.types import Literal, PathLike, _T
 
@@ -106,7 +106,7 @@ def git_working_dir(func: Callable[..., _T]) -> Callable[..., _T]:
     @wraps(func)
     def set_git_working_dir(self: "IndexFile", *args: Any, **kwargs: Any) -> _T:
         cur_wd = os.getcwd()
-        os.chdir(str(self.repo.working_tree_dir))
+        os.chdir(cast(PathLike, self.repo.working_tree_dir))
         try:
             return func(self, *args, **kwargs)
         finally:
diff --git a/git/objects/base.py b/git/objects/base.py
index eeaebc09b..faf600c6b 100644
--- a/git/objects/base.py
+++ b/git/objects/base.py
@@ -122,7 +122,7 @@ def new(cls, repo: "Repo", id: Union[str, "Reference"]) -> AnyGitObject:
         :return:
             New :class:`Object` instance of a type appropriate to the object type behind
             `id`. The id of the newly created object will be a binsha even though the
-            input id may have been a `~git.refs.reference.Reference` or rev-spec.
+            input id may have been a :class:`~git.refs.reference.Reference` or rev-spec.
 
         :param id:
             :class:`~git.refs.reference.Reference`, rev-spec, or hexsha.
@@ -218,7 +218,7 @@ class IndexObject(Object):
     """Base for all objects that can be part of the index file.
 
     The classes representing git object types that can be part of the index file are
-    :class:`~git.objects.tree.Tree and :class:`~git.objects.blob.Blob`. In addition,
+    :class:`~git.objects.tree.Tree` and :class:`~git.objects.blob.Blob`. In addition,
     :class:`~git.objects.submodule.base.Submodule`, which is not really a git object
     type but can be part of an index file, is also a subclass.
     """
diff --git a/git/objects/blob.py b/git/objects/blob.py
index 58de59642..f7d49c9cc 100644
--- a/git/objects/blob.py
+++ b/git/objects/blob.py
@@ -6,6 +6,7 @@
 __all__ = ["Blob"]
 
 from mimetypes import guess_type
+import os
 import sys
 
 if sys.version_info >= (3, 8):
@@ -44,5 +45,5 @@ def mime_type(self) -> str:
         """
         guesses = None
         if self.path:
-            guesses = guess_type(str(self.path))
+            guesses = guess_type(os.fspath(self.path))
         return guesses and guesses[0] or self.DEFAULT_MIME_TYPE
diff --git a/git/objects/commit.py b/git/objects/commit.py
index d957c9051..8c51254a2 100644
--- a/git/objects/commit.py
+++ b/git/objects/commit.py
@@ -289,7 +289,7 @@ def name_rev(self) -> str:
         """
         :return:
             String describing the commits hex sha based on the closest
-            `~git.refs.reference.Reference`.
+            :class:`~git.refs.reference.Reference`.
 
         :note:
             Mostly useful for UI purposes.
@@ -349,7 +349,7 @@ def iter_items(
         return cls._iter_from_process_or_stream(repo, proc)
 
     def iter_parents(self, paths: Union[PathLike, Sequence[PathLike]] = "", **kwargs: Any) -> Iterator["Commit"]:
-        R"""Iterate _all_ parents of this commit.
+        R"""Iterate *all* parents of this commit.
 
         :param paths:
             Optional path or list of paths limiting the :class:`Commit`\s to those that
@@ -377,15 +377,25 @@ def stats(self) -> Stats:
         :return:
             :class:`Stats`
         """
-        if not self.parents:
-            text = self.repo.git.diff_tree(self.hexsha, "--", numstat=True, no_renames=True, root=True)
-            text2 = ""
-            for line in text.splitlines()[1:]:
+
+        def process_lines(lines: List[str]) -> str:
+            text = ""
+            for file_info, line in zip(lines, lines[len(lines) // 2 :]):
+                change_type = file_info.split("\t")[0][-1]
                 (insertions, deletions, filename) = line.split("\t")
-                text2 += "%s\t%s\t%s\n" % (insertions, deletions, filename)
-            text = text2
+                text += "%s\t%s\t%s\t%s\n" % (change_type, insertions, deletions, filename)
+            return text
+
+        if not self.parents:
+            lines = self.repo.git.diff_tree(
+                self.hexsha, "--", numstat=True, no_renames=True, root=True, raw=True
+            ).splitlines()[1:]
+            text = process_lines(lines)
         else:
-            text = self.repo.git.diff(self.parents[0].hexsha, self.hexsha, "--", numstat=True, no_renames=True)
+            lines = self.repo.git.diff(
+                self.parents[0].hexsha, self.hexsha, "--", numstat=True, no_renames=True, raw=True
+            ).splitlines()
+            text = process_lines(lines)
         return Stats._list_from_string(self.repo, text)
 
     @property
@@ -890,7 +900,7 @@ def co_authors(self) -> List[Actor]:
         if self.message:
             results = re.findall(
                 r"^Co-authored-by: (.*) <(.*?)>$",
-                self.message,
+                str(self.message),
                 re.MULTILINE,
             )
             for author in results:
diff --git a/git/objects/submodule/base.py b/git/objects/submodule/base.py
index fa60bcdaf..d183672db 100644
--- a/git/objects/submodule/base.py
+++ b/git/objects/submodule/base.py
@@ -11,6 +11,7 @@
 import stat
 import sys
 import uuid
+import urllib
 
 import git
 from git.cmd import Git
@@ -65,7 +66,7 @@
 if TYPE_CHECKING:
     from git.index import IndexFile
     from git.objects.commit import Commit
-    from git.refs import Head
+    from git.refs import Head, RemoteReference
     from git.repo import Repo
 
 # -----------------------------------------------------------------------------
@@ -351,7 +352,12 @@ def _clone_repo(
             module_abspath_dir = osp.dirname(module_abspath)
             if not osp.isdir(module_abspath_dir):
                 os.makedirs(module_abspath_dir)
-            module_checkout_path = osp.join(str(repo.working_tree_dir), path)
+            module_checkout_path = osp.join(repo.working_tree_dir, path)  # type: ignore[arg-type]
+
+        if url.startswith("../"):
+            remote_name = cast("RemoteReference", repo.active_branch.tracking_branch()).remote_name
+            repo_remote_url = repo.remote(remote_name).url
+            url = os.path.join(repo_remote_url, url)
 
         clone = git.Repo.clone_from(
             url,
@@ -535,7 +541,7 @@ def add(
         if sm.exists():
             # Reretrieve submodule from tree.
             try:
-                sm = repo.head.commit.tree[str(path)]
+                sm = repo.head.commit.tree[os.fspath(path)]
                 sm._name = name
                 return sm
             except KeyError:
@@ -794,9 +800,13 @@ def update(
                     + "Cloning url '%s' to '%s' in submodule %r" % (self.url, checkout_module_abspath, self.name),
                 )
                 if not dry_run:
+                    if self.url.startswith("."):
+                        url = urllib.parse.urljoin(self.repo.remotes.origin.url + "/", self.url)
+                    else:
+                        url = self.url
                     mrepo = self._clone_repo(
                         self.repo,
-                        self.url,
+                        url,
                         self.path,
                         self.name,
                         n=True,
diff --git a/git/objects/tag.py b/git/objects/tag.py
index a3bb0b882..88671d316 100644
--- a/git/objects/tag.py
+++ b/git/objects/tag.py
@@ -14,7 +14,7 @@
 import sys
 
 from git.compat import defenc
-from git.util import hex_to_bin
+from git.util import Actor, hex_to_bin
 
 from . import base
 from .util import get_object_type_by_name, parse_actor_and_date
@@ -30,7 +30,6 @@
 
 if TYPE_CHECKING:
     from git.repo import Repo
-    from git.util import Actor
 
     from .blob import Blob
     from .commit import Commit
@@ -64,7 +63,7 @@ def __init__(
         binsha: bytes,
         object: Union[None, base.Object] = None,
         tag: Union[None, str] = None,
-        tagger: Union[None, "Actor"] = None,
+        tagger: Union[None, Actor] = None,
         tagged_date: Union[int, None] = None,
         tagger_tz_offset: Union[int, None] = None,
         message: Union[str, None] = None,
diff --git a/git/objects/tree.py b/git/objects/tree.py
index 09184a781..1845d0d0d 100644
--- a/git/objects/tree.py
+++ b/git/objects/tree.py
@@ -50,7 +50,9 @@
 
 # --------------------------------------------------------
 
-cmp: Callable[[str, str], int] = lambda a, b: (a > b) - (a < b)
+
+def cmp(a: str, b: str) -> int:
+    return (a > b) - (a < b)
 
 
 class TreeModifier:
diff --git a/git/objects/util.py b/git/objects/util.py
index 5c56e6134..a68d701f5 100644
--- a/git/objects/util.py
+++ b/git/objects/util.py
@@ -568,11 +568,11 @@ def addToStack(
                 yield rval
 
             # Only continue to next level if this is appropriate!
-            nd = d + 1
-            if depth > -1 and nd > depth:
+            next_d = d + 1
+            if depth > -1 and next_d > depth:
                 continue
 
-            addToStack(stack, item, branch_first, nd)
+            addToStack(stack, item, branch_first, next_d)
         # END for each item on work stack
 
 
diff --git a/git/refs/head.py b/git/refs/head.py
index 683634451..3c43993e7 100644
--- a/git/refs/head.py
+++ b/git/refs/head.py
@@ -22,7 +22,6 @@
 from git.types import Commit_ish, PathLike
 
 if TYPE_CHECKING:
-    from git.objects import Commit
     from git.refs import RemoteReference
     from git.repo import Repo
 
@@ -44,9 +43,6 @@ class HEAD(SymbolicReference):
 
     __slots__ = ()
 
-    # TODO: This can be removed once SymbolicReference.commit has static type hints.
-    commit: "Commit"
-
     def __init__(self, repo: "Repo", path: PathLike = _HEAD_NAME) -> None:
         if path != self._HEAD_NAME:
             raise ValueError("HEAD instance must point to %r, got %r" % (self._HEAD_NAME, path))
@@ -149,7 +145,7 @@ class Head(Reference):
     k_config_remote_ref = "merge"  # Branch to merge from remote.
 
     @classmethod
-    def delete(cls, repo: "Repo", *heads: "Union[Head, str]", force: bool = False, **kwargs: Any) -> None:
+    def delete(cls, repo: "Repo", *heads: "Union[Head, str]", force: bool = False, **kwargs: Any) -> None:  # type: ignore[override]
         """Delete the given heads.
 
         :param force:
diff --git a/git/refs/log.py b/git/refs/log.py
index 17e3a94b3..4751cff99 100644
--- a/git/refs/log.py
+++ b/git/refs/log.py
@@ -126,7 +126,7 @@ def from_line(cls, line: bytes) -> "RefLogEntry":
         elif len(fields) == 2:
             info, msg = fields
         else:
-            raise ValueError("Line must have up to two TAB-separated fields." " Got %s" % repr(line_str))
+            raise ValueError("Line must have up to two TAB-separated fields. Got %s" % repr(line_str))
         # END handle first split
 
         oldhexsha = info[:40]
@@ -145,7 +145,7 @@ def from_line(cls, line: bytes) -> "RefLogEntry":
         actor = Actor._from_string(info[82 : email_end + 1])
         time, tz_offset = parse_date(info[email_end + 2 :])  # skipcq: PYL-W0621
 
-        return RefLogEntry((oldhexsha, newhexsha, actor, (time, tz_offset), msg))
+        return RefLogEntry((oldhexsha, newhexsha, actor, (time, tz_offset), msg))  # type: ignore [arg-type]
 
 
 class RefLog(List[RefLogEntry], Serializable):
diff --git a/git/refs/reference.py b/git/refs/reference.py
index e5d473779..0c4327225 100644
--- a/git/refs/reference.py
+++ b/git/refs/reference.py
@@ -3,6 +3,7 @@
 
 __all__ = ["Reference"]
 
+import os
 from git.util import IterableObj, LazyMixin
 
 from .symbolic import SymbolicReference, T_References
@@ -65,7 +66,7 @@ def __init__(self, repo: "Repo", path: PathLike, check_path: bool = True) -> Non
             If ``False``, you can provide any path.
             Otherwise the path must start with the default path prefix of this type.
         """
-        if check_path and not str(path).startswith(self._common_path_default + "/"):
+        if check_path and not os.fspath(path).startswith(self._common_path_default + "/"):
             raise ValueError(f"Cannot instantiate {self.__class__.__name__!r} from path {path}")
         self.path: str  # SymbolicReference converts to string at the moment.
         super().__init__(repo, path)
diff --git a/git/refs/symbolic.py b/git/refs/symbolic.py
index 510850b2e..99af4f57c 100644
--- a/git/refs/symbolic.py
+++ b/git/refs/symbolic.py
@@ -4,6 +4,7 @@
 __all__ = ["SymbolicReference"]
 
 import os
+from pathlib import Path
 
 from gitdb.exc import BadName, BadObject
 
@@ -39,8 +40,8 @@
 if TYPE_CHECKING:
     from git.config import GitConfigParser
     from git.objects.commit import Actor
-    from git.refs import Head, TagReference, RemoteReference, Reference
     from git.refs.log import RefLogEntry
+    from git.refs.reference import Reference
     from git.repo import Repo
 
 
@@ -76,10 +77,10 @@ class SymbolicReference:
 
     def __init__(self, repo: "Repo", path: PathLike, check_path: bool = False) -> None:
         self.repo = repo
-        self.path = path
+        self.path: PathLike = path
 
     def __str__(self) -> str:
-        return str(self.path)
+        return os.fspath(self.path)
 
     def __repr__(self) -> str:
         return '<git.%s "%s">' % (self.__class__.__name__, self.path)
@@ -103,7 +104,7 @@ def name(self) -> str:
             In case of symbolic references, the shortest assumable name is the path
             itself.
         """
-        return str(self.path)
+        return os.fspath(self.path)
 
     @property
     def abspath(self) -> PathLike:
@@ -178,7 +179,7 @@ def _check_ref_name_valid(ref_path: PathLike) -> None:
         """
         previous: Union[str, None] = None
         one_before_previous: Union[str, None] = None
-        for c in str(ref_path):
+        for c in os.fspath(ref_path):
             if c in " ~^:?*[\\":
                 raise ValueError(
                     f"Invalid reference '{ref_path}': references cannot contain spaces, tildes (~), carets (^),"
@@ -212,7 +213,7 @@ def _check_ref_name_valid(ref_path: PathLike) -> None:
             raise ValueError(f"Invalid reference '{ref_path}': references cannot end with a forward slash (/)")
         elif previous == "@" and one_before_previous is None:
             raise ValueError(f"Invalid reference '{ref_path}': references cannot be '@'")
-        elif any(component.endswith(".lock") for component in str(ref_path).split("/")):
+        elif any(component.endswith(".lock") for component in Path(ref_path).parts):
             raise ValueError(
                 f"Invalid reference '{ref_path}': references cannot have slash-separated components that end with"
                 " '.lock'"
@@ -235,7 +236,7 @@ def _get_ref_info_helper(
         tokens: Union[None, List[str], Tuple[str, str]] = None
         repodir = _git_dir(repo, ref_path)
         try:
-            with open(os.path.join(repodir, str(ref_path)), "rt", encoding="UTF-8") as fp:
+            with open(os.path.join(repodir, ref_path), "rt", encoding="UTF-8") as fp:  # type: ignore[arg-type]
                 value = fp.read().rstrip()
             # Don't only split on spaces, but on whitespace, which allows to parse lines like:
             # 60b64ef992065e2600bfef6187a97f92398a9144                branch 'master' of git-server:/path/to/repo
@@ -387,19 +388,25 @@ def set_object(
         # set the commit on our reference
         return self._get_reference().set_object(object, logmsg)
 
-    commit = property(
-        _get_commit,
-        set_commit,  # type: ignore[arg-type]
-        doc="Query or set commits directly",
-    )
+    @property
+    def commit(self) -> "Commit":
+        """Query or set commits directly"""
+        return self._get_commit()
+
+    @commit.setter
+    def commit(self, commit: Union[Commit, "SymbolicReference", str]) -> "SymbolicReference":
+        return self.set_commit(commit)
+
+    @property
+    def object(self) -> AnyGitObject:
+        """Return the object our ref currently refers to"""
+        return self._get_object()
 
-    object = property(
-        _get_object,
-        set_object,  # type: ignore[arg-type]
-        doc="Return the object our ref currently refers to",
-    )
+    @object.setter
+    def object(self, object: Union[AnyGitObject, "SymbolicReference", str]) -> "SymbolicReference":
+        return self.set_object(object)
 
-    def _get_reference(self) -> "SymbolicReference":
+    def _get_reference(self) -> "Reference":
         """
         :return:
             :class:`~git.refs.reference.Reference` object we point to
@@ -411,7 +418,7 @@ def _get_reference(self) -> "SymbolicReference":
         sha, target_ref_path = self._get_ref_info(self.repo, self.path)
         if target_ref_path is None:
             raise TypeError("%s is a detached symbolic reference as it points to %r" % (self, sha))
-        return self.from_path(self.repo, target_ref_path)
+        return cast("Reference", self.from_path(self.repo, target_ref_path))
 
     def set_reference(
         self,
@@ -496,12 +503,14 @@ def set_reference(
         return self
 
     # Aliased reference
-    reference: Union["Head", "TagReference", "RemoteReference", "Reference"]
-    reference = property(  # type: ignore[assignment]
-        _get_reference,
-        set_reference,  # type: ignore[arg-type]
-        doc="Returns the Reference we point to",
-    )
+    @property
+    def reference(self) -> "Reference":
+        return self._get_reference()
+
+    @reference.setter
+    def reference(self, ref: Union[AnyGitObject, "SymbolicReference", str]) -> "SymbolicReference":
+        return self.set_reference(ref)
+
     ref = reference
 
     def is_valid(self) -> bool:
@@ -606,7 +615,7 @@ def to_full_path(cls, path: Union[PathLike, "SymbolicReference"]) -> PathLike:
         full_ref_path = path
         if not cls._common_path_default:
             return full_ref_path
-        if not str(path).startswith(cls._common_path_default + "/"):
+        if not os.fspath(path).startswith(cls._common_path_default + "/"):
             full_ref_path = "%s/%s" % (cls._common_path_default, path)
         return full_ref_path
 
@@ -698,7 +707,7 @@ def _create(
         if not force and os.path.isfile(abs_ref_path):
             target_data = str(target)
             if isinstance(target, SymbolicReference):
-                target_data = str(target.path)
+                target_data = os.fspath(target.path)
             if not resolve:
                 target_data = "ref: " + target_data
             with open(abs_ref_path, "rb") as fd:
@@ -834,7 +843,7 @@ def _iter_items(
 
         # Read packed refs.
         for _sha, rela_path in cls._iter_packed_refs(repo):
-            if rela_path.startswith(str(common_path)):
+            if rela_path.startswith(os.fspath(common_path)):
                 rela_paths.add(rela_path)
             # END relative path matches common path
         # END packed refs reading
@@ -908,8 +917,7 @@ def from_path(cls: Type[T_References], repo: "Repo", path: PathLike) -> T_Refere
             SymbolicReference,
         ):
             try:
-                instance: T_References
-                instance = ref_type(repo, path)
+                instance = cast(T_References, ref_type(repo, path))
                 if instance.__class__ is SymbolicReference and instance.is_detached:
                     raise ValueError("SymbolicRef was detached, we drop it")
                 else:
@@ -923,4 +931,4 @@ def from_path(cls: Type[T_References], repo: "Repo", path: PathLike) -> T_Refere
 
     def is_remote(self) -> bool:
         """:return: True if this symbolic reference points to a remote branch"""
-        return str(self.path).startswith(self._remote_common_path_default + "/")
+        return os.fspath(self.path).startswith(self._remote_common_path_default + "/")
diff --git a/git/refs/tag.py b/git/refs/tag.py
index 1e38663ae..4525b09cb 100644
--- a/git/refs/tag.py
+++ b/git/refs/tag.py
@@ -45,8 +45,8 @@ class TagReference(Reference):
     _common_default = "tags"
     _common_path_default = Reference._common_path_default + "/" + _common_default
 
-    @property
-    def commit(self) -> "Commit":  # type: ignore[override]  # LazyMixin has unrelated commit method
+    @property  # type: ignore[misc]
+    def commit(self) -> "Commit":  # LazyMixin has unrelated commit method
         """:return: Commit object the tag ref points to
 
         :raise ValueError:
@@ -80,8 +80,8 @@ def tag(self) -> Union["TagObject", None]:
         return None
 
     # Make object read-only. It should be reasonably hard to adjust an existing tag.
-    @property
-    def object(self) -> AnyGitObject:  # type: ignore[override]
+    @property  # type: ignore[misc]
+    def object(self) -> AnyGitObject:
         return Reference._get_object(self)
 
     @classmethod
diff --git a/git/remote.py b/git/remote.py
index 37c991d27..20e42b412 100644
--- a/git/remote.py
+++ b/git/remote.py
@@ -250,7 +250,7 @@ def _from_line(cls, remote: "Remote", line: str) -> "PushInfo":
                 flags |= cls.NEW_TAG
             elif "[new branch]" in summary:
                 flags |= cls.NEW_HEAD
-            # uptodate encoded in control character
+            # `uptodate` encoded in control character
         else:
             # Fast-forward or forced update - was encoded in control character,
             # but we parse the old and new commit.
@@ -828,8 +828,15 @@ def remove(cls, repo: "Repo", name: str) -> str:
             name._clear_cache()
         return name
 
-    # `rm` is an alias.
-    rm = remove
+    @classmethod
+    def rm(cls, repo: "Repo", name: str) -> str:
+        """Alias of remove.
+        Remove the remote with the given name.
+
+        :return:
+            The passed remote name to remove
+        """
+        return cls.remove(repo, name)
 
     def rename(self, new_name: str) -> "Remote":
         """Rename self to the given `new_name`.
@@ -887,7 +894,7 @@ def _get_fetch_info_from_stderr(
             None,
             progress_handler,
             finalizer=None,
-            decode_streams=True,
+            decode_streams=False,
             kill_after_timeout=kill_after_timeout,
         )
 
@@ -1064,7 +1071,7 @@ def fetch(
             Git.check_unsafe_options(options=list(kwargs.keys()), unsafe_options=self.unsafe_git_fetch_options)
 
         proc = self.repo.git.fetch(
-            "--", self, *args, as_process=True, with_stdout=False, universal_newlines=False, v=verbose, **kwargs
+            "--", self, *args, as_process=True, with_stdout=False, universal_newlines=True, v=verbose, **kwargs
         )
         res = self._get_fetch_info_from_stderr(proc, progress, kill_after_timeout=kill_after_timeout)
         if hasattr(self.repo.odb, "update_cache"):
@@ -1118,7 +1125,7 @@ def pull(
             Git.check_unsafe_options(options=list(kwargs.keys()), unsafe_options=self.unsafe_git_pull_options)
 
         proc = self.repo.git.pull(
-            "--", self, refspec, with_stdout=False, as_process=True, universal_newlines=False, v=True, **kwargs
+            "--", self, refspec, with_stdout=False, as_process=True, universal_newlines=True, v=True, **kwargs
         )
         res = self._get_fetch_info_from_stderr(proc, progress, kill_after_timeout=kill_after_timeout)
         if hasattr(self.repo.odb, "update_cache"):
diff --git a/git/repo/base.py b/git/repo/base.py
index 51ea76901..1f543cc57 100644
--- a/git/repo/base.py
+++ b/git/repo/base.py
@@ -126,6 +126,7 @@ class Repo:
     working_dir: PathLike
     """The working directory of the git command."""
 
+    # stored as string for easier processing, but annotated as path for clearer intention
     _working_tree_dir: Optional[PathLike] = None
 
     git_dir: PathLike
@@ -179,7 +180,7 @@ def __init__(
         R"""Create a new :class:`Repo` instance.
 
         :param path:
-            The path to either the root git directory or the bare git repo::
+            The path to either the worktree directory or the .git directory itself::
 
                 repo = Repo("/Users/mtrier/Development/git-python")
                 repo = Repo("/Users/mtrier/Development/git-python.git")
@@ -215,15 +216,13 @@ def __init__(
         epath = path or os.getenv("GIT_DIR")
         if not epath:
             epath = os.getcwd()
+        epath = os.fspath(epath)
         if Git.is_cygwin():
             # Given how the tests are written, this seems more likely to catch Cygwin
             # git used from Windows than Windows git used from Cygwin. Therefore
             # changing to Cygwin-style paths is the relevant operation.
-            epath = cygpath(str(epath))
+            epath = cygpath(epath)
 
-        epath = epath or path or os.getcwd()
-        if not isinstance(epath, str):
-            epath = str(epath)
         if expand_vars and re.search(self.re_envvars, epath):
             warnings.warn(
                 "The use of environment variables in paths is deprecated"
@@ -354,21 +353,19 @@ def __ne__(self, rhs: object) -> bool:
     def __hash__(self) -> int:
         return hash(self.git_dir)
 
-    # Description property
-    def _get_description(self) -> str:
+    @property
+    def description(self) -> str:
+        """The project's description"""
         filename = osp.join(self.git_dir, "description")
         with open(filename, "rb") as fp:
             return fp.read().rstrip().decode(defenc)
 
-    def _set_description(self, descr: str) -> None:
+    @description.setter
+    def description(self, descr: str) -> None:
         filename = osp.join(self.git_dir, "description")
         with open(filename, "wb") as fp:
             fp.write((descr + "\n").encode(defenc))
 
-    description = property(_get_description, _set_description, doc="the project's description")
-    del _get_description
-    del _set_description
-
     @property
     def working_tree_dir(self) -> Optional[PathLike]:
         """
@@ -402,6 +399,17 @@ def heads(self) -> "IterableList[Head]":
         """
         return Head.list_items(self)
 
+    @property
+    def branches(self) -> "IterableList[Head]":
+        """Alias for heads.
+        A list of :class:`~git.refs.head.Head` objects representing the branch heads
+        in this repo.
+
+        :return:
+            ``git.IterableList(Head, ...)``
+        """
+        return self.heads
+
     @property
     def references(self) -> "IterableList[Reference]":
         """A list of :class:`~git.refs.reference.Reference` objects representing tags,
@@ -412,11 +420,16 @@ def references(self) -> "IterableList[Reference]":
         """
         return Reference.list_items(self)
 
-    # Alias for references.
-    refs = references
+    @property
+    def refs(self) -> "IterableList[Reference]":
+        """Alias for references.
+        A list of :class:`~git.refs.reference.Reference` objects representing tags,
+        heads and remote references.
 
-    # Alias for heads.
-    branches = heads
+        :return:
+            ``git.IterableList(Reference, ...)``
+        """
+        return self.references
 
     @property
     def index(self) -> "IndexFile":
@@ -498,7 +511,7 @@ def create_submodule(self, *args: Any, **kwargs: Any) -> Submodule:
     def iter_submodules(self, *args: Any, **kwargs: Any) -> Iterator[Submodule]:
         """An iterator yielding Submodule instances.
 
-        See the `~git.objects.util.Traversable` interface for a description of `args`
+        See the :class:`~git.objects.util.Traversable` interface for a description of `args`
         and `kwargs`.
 
         :return:
@@ -506,7 +519,7 @@ def iter_submodules(self, *args: Any, **kwargs: Any) -> Iterator[Submodule]:
         """
         return RootModule(self).traverse(*args, **kwargs)
 
-    def submodule_update(self, *args: Any, **kwargs: Any) -> Iterator[Submodule]:
+    def submodule_update(self, *args: Any, **kwargs: Any) -> RootModule:
         """Update the submodules, keeping the repository consistent as it will
         take the previous state into consideration.
 
@@ -670,11 +683,7 @@ def _config_reader(
         git_dir: Optional[PathLike] = None,
     ) -> GitConfigParser:
         if config_level is None:
-            files = [
-                self._get_config_path(cast(Lit_config_levels, f), git_dir)
-                for f in self.config_level
-                if cast(Lit_config_levels, f)
-            ]
+            files = [self._get_config_path(f, git_dir) for f in self.config_level if f]
         else:
             files = [self._get_config_path(config_level, git_dir)]
         return GitConfigParser(files, read_only=True, repo=self)
@@ -869,13 +878,14 @@ def _set_daemon_export(self, value: object) -> None:
         elif not value and fileexists:
             os.unlink(filename)
 
-    daemon_export = property(
-        _get_daemon_export,
-        _set_daemon_export,
-        doc="If True, git-daemon may export this repository",
-    )
-    del _get_daemon_export
-    del _set_daemon_export
+    @property
+    def daemon_export(self) -> bool:
+        """If True, git-daemon may export this repository"""
+        return self._get_daemon_export()
+
+    @daemon_export.setter
+    def daemon_export(self, value: object) -> None:
+        self._set_daemon_export(value)
 
     def _get_alternates(self) -> List[str]:
         """The list of alternates for this repo from which objects can be retrieved.
@@ -913,11 +923,14 @@ def _set_alternates(self, alts: List[str]) -> None:
             with open(alternates_path, "wb") as f:
                 f.write("\n".join(alts).encode(defenc))
 
-    alternates = property(
-        _get_alternates,
-        _set_alternates,
-        doc="Retrieve a list of alternates paths or set a list paths to be used as alternates",
-    )
+    @property
+    def alternates(self) -> List[str]:
+        """Retrieve a list of alternates paths or set a list paths to be used as alternates"""
+        return self._get_alternates()
+
+    @alternates.setter
+    def alternates(self, alts: List[str]) -> None:
+        self._set_alternates(alts)
 
     def is_dirty(
         self,
@@ -943,7 +956,7 @@ def is_dirty(
         if not submodules:
             default_args.append("--ignore-submodules")
         if path:
-            default_args.extend(["--", str(path)])
+            default_args.extend(["--", os.fspath(path)])
         if index:
             # diff index against HEAD.
             if osp.isfile(self.index.path) and len(self.git.diff("--cached", *default_args)):
@@ -1343,9 +1356,9 @@ def _clone(
     ) -> "Repo":
         odbt = kwargs.pop("odbt", odb_default_type)
 
-        # When pathlib.Path or other class-based path is passed
-        if not isinstance(path, str):
-            path = str(path)
+        # url may be a path and this has no effect if it is a string
+        url = os.fspath(url)
+        path = os.fspath(path)
 
         ## A bug win cygwin's Git, when `--bare` or `--separate-git-dir`
         #  it prepends the cwd or(?) the `url` into the `path, so::
@@ -1362,7 +1375,7 @@ def _clone(
             multi = shlex.split(" ".join(multi_options))
 
         if not allow_unsafe_protocols:
-            Git.check_unsafe_protocols(str(url))
+            Git.check_unsafe_protocols(url)
         if not allow_unsafe_options:
             Git.check_unsafe_options(options=list(kwargs.keys()), unsafe_options=cls.unsafe_git_clone_options)
         if not allow_unsafe_options and multi_options:
@@ -1371,7 +1384,7 @@ def _clone(
         proc = git.clone(
             multi,
             "--",
-            Git.polish_url(str(url)),
+            Git.polish_url(url),
             clone_path,
             with_extended_output=True,
             as_process=True,
@@ -1466,7 +1479,7 @@ def clone(
             self.common_dir,
             path,
             type(self.odb),
-            progress,
+            progress,  # type: ignore[arg-type]
             multi_options,
             allow_unsafe_protocols=allow_unsafe_protocols,
             allow_unsafe_options=allow_unsafe_options,
@@ -1527,7 +1540,7 @@ def clone_from(
             url,
             to_path,
             GitCmdObjectDB,
-            progress,
+            progress,  # type: ignore[arg-type]
             multi_options,
             allow_unsafe_protocols=allow_unsafe_protocols,
             allow_unsafe_options=allow_unsafe_options,
diff --git a/git/repo/fun.py b/git/repo/fun.py
index 182cf82ed..3f00e60ea 100644
--- a/git/repo/fun.py
+++ b/git/repo/fun.py
@@ -286,7 +286,7 @@ def rev_parse(repo: "Repo", rev: str) -> AnyGitObject:
             # END handle refname
         else:
             if ref is not None:
-                obj = cast("Commit", ref.commit)
+                obj = ref.commit
             # END handle ref
         # END initialize obj on first token
 
@@ -301,7 +301,13 @@ def rev_parse(repo: "Repo", rev: str) -> AnyGitObject:
 
             # Handle type.
             if output_type == "commit":
-                pass  # Default.
+                obj = cast("TagObject", obj)
+                if obj and obj.type == "tag":
+                    obj = deref_tag(obj)
+                else:
+                    # Cannot do anything for non-tags.
+                    pass
+                # END handle tag
             elif output_type == "tree":
                 try:
                     obj = cast(AnyGitObject, obj)
@@ -399,7 +405,7 @@ def rev_parse(repo: "Repo", rev: str) -> AnyGitObject:
             # END end handle tag
         except (IndexError, AttributeError) as e:
             raise BadName(
-                f"Invalid revision spec '{rev}' - not enough " f"parent commits to reach '{token}{int(num)}'"
+                f"Invalid revision spec '{rev}' - not enough parent commits to reach '{token}{int(num)}'"
             ) from e
         # END exception handling
     # END parse loop
diff --git a/git/types.py b/git/types.py
index 584450146..100fff43f 100644
--- a/git/types.py
+++ b/git/types.py
@@ -13,7 +13,6 @@
     Sequence as Sequence,
     Tuple,
     TYPE_CHECKING,
-    Type,
     TypeVar,
     Union,
 )
@@ -130,7 +129,8 @@
 https://git-scm.com/docs/gitglossary#def_object_type
 """
 
-Lit_commit_ish: Type[Literal["commit", "tag"]]
+if TYPE_CHECKING:
+    Lit_commit_ish = Literal["commit", "tag"]
 """Deprecated. Type of literal strings identifying typically-commitish git object types.
 
 Prior to a bugfix, this type had been defined more broadly. Any usage is in practice
@@ -248,6 +248,7 @@ class Files_TD(TypedDict):
     insertions: int
     deletions: int
     lines: int
+    change_type: str
 
 
 class Total_TD(TypedDict):
diff --git a/git/util.py b/git/util.py
index 11f963e02..c3ffdd62b 100644
--- a/git/util.py
+++ b/git/util.py
@@ -36,7 +36,7 @@
 import logging
 import os
 import os.path as osp
-import pathlib
+from pathlib import Path
 import platform
 import re
 import shutil
@@ -272,9 +272,9 @@ def stream_copy(source: BinaryIO, destination: BinaryIO, chunk_size: int = 512 *
 def join_path(a: PathLike, *p: PathLike) -> PathLike:
     R"""Join path tokens together similar to osp.join, but always use ``/`` instead of
     possibly ``\`` on Windows."""
-    path = str(a)
+    path = os.fspath(a)
     for b in p:
-        b = str(b)
+        b = os.fspath(b)
         if not b:
             continue
         if b.startswith("/"):
@@ -290,18 +290,18 @@ def join_path(a: PathLike, *p: PathLike) -> PathLike:
 if sys.platform == "win32":
 
     def to_native_path_windows(path: PathLike) -> PathLike:
-        path = str(path)
+        path = os.fspath(path)
         return path.replace("/", "\\")
 
     def to_native_path_linux(path: PathLike) -> str:
-        path = str(path)
+        path = os.fspath(path)
         return path.replace("\\", "/")
 
     to_native_path = to_native_path_windows
 else:
     # No need for any work on Linux.
     def to_native_path_linux(path: PathLike) -> str:
-        return str(path)
+        return os.fspath(path)
 
     to_native_path = to_native_path_linux
 
@@ -372,7 +372,7 @@ def is_exec(fpath: str) -> bool:
     progs = []
     if not path:
         path = os.environ["PATH"]
-    for folder in str(path).split(os.pathsep):
+    for folder in os.fspath(path).split(os.pathsep):
         folder = folder.strip('"')
         if folder:
             exe_path = osp.join(folder, program)
@@ -397,7 +397,7 @@ def _cygexpath(drive: Optional[str], path: str) -> str:
                 p = cygpath(p)
         elif drive:
             p = "/proc/cygdrive/%s/%s" % (drive.lower(), p)
-    p_str = str(p)  # ensure it is a str and not AnyPath
+    p_str = os.fspath(p)  # ensure it is a str and not AnyPath
     return p_str.replace("\\", "/")
 
 
@@ -418,7 +418,7 @@ def _cygexpath(drive: Optional[str], path: str) -> str:
 
 def cygpath(path: str) -> str:
     """Use :meth:`git.cmd.Git.polish_url` instead, that works on any environment."""
-    path = str(path)  # Ensure is str and not AnyPath.
+    path = os.fspath(path)  # Ensure is str and not AnyPath.
     # Fix to use Paths when 3.5 dropped. Or to be just str if only for URLs?
     if not path.startswith(("/cygdrive", "//", "/proc/cygdrive")):
         for regex, parser, recurse in _cygpath_parsers:
@@ -438,7 +438,7 @@ def cygpath(path: str) -> str:
 
 
 def decygpath(path: PathLike) -> str:
-    path = str(path)
+    path = os.fspath(path)
     m = _decygpath_regex.match(path)
     if m:
         drive, rest_path = m.groups()
@@ -464,6 +464,12 @@ def _is_cygwin_git(git_executable: str) -> bool:
 
             # Just a name given, not a real path.
             uname_cmd = osp.join(git_dir, "uname")
+
+            if not (Path(uname_cmd).is_file() and os.access(uname_cmd, os.X_OK)):
+                _logger.debug(f"Failed checking if running in CYGWIN: {uname_cmd} is not an executable")
+                _is_cygwin_cache[git_executable] = is_cygwin
+                return is_cygwin
+
             process = subprocess.Popen([uname_cmd], stdout=subprocess.PIPE, universal_newlines=True)
             uname_out, _ = process.communicate()
             # retcode = process.poll()
@@ -484,7 +490,9 @@ def is_cygwin_git(git_executable: PathLike) -> bool: ...
 
 
 def is_cygwin_git(git_executable: Union[None, PathLike]) -> bool:
-    if sys.platform == "win32":  # TODO: See if we can use `sys.platform != "cygwin"`.
+    # TODO: when py3.7 support is dropped, use the new interpolation f"{variable=}"
+    _logger.debug(f"sys.platform={sys.platform!r}, git_executable={git_executable!r}")
+    if sys.platform != "cygwin":
         return False
     elif git_executable is None:
         return False
@@ -515,7 +523,7 @@ def expand_path(p: PathLike, expand_vars: bool = ...) -> str:
 
 
 def expand_path(p: Union[None, PathLike], expand_vars: bool = True) -> Optional[PathLike]:
-    if isinstance(p, pathlib.Path):
+    if isinstance(p, Path):
         return p.resolve()
     try:
         p = osp.expanduser(p)  # type: ignore[arg-type]
@@ -910,6 +918,7 @@ class Stats:
       deletions = number of deleted lines as int
       insertions = number of inserted lines as int
       lines = total number of lines changed as int, or deletions + insertions
+      change_type = type of change as str, A|C|D|M|R|T|U|X|B
 
     ``full-stat-dict``
 
@@ -938,7 +947,7 @@ def _list_from_string(cls, repo: "Repo", text: str) -> "Stats":
             "files": {},
         }
         for line in text.splitlines():
-            (raw_insertions, raw_deletions, filename) = line.split("\t")
+            (change_type, raw_insertions, raw_deletions, filename) = line.split("\t")
             insertions = raw_insertions != "-" and int(raw_insertions) or 0
             deletions = raw_deletions != "-" and int(raw_deletions) or 0
             hsh["total"]["insertions"] += insertions
@@ -949,6 +958,7 @@ def _list_from_string(cls, repo: "Repo", text: str) -> "Stats":
                 "insertions": insertions,
                 "deletions": deletions,
                 "lines": insertions + deletions,
+                "change_type": change_type,
             }
             hsh["files"][filename.strip()] = files_dict
         return Stats(hsh["total"], hsh["files"])
@@ -1133,7 +1143,7 @@ def _obtain_lock(self) -> None:
         # END endless loop
 
 
-class IterableList(List[T_IterableObj]):
+class IterableList(List[T_IterableObj]):  # type: ignore[type-var]
     """List of iterable objects allowing to query an object by id or by named index::
 
      heads = repo.heads
@@ -1198,24 +1208,20 @@ def __getattr__(self, attr: str) -> T_IterableObj:
         return list.__getattribute__(self, attr)
 
     def __getitem__(self, index: Union[SupportsIndex, int, slice, str]) -> T_IterableObj:  # type: ignore[override]
-        assert isinstance(index, (int, str, slice)), "Index of IterableList should be an int or str"
-
         if isinstance(index, int):
             return list.__getitem__(self, index)
         elif isinstance(index, slice):
             raise ValueError("Index should be an int or str")
         else:
             try:
-                return getattr(self, index)
+                return getattr(self, cast(str, index))
             except AttributeError as e:
-                raise IndexError("No item found with id %r" % (self._prefix + index)) from e
+                raise IndexError(f"No item found with id {self._prefix}{index}") from e
         # END handle getattr
 
     def __delitem__(self, index: Union[SupportsIndex, int, slice, str]) -> None:
-        assert isinstance(index, (int, str)), "Index of IterableList should be an int or str"
-
         delindex = cast(int, index)
-        if not isinstance(index, int):
+        if isinstance(index, str):
             delindex = -1
             name = self._prefix + index
             for i, item in enumerate(self):
diff --git a/pyproject.toml b/pyproject.toml
index ee54edb78..149f2dc92 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,7 +19,6 @@ testpaths = "test"  # Space separated list of paths from root e.g test tests doc
 # filterwarnings ignore::WarningType  # ignores those warnings
 
 [tool.mypy]
-python_version = "3.8"
 files = ["git/", "test/deprecation/"]
 disallow_untyped_defs = true
 no_implicit_optional = true
@@ -60,16 +59,14 @@ lint.select = [
     # "UP",  # See: https://docs.astral.sh/ruff/rules/#pyupgrade-up
 ]
 lint.extend-select = [
-    # "A",     # See: https://pypi.org/project/flake8-builtins
-    "B",       # See: https://pypi.org/project/flake8-bugbear
-    "C4",      # See: https://pypi.org/project/flake8-comprehensions
-    "TCH004",  # See: https://docs.astral.sh/ruff/rules/runtime-import-in-type-checking-block/
+    # "A",    # See: https://pypi.org/project/flake8-builtins
+    "B",      # See: https://pypi.org/project/flake8-bugbear
+    "C4",     # See: https://pypi.org/project/flake8-comprehensions
+    "TC004",  # See: https://docs.astral.sh/ruff/rules/runtime-import-in-type-checking-block/
 ]
 lint.ignore = [
-    "E203",  # Whitespace before ':'
-    "E731",  # Do not assign a `lambda` expression, use a `def`
+    # If it becomes necessary to ignore any rules, list them here.
 ]
-lint.ignore-init-module-imports = true
 lint.unfixable = [
     "F401",  # Module imported but unused
 ]
@@ -78,3 +75,12 @@ lint.unfixable = [
 "test/**" = [
     "B018",  # useless-expression
 ]
+"fuzzing/fuzz-targets/**" = [
+  "E402",  # environment setup must happen before the `git` module is imported, thus cannot happen at top of file
+]
+
+
+[tool.codespell]
+ignore-words-list="afile,assertIn,doesnt,gud,uptodate"
+#count = true
+quiet-level = 3
diff --git a/requirements-dev.txt b/requirements-dev.txt
index f626644af..066b192b8 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -1,8 +1,8 @@
--r requirements.txt
--r test-requirements.txt
-
-# For additional local testing/linting - to be added elsewhere eventually.
-ruff
-shellcheck
-pytest-icdiff
-# pytest-profiling
+-r requirements.txt
+-r test-requirements.txt
+
+# For additional local testing/linting - to be added elsewhere eventually.
+ruff >=0.8
+shellcheck
+pytest-icdiff
+# pytest-profiling
diff --git a/requirements.txt b/requirements.txt
index 7159416a9..61d8403b0 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,2 +1,2 @@
 gitdb>=4.0.1,<5
-typing-extensions>=3.7.4.3;python_version<"3.8"
+typing-extensions>=3.10.0.2;python_version<"3.10"
diff --git a/setup.py b/setup.py
index f28fedb85..a7b1eab00 100755
--- a/setup.py
+++ b/setup.py
@@ -95,7 +95,6 @@ def _stamp_version(filename: str) -> None:
         # "Development Status :: 7 - Inactive",
         "Environment :: Console",
         "Intended Audience :: Developers",
-        "License :: OSI Approved :: BSD License",
         "Operating System :: OS Independent",
         "Operating System :: POSIX",
         "Operating System :: Microsoft :: Windows",
diff --git a/test-requirements.txt b/test-requirements.txt
index 75e9e81fa..e6e01c683 100644
--- a/test-requirements.txt
+++ b/test-requirements.txt
@@ -1,7 +1,7 @@
 coverage[toml]
 ddt >= 1.1.1, != 1.4.3
 mock ; python_version < "3.8"
-mypy
+mypy==1.18.2 ; python_version >= "3.9" # pin mypy version to avoid new errors
 pre-commit
 pytest >= 7.3.1
 pytest-cov
diff --git a/test/deprecation/test_types.py b/test/deprecation/test_types.py
index f97375a85..d3c6af645 100644
--- a/test/deprecation/test_types.py
+++ b/test/deprecation/test_types.py
@@ -36,7 +36,7 @@ def test_can_access_lit_commit_ish_but_it_is_not_usable() -> None:
     assert 'Literal["commit", "tag"]' in message, "Has new definition."
     assert "GitObjectTypeString" in message, "Has new type name for old definition."
 
-    _: Lit_commit_ish = "commit"  # type: ignore[valid-type]
+    _: Lit_commit_ish = "commit"
 
     # It should be as documented (even though deliberately unusable in static checks).
     assert Lit_commit_ish == Literal["commit", "tag"]
diff --git a/test/fixtures/diff_numstat b/test/fixtures/diff_numstat
index 44c6ca2d5..b76e467eb 100644
--- a/test/fixtures/diff_numstat
+++ b/test/fixtures/diff_numstat
@@ -1,2 +1,3 @@
-29	18	a.txt
-0	5	b.txt
+M	29	18	a.txt
+M	0	5	b.txt
+A	7	0	c.txt
\ No newline at end of file
diff --git a/test/fixtures/git_config_with_empty_quotes b/test/fixtures/git_config_with_empty_quotes
new file mode 100644
index 000000000..f11fe4248
--- /dev/null
+++ b/test/fixtures/git_config_with_empty_quotes
@@ -0,0 +1,2 @@
+[core]
+  filemode = ""
diff --git a/test/fixtures/git_config_with_extra_whitespace b/test/fixtures/git_config_with_extra_whitespace
new file mode 100644
index 000000000..0f727cb5d
--- /dev/null
+++ b/test/fixtures/git_config_with_extra_whitespace
@@ -0,0 +1,2 @@
+[init]
+  defaultBranch =  trunk  
diff --git a/test/fixtures/git_config_with_quotes b/test/fixtures/git_config_with_quotes
new file mode 100644
index 000000000..40e6710d9
--- /dev/null
+++ b/test/fixtures/git_config_with_quotes
@@ -0,0 +1,3 @@
+[user]
+  name = "Cody Veal"
+  email = "cveal05@gmail.com"
diff --git a/test/fixtures/git_config_with_quotes_escapes b/test/fixtures/git_config_with_quotes_escapes
new file mode 100644
index 000000000..33332c221
--- /dev/null
+++ b/test/fixtures/git_config_with_quotes_escapes
@@ -0,0 +1,9 @@
+[custom]
+  hasnewline = "first\nsecond"
+  hasbackslash = "foo\\bar"
+  hasquote = "ab\"cd"
+  hastrailingbackslash = "word\\"
+  hasunrecognized = "p\qrs"
+  hasunescapedquotes = "ab"cd"e"
+  ordinary = "hello world"
+  unquoted = good evening
diff --git a/test/fixtures/git_config_with_quotes_whitespace_inside b/test/fixtures/git_config_with_quotes_whitespace_inside
new file mode 100644
index 000000000..c6014cc61
--- /dev/null
+++ b/test/fixtures/git_config_with_quotes_whitespace_inside
@@ -0,0 +1,2 @@
+[core]
+  commentString = "# "
diff --git a/test/fixtures/git_config_with_quotes_whitespace_outside b/test/fixtures/git_config_with_quotes_whitespace_outside
new file mode 100644
index 000000000..4b1615a51
--- /dev/null
+++ b/test/fixtures/git_config_with_quotes_whitespace_outside
@@ -0,0 +1,2 @@
+[init]
+  defaultBranch =  "trunk"  
diff --git a/test/fixtures/index_extended_flags b/test/fixtures/index_extended_flags
new file mode 100644
index 000000000..f03713b68
Binary files /dev/null and b/test/fixtures/index_extended_flags differ
diff --git a/test/lib/helper.py b/test/lib/helper.py
index 5d91447ea..6a8b714e6 100644
--- a/test/lib/helper.py
+++ b/test/lib/helper.py
@@ -10,6 +10,7 @@
     "with_rw_directory",
     "with_rw_repo",
     "with_rw_and_rw_remote_repo",
+    "PathLikeMock",
     "TestBase",
     "VirtualEnvironment",
     "TestCase",
@@ -20,6 +21,7 @@
 ]
 
 import contextlib
+from dataclasses import dataclass
 from functools import wraps
 import gc
 import io
@@ -49,6 +51,15 @@
 
 _logger = logging.getLogger(__name__)
 
+
+@dataclass
+class PathLikeMock:
+    path: str
+
+    def __fspath__(self) -> str:
+        return self.path
+
+
 # { Routines
 
 
@@ -149,7 +160,7 @@ def repo_creator(self):
             os.chdir(rw_repo.working_dir)
             try:
                 return func(self, rw_repo)
-            except:  # noqa: E722 B001
+            except:  # noqa: E722
                 _logger.info("Keeping repo after failure: %s", repo_dir)
                 repo_dir = None
                 raise
@@ -309,7 +320,7 @@ def remote_repo_creator(self):
                     with cwd(rw_repo.working_dir):
                         try:
                             return func(self, rw_repo, rw_daemon_repo)
-                        except:  # noqa: E722 B001
+                        except:  # noqa: E722
                             _logger.info(
                                 "Keeping repos after failure: \n  rw_repo_dir: %s \n  rw_daemon_repo_dir: %s",
                                 rw_repo_dir,
@@ -415,9 +426,15 @@ def __init__(self, env_dir, *, with_pip):
 
         if with_pip:
             # The upgrade_deps parameter to venv.create is 3.9+ only, so do it this way.
-            command = [self.python, "-m", "pip", "install", "--upgrade", "pip"]
-            if sys.version_info < (3, 12):
-                command.append("setuptools")
+            command = [
+                self.python,
+                "-m",
+                "pip",
+                "install",
+                "--upgrade",
+                "pip",
+                'setuptools; python_version<"3.12"',
+            ]
             subprocess.check_output(command)
 
     @property
diff --git a/test/test_clone.py b/test/test_clone.py
index 126ef0063..143a3b51f 100644
--- a/test/test_clone.py
+++ b/test/test_clone.py
@@ -1,12 +1,23 @@
 # This module is part of GitPython and is released under the
 # 3-Clause BSD License: https://opensource.org/license/bsd-3-clause/
 
+import os
+import os.path as osp
+import pathlib
+import sys
+import tempfile
+from unittest import skip
+
+from git import GitCommandError, Repo
+from git.exc import UnsafeOptionError, UnsafeProtocolError
+
+from test.lib import TestBase, with_rw_directory, with_rw_repo, PathLikeMock
+
 from pathlib import Path
 import re
 
 import git
-
-from test.lib import TestBase, with_rw_directory
+import pytest
 
 
 class TestClone(TestBase):
@@ -29,3 +40,287 @@ def test_checkout_in_non_empty_dir(self, rw_dir):
             )
         else:
             self.fail("GitCommandError not raised")
+
+    @with_rw_directory
+    def test_clone_from_pathlib(self, rw_dir):
+        original_repo = Repo.init(osp.join(rw_dir, "repo"))
+
+        Repo.clone_from(pathlib.Path(original_repo.git_dir), pathlib.Path(rw_dir) / "clone_pathlib")
+
+    @with_rw_directory
+    def test_clone_from_pathlike(self, rw_dir):
+        original_repo = Repo.init(osp.join(rw_dir, "repo"))
+        Repo.clone_from(PathLikeMock(original_repo.git_dir), PathLikeMock(os.path.join(rw_dir, "clone_pathlike")))
+
+    @with_rw_directory
+    def test_clone_from_pathlib_withConfig(self, rw_dir):
+        original_repo = Repo.init(osp.join(rw_dir, "repo"))
+
+        cloned = Repo.clone_from(
+            original_repo.git_dir,
+            pathlib.Path(rw_dir) / "clone_pathlib_withConfig",
+            multi_options=[
+                "--recurse-submodules=repo",
+                "--config core.filemode=false",
+                "--config submodule.repo.update=checkout",
+                "--config filter.lfs.clean='git-lfs clean -- %f'",
+            ],
+            allow_unsafe_options=True,
+        )
+
+        self.assertEqual(cloned.config_reader().get_value("submodule", "active"), "repo")
+        self.assertEqual(cloned.config_reader().get_value("core", "filemode"), False)
+        self.assertEqual(cloned.config_reader().get_value('submodule "repo"', "update"), "checkout")
+        self.assertEqual(
+            cloned.config_reader().get_value('filter "lfs"', "clean"),
+            "git-lfs clean -- %f",
+        )
+
+    def test_clone_from_with_path_contains_unicode(self):
+        with tempfile.TemporaryDirectory() as tmpdir:
+            unicode_dir_name = "\u0394"
+            path_with_unicode = os.path.join(tmpdir, unicode_dir_name)
+            os.makedirs(path_with_unicode)
+
+            try:
+                Repo.clone_from(
+                    url=self._small_repo_url(),
+                    to_path=path_with_unicode,
+                )
+            except UnicodeEncodeError:
+                self.fail("Raised UnicodeEncodeError")
+
+    @with_rw_directory
+    @skip(
+        """The referenced repository was removed, and one needs to set up a new
+        password controlled repo under the org's control."""
+    )
+    def test_leaking_password_in_clone_logs(self, rw_dir):
+        password = "fakepassword1234"
+        try:
+            Repo.clone_from(
+                url="https://fakeuser:{}@fakerepo.example.com/testrepo".format(password),
+                to_path=rw_dir,
+            )
+        except GitCommandError as err:
+            assert password not in str(err), "The error message '%s' should not contain the password" % err
+        # Working example from a blank private project.
+        Repo.clone_from(
+            url="https://gitlab+deploy-token-392045:mLWhVus7bjLsy8xj8q2V@gitlab.com/mercierm/test_git_python",
+            to_path=rw_dir,
+        )
+
+    @with_rw_repo("HEAD")
+    def test_clone_unsafe_options(self, rw_repo):
+        with tempfile.TemporaryDirectory() as tdir:
+            tmp_dir = pathlib.Path(tdir)
+            tmp_file = tmp_dir / "pwn"
+            unsafe_options = [
+                f"--upload-pack='touch {tmp_file}'",
+                f"-u 'touch {tmp_file}'",
+                "--config=protocol.ext.allow=always",
+                "-c protocol.ext.allow=always",
+            ]
+            for unsafe_option in unsafe_options:
+                with self.assertRaises(UnsafeOptionError):
+                    rw_repo.clone(tmp_dir, multi_options=[unsafe_option])
+                assert not tmp_file.exists()
+
+            unsafe_options = [
+                {"upload-pack": f"touch {tmp_file}"},
+                {"u": f"touch {tmp_file}"},
+                {"config": "protocol.ext.allow=always"},
+                {"c": "protocol.ext.allow=always"},
+            ]
+            for unsafe_option in unsafe_options:
+                with self.assertRaises(UnsafeOptionError):
+                    rw_repo.clone(tmp_dir, **unsafe_option)
+                assert not tmp_file.exists()
+
+    @pytest.mark.xfail(
+        sys.platform == "win32",
+        reason=(
+            "File not created. A separate Windows command may be needed. This and the "
+            "currently passing test test_clone_unsafe_options must be adjusted in the "
+            "same way. Until then, test_clone_unsafe_options is unreliable on Windows."
+        ),
+        raises=AssertionError,
+    )
+    @with_rw_repo("HEAD")
+    def test_clone_unsafe_options_allowed(self, rw_repo):
+        with tempfile.TemporaryDirectory() as tdir:
+            tmp_dir = pathlib.Path(tdir)
+            tmp_file = tmp_dir / "pwn"
+            unsafe_options = [
+                f"--upload-pack='touch {tmp_file}'",
+                f"-u 'touch {tmp_file}'",
+            ]
+            for i, unsafe_option in enumerate(unsafe_options):
+                destination = tmp_dir / str(i)
+                assert not tmp_file.exists()
+                # The options will be allowed, but the command will fail.
+                with self.assertRaises(GitCommandError):
+                    rw_repo.clone(destination, multi_options=[unsafe_option], allow_unsafe_options=True)
+                assert tmp_file.exists()
+                tmp_file.unlink()
+
+            unsafe_options = [
+                "--config=protocol.ext.allow=always",
+                "-c protocol.ext.allow=always",
+            ]
+            for i, unsafe_option in enumerate(unsafe_options):
+                destination = tmp_dir / str(i)
+                assert not destination.exists()
+                rw_repo.clone(destination, multi_options=[unsafe_option], allow_unsafe_options=True)
+                assert destination.exists()
+
+    @with_rw_repo("HEAD")
+    def test_clone_safe_options(self, rw_repo):
+        with tempfile.TemporaryDirectory() as tdir:
+            tmp_dir = pathlib.Path(tdir)
+            options = [
+                "--depth=1",
+                "--single-branch",
+                "-q",
+            ]
+            for option in options:
+                destination = tmp_dir / option
+                assert not destination.exists()
+                rw_repo.clone(destination, multi_options=[option])
+                assert destination.exists()
+
+    @with_rw_repo("HEAD")
+    def test_clone_from_unsafe_options(self, rw_repo):
+        with tempfile.TemporaryDirectory() as tdir:
+            tmp_dir = pathlib.Path(tdir)
+            tmp_file = tmp_dir / "pwn"
+            unsafe_options = [
+                f"--upload-pack='touch {tmp_file}'",
+                f"-u 'touch {tmp_file}'",
+                "--config=protocol.ext.allow=always",
+                "-c protocol.ext.allow=always",
+            ]
+            for unsafe_option in unsafe_options:
+                with self.assertRaises(UnsafeOptionError):
+                    Repo.clone_from(rw_repo.working_dir, tmp_dir, multi_options=[unsafe_option])
+                assert not tmp_file.exists()
+
+            unsafe_options = [
+                {"upload-pack": f"touch {tmp_file}"},
+                {"u": f"touch {tmp_file}"},
+                {"config": "protocol.ext.allow=always"},
+                {"c": "protocol.ext.allow=always"},
+            ]
+            for unsafe_option in unsafe_options:
+                with self.assertRaises(UnsafeOptionError):
+                    Repo.clone_from(rw_repo.working_dir, tmp_dir, **unsafe_option)
+                assert not tmp_file.exists()
+
+    @pytest.mark.xfail(
+        sys.platform == "win32",
+        reason=(
+            "File not created. A separate Windows command may be needed. This and the "
+            "currently passing test test_clone_from_unsafe_options must be adjusted in the "
+            "same way. Until then, test_clone_from_unsafe_options is unreliable on Windows."
+        ),
+        raises=AssertionError,
+    )
+    @with_rw_repo("HEAD")
+    def test_clone_from_unsafe_options_allowed(self, rw_repo):
+        with tempfile.TemporaryDirectory() as tdir:
+            tmp_dir = pathlib.Path(tdir)
+            tmp_file = tmp_dir / "pwn"
+            unsafe_options = [
+                f"--upload-pack='touch {tmp_file}'",
+                f"-u 'touch {tmp_file}'",
+            ]
+            for i, unsafe_option in enumerate(unsafe_options):
+                destination = tmp_dir / str(i)
+                assert not tmp_file.exists()
+                # The options will be allowed, but the command will fail.
+                with self.assertRaises(GitCommandError):
+                    Repo.clone_from(
+                        rw_repo.working_dir, destination, multi_options=[unsafe_option], allow_unsafe_options=True
+                    )
+                assert tmp_file.exists()
+                tmp_file.unlink()
+
+            unsafe_options = [
+                "--config=protocol.ext.allow=always",
+                "-c protocol.ext.allow=always",
+            ]
+            for i, unsafe_option in enumerate(unsafe_options):
+                destination = tmp_dir / str(i)
+                assert not destination.exists()
+                Repo.clone_from(
+                    rw_repo.working_dir, destination, multi_options=[unsafe_option], allow_unsafe_options=True
+                )
+                assert destination.exists()
+
+    @with_rw_repo("HEAD")
+    def test_clone_from_safe_options(self, rw_repo):
+        with tempfile.TemporaryDirectory() as tdir:
+            tmp_dir = pathlib.Path(tdir)
+            options = [
+                "--depth=1",
+                "--single-branch",
+                "-q",
+            ]
+            for option in options:
+                destination = tmp_dir / option
+                assert not destination.exists()
+                Repo.clone_from(rw_repo.common_dir, destination, multi_options=[option])
+                assert destination.exists()
+
+    def test_clone_from_unsafe_protocol(self):
+        with tempfile.TemporaryDirectory() as tdir:
+            tmp_dir = pathlib.Path(tdir)
+            tmp_file = tmp_dir / "pwn"
+            urls = [
+                f"ext::sh -c touch% {tmp_file}",
+                "fd::17/foo",
+            ]
+            for url in urls:
+                with self.assertRaises(UnsafeProtocolError):
+                    Repo.clone_from(url, tmp_dir / "repo")
+                assert not tmp_file.exists()
+
+    def test_clone_from_unsafe_protocol_allowed(self):
+        with tempfile.TemporaryDirectory() as tdir:
+            tmp_dir = pathlib.Path(tdir)
+            tmp_file = tmp_dir / "pwn"
+            urls = [
+                f"ext::sh -c touch% {tmp_file}",
+                "fd::/foo",
+            ]
+            for url in urls:
+                # The URL will be allowed into the command, but the command will
+                # fail since we don't have that protocol enabled in the Git config file.
+                with self.assertRaises(GitCommandError):
+                    Repo.clone_from(url, tmp_dir / "repo", allow_unsafe_protocols=True)
+                assert not tmp_file.exists()
+
+    def test_clone_from_unsafe_protocol_allowed_and_enabled(self):
+        with tempfile.TemporaryDirectory() as tdir:
+            tmp_dir = pathlib.Path(tdir)
+            tmp_file = tmp_dir / "pwn"
+            urls = [
+                f"ext::sh -c touch% {tmp_file}",
+            ]
+            allow_ext = [
+                "--config=protocol.ext.allow=always",
+            ]
+            for url in urls:
+                # The URL will be allowed into the command, and the protocol is enabled,
+                # but the command will fail since it can't read from the remote repo.
+                assert not tmp_file.exists()
+                with self.assertRaises(GitCommandError):
+                    Repo.clone_from(
+                        url,
+                        tmp_dir / "repo",
+                        multi_options=allow_ext,
+                        allow_unsafe_protocols=True,
+                        allow_unsafe_options=True,
+                    )
+                assert tmp_file.exists()
+                tmp_file.unlink()
diff --git a/test/test_commit.py b/test/test_commit.py
index 5832258de..37c66e3e7 100644
--- a/test/test_commit.py
+++ b/test/test_commit.py
@@ -135,9 +135,12 @@ def test_stats(self):
         commit = self.rorepo.commit("33ebe7acec14b25c5f84f35a664803fcab2f7781")
         stats = commit.stats
 
-        def check_entries(d):
+        def check_entries(d, has_change_type=False):
             assert isinstance(d, dict)
-            for key in ("insertions", "deletions", "lines"):
+            keys = ("insertions", "deletions", "lines")
+            if has_change_type:
+                keys += ("change_type",)
+            for key in keys:
                 assert key in d
 
         # END assertion helper
@@ -148,7 +151,7 @@ def check_entries(d):
         assert "files" in stats.total
 
         for _filepath, d in stats.files.items():
-            check_entries(d)
+            check_entries(d, True)
         # END for each stated file
 
         # Check that data is parsed properly.
diff --git a/test/test_config.py b/test/test_config.py
index 92997422d..56ac0f304 100644
--- a/test/test_config.py
+++ b/test/test_config.py
@@ -373,6 +373,41 @@ def test_conditional_includes_from_branch_name_error(self, rw_dir):
             assert not config._has_includes()
             assert config._included_paths() == []
 
+    @with_rw_directory
+    def test_conditional_includes_remote_url(self, rw_dir):
+        # Initiate mocked repository.
+        repo = mock.Mock()
+        repo.remotes = [mock.Mock(url="https://github.com/foo/repo")]
+
+        # Initiate config files.
+        path1 = osp.join(rw_dir, "config1")
+        path2 = osp.join(rw_dir, "config2")
+        template = '[includeIf "hasconfig:remote.*.url:{}"]\n    path={}\n'
+
+        # Ensure that config with hasconfig and full url is correct.
+        with open(path1, "w") as stream:
+            stream.write(template.format("https://github.com/foo/repo", path2))
+
+        with GitConfigParser(path1, repo=repo) as config:
+            assert config._has_includes()
+            assert config._included_paths() == [("path", path2)]
+
+        # Ensure that config with hasconfig and incorrect url is incorrect.
+        with open(path1, "w") as stream:
+            stream.write(template.format("incorrect", path2))
+
+        with GitConfigParser(path1, repo=repo) as config:
+            assert not config._has_includes()
+            assert config._included_paths() == []
+
+        # Ensure that config with hasconfig and url using glob pattern is correct.
+        with open(path1, "w") as stream:
+            stream.write(template.format("**/**github.com*/**", path2))
+
+        with GitConfigParser(path1, repo=repo) as config:
+            assert config._has_includes()
+            assert config._included_paths() == [("path", path2)]
+
     def test_rename(self):
         file_obj = self._to_memcache(fixture_path("git_config"))
         with GitConfigParser(file_obj, read_only=False, merge_includes=False) as cw:
@@ -391,13 +426,17 @@ def test_complex_aliases(self):
         with GitConfigParser(file_obj, read_only=False) as w_config:
             self.assertEqual(
                 w_config.get("alias", "rbi"),
-                '"!g() { git rebase -i origin/${1:-master} ; } ; g"',
+                "!g() { git rebase -i origin/${1:-master} ; } ; g",
             )
         self.assertEqual(
             file_obj.getvalue(),
             self._to_memcache(fixture_path(".gitconfig")).getvalue(),
         )
 
+    def test_config_with_extra_whitespace(self):
+        cr = GitConfigParser(fixture_path("git_config_with_extra_whitespace"), read_only=True)
+        self.assertEqual(cr.get("init", "defaultBranch"), "trunk")
+
     def test_empty_config_value(self):
         cr = GitConfigParser(fixture_path("git_config_with_empty_value"), read_only=True)
 
@@ -406,6 +445,44 @@ def test_empty_config_value(self):
         with self.assertRaises(cp.NoOptionError):
             cr.get_value("color", "ui")
 
+    def test_config_with_quotes(self):
+        cr = GitConfigParser(fixture_path("git_config_with_quotes"), read_only=True)
+
+        self.assertEqual(cr.get("user", "name"), "Cody Veal")
+        self.assertEqual(cr.get("user", "email"), "cveal05@gmail.com")
+
+    def test_config_with_empty_quotes(self):
+        cr = GitConfigParser(fixture_path("git_config_with_empty_quotes"), read_only=True)
+        self.assertEqual(cr.get("core", "filemode"), "", "quotes can form a literal empty string as value")
+
+    def test_config_with_quotes_with_literal_whitespace(self):
+        cr = GitConfigParser(fixture_path("git_config_with_quotes_whitespace_inside"), read_only=True)
+        self.assertEqual(cr.get("core", "commentString"), "# ")
+
+    def test_config_with_quotes_with_whitespace_outside_value(self):
+        cr = GitConfigParser(fixture_path("git_config_with_quotes_whitespace_outside"), read_only=True)
+        self.assertEqual(cr.get("init", "defaultBranch"), "trunk")
+
+    def test_config_with_quotes_containing_escapes(self):
+        """For now just suppress quote removal. But it would be good to interpret most of these."""
+        cr = GitConfigParser(fixture_path("git_config_with_quotes_escapes"), read_only=True)
+
+        # These can eventually be supported by substituting the represented character.
+        self.assertEqual(cr.get("custom", "hasnewline"), R'"first\nsecond"')
+        self.assertEqual(cr.get("custom", "hasbackslash"), R'"foo\\bar"')
+        self.assertEqual(cr.get("custom", "hasquote"), R'"ab\"cd"')
+        self.assertEqual(cr.get("custom", "hastrailingbackslash"), R'"word\\"')
+        self.assertEqual(cr.get("custom", "hasunrecognized"), R'"p\qrs"')
+
+        # It is less obvious whether and what to eventually do with this.
+        self.assertEqual(cr.get("custom", "hasunescapedquotes"), '"ab"cd"e"')
+
+        # Cases where quote removal is clearly safe should happen even after those.
+        self.assertEqual(cr.get("custom", "ordinary"), "hello world")
+
+        # Cases without quotes should still parse correctly even after those, too.
+        self.assertEqual(cr.get("custom", "unquoted"), "good evening")
+
     def test_get_values_works_without_requiring_any_other_calls_first(self):
         file_obj = self._to_memcache(fixture_path("git_config_multiple"))
         cr = GitConfigParser(file_obj, read_only=True)
diff --git a/test/test_diff.py b/test/test_diff.py
index 928a9f428..612fbd9e0 100644
--- a/test/test_diff.py
+++ b/test/test_diff.py
@@ -529,3 +529,22 @@ def test_diff_patch_with_external_engine(self, rw_dir):
         self.assertEqual(len(index_against_head), 1)
         index_against_working_tree = repo.index.diff(None, create_patch=True)
         self.assertEqual(len(index_against_working_tree), 1)
+
+    @with_rw_directory
+    def test_beginning_space(self, rw_dir):
+        # Create a file beginning by a whitespace
+        repo = Repo.init(rw_dir)
+        file = osp.join(rw_dir, " file.txt")
+        with open(file, "w") as f:
+            f.write("hello world")
+        repo.git.add(Git.polish_url(file))
+        repo.index.commit("first commit")
+
+        # Diff the commit with an empty tree
+        # and check the paths
+        diff_index = repo.head.commit.diff(NULL_TREE)
+        d = diff_index[0]
+        a_path = d.a_path
+        b_path = d.b_path
+        self.assertEqual(a_path, " file.txt")
+        self.assertEqual(b_path, " file.txt")
diff --git a/test/test_docs.py b/test/test_docs.py
index b3547c1de..cc0bbf26a 100644
--- a/test/test_docs.py
+++ b/test/test_docs.py
@@ -469,11 +469,11 @@ def test_references_and_objects(self, rw_dir):
         # ![30-test_references_and_objects]
 
         # [31-test_references_and_objects]
-        git = repo.git
-        git.checkout("HEAD", b="my_new_branch")  # Create a new branch.
-        git.branch("another-new-one")
-        git.branch("-D", "another-new-one")  # Pass strings for full control over argument order.
-        git.for_each_ref()  # '-' becomes '_' when calling it.
+        git_cmd = repo.git
+        git_cmd.checkout("HEAD", b="my_new_branch")  # Create a new branch.
+        git_cmd.branch("another-new-one")
+        git_cmd.branch("-D", "another-new-one")  # Pass strings for full control over argument order.
+        git_cmd.for_each_ref()  # '-' becomes '_' when calling it.
         # ![31-test_references_and_objects]
 
         repo.git.clear_cache()
diff --git a/test/test_exc.py b/test/test_exc.py
index c1eae7240..2e979f5a1 100644
--- a/test/test_exc.py
+++ b/test/test_exc.py
@@ -52,7 +52,7 @@
 
 _streams_n_substrings = (
     None,
-    "steram",
+    "stream",
     "ομορφο stream",
 )
 
diff --git a/test/test_fun.py b/test/test_fun.py
index b8593b400..a456b8aab 100644
--- a/test/test_fun.py
+++ b/test/test_fun.py
@@ -243,6 +243,7 @@ def test_tree_traversal(self):
         B_old = self.rorepo.tree("1f66cfbbce58b4b552b041707a12d437cc5f400a")  # old base tree
 
         # Two very different trees.
+
         entries = traverse_trees_recursive(odb, [B_old.binsha, H.binsha], "")
         self._assert_tree_entries(entries, 2)
 
@@ -251,7 +252,10 @@ def test_tree_traversal(self):
         self._assert_tree_entries(oentries, 2)
 
         # Single tree.
-        is_no_tree = lambda i, d: i.type != "tree"
+
+        def is_no_tree(i, _d):
+            return i.type != "tree"
+
         entries = traverse_trees_recursive(odb, [B.binsha], "")
         assert len(entries) == len(list(B.traverse(predicate=is_no_tree)))
         self._assert_tree_entries(entries, 1)
diff --git a/test/test_git.py b/test/test_git.py
index 94e68ecf0..4a54d0d9b 100644
--- a/test/test_git.py
+++ b/test/test_git.py
@@ -747,7 +747,7 @@ def test_environment(self, rw_dir):
 
         path = osp.join(rw_dir, "failing-script.sh")
         with open(path, "wt") as stream:
-            stream.write("#!/usr/bin/env sh\n" "echo FOO\n")
+            stream.write("#!/usr/bin/env sh\necho FOO\n")
         os.chmod(path, 0o777)
 
         rw_repo = Repo.init(osp.join(rw_dir, "repo"))
@@ -762,17 +762,18 @@ def test_environment(self, rw_dir):
     def test_handle_process_output(self):
         from git.cmd import handle_process_output, safer_popen
 
-        line_count = 5002
-        count = [None, 0, 0]
+        expected_line_count = 5002
+        actual_lines = [None, [], []]
 
-        def counter_stdout(line):
-            count[1] += 1
+        def stdout_handler(line):
+            actual_lines[1].append(line)
 
-        def counter_stderr(line):
-            count[2] += 1
+        def stderr_handler(line):
+            actual_lines[2].append(line)
 
         cmdline = [
             sys.executable,
+            "-S",  # Keep any `CoverageWarning` messages out of the subprocess stderr.
             fixture_path("cat_file.py"),
             str(fixture_path("issue-301_stderr")),
         ]
@@ -784,10 +785,10 @@ def counter_stderr(line):
             shell=False,
         )
 
-        handle_process_output(proc, counter_stdout, counter_stderr, finalize_process)
+        handle_process_output(proc, stdout_handler, stderr_handler, finalize_process)
 
-        self.assertEqual(count[1], line_count)
-        self.assertEqual(count[2], line_count)
+        self.assertEqual(len(actual_lines[1]), expected_line_count, repr(actual_lines[1]))
+        self.assertEqual(len(actual_lines[2]), expected_line_count, repr(actual_lines[2]))
 
     def test_execute_kwargs_set_agrees_with_method(self):
         parameter_names = inspect.signature(cmd.Git.execute).parameters.keys()
diff --git a/test/test_index.py b/test/test_index.py
index b92258c92..33490f907 100644
--- a/test/test_index.py
+++ b/test/test_index.py
@@ -16,6 +16,7 @@
 import subprocess
 import sys
 import tempfile
+from unittest import mock
 
 from gitdb.base import IStream
 
@@ -36,14 +37,7 @@
 from git.objects import Blob
 from git.util import Actor, cwd, hex_to_bin, rmtree
 
-from test.lib import (
-    TestBase,
-    VirtualEnvironment,
-    fixture,
-    fixture_path,
-    with_rw_directory,
-    with_rw_repo,
-)
+from test.lib import TestBase, VirtualEnvironment, fixture, fixture_path, with_rw_directory, with_rw_repo, PathLikeMock
 
 HOOKS_SHEBANG = "#!/usr/bin/env sh\n"
 
@@ -329,7 +323,10 @@ def test_index_file_from_tree(self, rw_repo):
         assert len([e for e in three_way_index.entries.values() if e.stage != 0])
 
         # ITERATE BLOBS
-        merge_required = lambda t: t[0] != 0
+
+        def merge_required(t):
+            return t[0] != 0
+
         merge_blobs = list(three_way_index.iter_blobs(merge_required))
         assert merge_blobs
         assert merge_blobs[0][0] in (1, 2, 3)
@@ -583,11 +580,15 @@ def mixed_iterator():
                     yield entry.path
                 elif type_id == 1:  # path (PathLike)
                     yield Path(entry.path)
-                elif type_id == 2:  # blob
+                elif type_id == 2:  # path mock (PathLike)
+                    yield PathLikeMock(entry.path)
+                elif type_id == 3:  # path mock in a blob
                     yield Blob(rw_repo, entry.binsha, entry.mode, entry.path)
-                elif type_id == 3:  # BaseIndexEntry
+                elif type_id == 4:  # blob
+                    yield Blob(rw_repo, entry.binsha, entry.mode, entry.path)
+                elif type_id == 5:  # BaseIndexEntry
                     yield BaseIndexEntry(entry[:4])
-                elif type_id == 4:  # IndexEntry
+                elif type_id == 6:  # IndexEntry
                     yield entry
                 else:
                     raise AssertionError("Invalid Type")
@@ -1015,10 +1016,31 @@ class Mocked:
         rel = index._to_relative_path(path)
         self.assertEqual(rel, os.path.relpath(path, root))
 
+    def test__to_relative_path_absolute_trailing_slash(self):
+        repo_root = os.path.join(osp.abspath(os.sep), "directory1", "repo_root")
+
+        class Mocked:
+            bare = False
+            git_dir = repo_root
+            working_tree_dir = repo_root
+
+        repo = Mocked()
+        path = os.path.join(repo_root, f"directory2{os.sep}")
+        index = IndexFile(repo)
+
+        expected_path = f"directory2{os.sep}"
+        actual_path = index._to_relative_path(path)
+        self.assertEqual(expected_path, actual_path)
+
+        with mock.patch("git.index.base.os.path") as ospath_mock:
+            ospath_mock.relpath.return_value = f"directory2{os.sep}"
+            actual_path = index._to_relative_path(path)
+            self.assertEqual(expected_path, actual_path)
+
     @pytest.mark.xfail(
         type(_win_bash_status) is WinBashStatus.Absent,
         reason="Can't run a hook on Windows without bash.exe.",
-        rasies=HookExecutionError,
+        raises=HookExecutionError,
     )
     @pytest.mark.xfail(
         type(_win_bash_status) is WinBashStatus.WslNoDistro,
@@ -1077,7 +1099,7 @@ def test_hook_uses_shell_not_from_cwd(self, rw_dir, case):
     @pytest.mark.xfail(
         type(_win_bash_status) is WinBashStatus.Absent,
         reason="Can't run a hook on Windows without bash.exe.",
-        rasies=HookExecutionError,
+        raises=HookExecutionError,
     )
     @pytest.mark.xfail(
         type(_win_bash_status) is WinBashStatus.WslNoDistro,
@@ -1120,7 +1142,7 @@ def test_pre_commit_hook_fail(self, rw_repo):
     @pytest.mark.xfail(
         type(_win_bash_status) is WinBashStatus.Absent,
         reason="Can't run a hook on Windows without bash.exe.",
-        rasies=HookExecutionError,
+        raises=HookExecutionError,
     )
     @pytest.mark.xfail(
         type(_win_bash_status) is WinBashStatus.Wsl,
@@ -1173,7 +1195,7 @@ def test_commit_msg_hook_fail(self, rw_repo):
             raise AssertionError("Should have caught a HookExecutionError")
 
     @with_rw_repo("HEAD")
-    def test_index_add_pathlike(self, rw_repo):
+    def test_index_add_pathlib(self, rw_repo):
         git_dir = Path(rw_repo.git_dir)
 
         file = git_dir / "file.txt"
@@ -1181,6 +1203,69 @@ def test_index_add_pathlike(self, rw_repo):
 
         rw_repo.index.add(file)
 
+    @with_rw_repo("HEAD")
+    def test_index_add_pathlike(self, rw_repo):
+        git_dir = Path(rw_repo.git_dir)
+
+        file = git_dir / "file.txt"
+        file.touch()
+
+        rw_repo.index.add(PathLikeMock(str(file)))
+
+    @with_rw_repo("HEAD")
+    def test_index_add_non_normalized_path(self, rw_repo):
+        git_dir = Path(rw_repo.git_dir)
+
+        file = git_dir / "file.txt"
+        file.touch()
+        non_normalized_path = file.as_posix()
+        if os.name != "nt":
+            non_normalized_path = "/" + non_normalized_path[1:].replace("/", "//")
+
+        rw_repo.index.add(non_normalized_path)
+
+    def test_index_file_v3(self):
+        index = IndexFile(self.rorepo, fixture_path("index_extended_flags"))
+        assert index.entries
+        assert index.version == 3
+        assert len(index.entries) == 4
+        assert index.entries[("init.t", 0)].skip_worktree
+
+        # Write the data - it must match the original.
+        with tempfile.NamedTemporaryFile() as tmpfile:
+            index.write(tmpfile.name)
+            assert Path(tmpfile.name).read_bytes() == Path(fixture_path("index_extended_flags")).read_bytes()
+
+    @with_rw_directory
+    def test_index_file_v3_with_git_command(self, tmp_dir):
+        tmp_dir = Path(tmp_dir)
+        with cwd(tmp_dir):
+            git = Git(tmp_dir)
+            git.init()
+
+            file = tmp_dir / "file.txt"
+            file.write_text("hello")
+            git.add("--intent-to-add", "file.txt")  # intent-to-add sets extended flag
+
+            repo = Repo(tmp_dir)
+            index = repo.index
+
+            assert len(index.entries) == 1
+            assert index.version == 3
+            entry = list(index.entries.values())[0]
+            assert entry.path == "file.txt"
+            assert entry.intent_to_add
+
+            file2 = tmp_dir / "file2.txt"
+            file2.write_text("world")
+            index.add(["file2.txt"])
+            index.write()
+
+            status_str = git.status(porcelain=True)
+            status_lines = status_str.splitlines()
+            assert " A file.txt" in status_lines
+            assert "A  file2.txt" in status_lines
+
 
 class TestIndexUtils:
     @pytest.mark.parametrize("file_path_type", [str, Path])
diff --git a/test/test_installation.py b/test/test_installation.py
index ae6472e98..7c82bd403 100644
--- a/test/test_installation.py
+++ b/test/test_installation.py
@@ -2,6 +2,7 @@
 # 3-Clause BSD License: https://opensource.org/license/bsd-3-clause/
 
 import ast
+import functools
 import os
 import subprocess
 
@@ -11,50 +12,22 @@
 class TestInstallation(TestBase):
     @with_rw_directory
     def test_installation(self, rw_dir):
-        venv = self._set_up_venv(rw_dir)
+        venv, run = self._set_up_venv(rw_dir)
 
-        result = subprocess.run(
-            [venv.pip, "install", "."],
-            stdout=subprocess.PIPE,
-            cwd=venv.sources,
-        )
-        self.assertEqual(
-            0,
-            result.returncode,
-            msg=result.stderr or result.stdout or "Can't install project",
-        )
+        result = run([venv.pip, "install", "."])
+        self._check_result(result, "Can't install project")
 
-        result = subprocess.run(
-            [venv.python, "-c", "import git"],
-            stdout=subprocess.PIPE,
-            cwd=venv.sources,
-        )
-        self.assertEqual(
-            0,
-            result.returncode,
-            msg=result.stderr or result.stdout or "Self-test failed",
-        )
+        result = run([venv.python, "-c", "import git"])
+        self._check_result(result, "Self-test failed")
 
-        result = subprocess.run(
-            [venv.python, "-c", "import gitdb; import smmap"],
-            stdout=subprocess.PIPE,
-            cwd=venv.sources,
-        )
-        self.assertEqual(
-            0,
-            result.returncode,
-            msg=result.stderr or result.stdout or "Dependencies not installed",
-        )
+        result = run([venv.python, "-c", "import gitdb; import smmap"])
+        self._check_result(result, "Dependencies not installed")
 
         # Even IF gitdb or any other dependency is supplied during development by
         # inserting its location into PYTHONPATH or otherwise patched into sys.path,
         # make sure it is not wrongly inserted as the *first* entry.
-        result = subprocess.run(
-            [venv.python, "-c", "import sys; import git; print(sys.path)"],
-            stdout=subprocess.PIPE,
-            cwd=venv.sources,
-        )
-        syspath = result.stdout.decode("utf-8").splitlines()[0]
+        result = run([venv.python, "-c", "import sys; import git; print(sys.path)"])
+        syspath = result.stdout.splitlines()[0]
         syspath = ast.literal_eval(syspath)
         self.assertEqual(
             "",
@@ -64,10 +37,37 @@ def test_installation(self, rw_dir):
 
     @staticmethod
     def _set_up_venv(rw_dir):
+        # Initialize the virtual environment.
         venv = VirtualEnvironment(rw_dir, with_pip=True)
+
+        # Make its src directory a symlink to our own top-level source tree.
         os.symlink(
             os.path.dirname(os.path.dirname(__file__)),
             venv.sources,
             target_is_directory=True,
         )
-        return venv
+
+        # Create a convenience function to run commands in it.
+        run = functools.partial(
+            subprocess.run,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+            universal_newlines=True,
+            cwd=venv.sources,
+            env={**os.environ, "PYTHONWARNINGS": "error"},
+        )
+
+        return venv, run
+
+    def _check_result(self, result, failure_summary):
+        self.assertEqual(
+            0,
+            result.returncode,
+            msg=self._prepare_failure_message(result, failure_summary),
+        )
+
+    @staticmethod
+    def _prepare_failure_message(result, failure_summary):
+        stdout = result.stdout.rstrip()
+        stderr = result.stderr.rstrip()
+        return f"{failure_summary}\n\nstdout:\n{stdout}\n\nstderr:\n{stderr}"
diff --git a/test/test_quick_doc.py b/test/test_quick_doc.py
index 4ef75f4aa..98658e02f 100644
--- a/test/test_quick_doc.py
+++ b/test/test_quick_doc.py
@@ -173,7 +173,7 @@ def test_cloned_repo_object(self, local_dir):
         # [15-test_cloned_repo_object]
         def print_files_from_git(root, level=0):
             for entry in root:
-                print(f'{"-" * 4 * level}| {entry.path}, {entry.type}')
+                print(f"{'-' * 4 * level}| {entry.path}, {entry.type}")
                 if entry.type == "tree":
                     print_files_from_git(entry, level + 1)
 
diff --git a/test/test_refs.py b/test/test_refs.py
index 08096e69e..329515807 100644
--- a/test/test_refs.py
+++ b/test/test_refs.py
@@ -25,7 +25,7 @@
 import git.refs as refs
 from git.util import Actor
 
-from test.lib import TestBase, with_rw_repo
+from test.lib import TestBase, with_rw_repo, PathLikeMock
 
 
 class TestRefs(TestBase):
@@ -43,6 +43,25 @@ def test_from_path(self):
         self.assertRaises(ValueError, TagReference, self.rorepo, "refs/invalid/tag")
         # Works without path check.
         TagReference(self.rorepo, "refs/invalid/tag", check_path=False)
+        # Check remoteness
+        assert Reference(self.rorepo, "refs/remotes/origin").is_remote()
+
+    def test_from_pathlike(self):
+        # Should be able to create any reference directly.
+        for ref_type in (Reference, Head, TagReference, RemoteReference):
+            for name in ("rela_name", "path/rela_name"):
+                full_path = ref_type.to_full_path(PathLikeMock(name))
+                instance = ref_type.from_path(self.rorepo, PathLikeMock(full_path))
+                assert isinstance(instance, ref_type)
+            # END for each name
+        # END for each type
+
+        # Invalid path.
+        self.assertRaises(ValueError, TagReference, self.rorepo, "refs/invalid/tag")
+        # Works without path check.
+        TagReference(self.rorepo, PathLikeMock("refs/invalid/tag"), check_path=False)
+        # Check remoteness
+        assert Reference(self.rorepo, PathLikeMock("refs/remotes/origin")).is_remote()
 
     def test_tag_base(self):
         tag_object_refs = []
diff --git a/test/test_remote.py b/test/test_remote.py
index 5ddb41bc0..b1d686f05 100644
--- a/test/test_remote.py
+++ b/test/test_remote.py
@@ -44,7 +44,7 @@
 class TestRemoteProgress(RemoteProgress):
     __slots__ = ("_seen_lines", "_stages_per_op", "_num_progress_messages")
 
-    def __init__(self):
+    def __init__(self) -> None:
         super().__init__()
         self._seen_lines = []
         self._stages_per_op = {}
@@ -103,6 +103,9 @@ def assert_received_message(self):
         assert self._num_progress_messages
 
 
+TestRemoteProgress.__test__ = False  # type: ignore
+
+
 class TestRemote(TestBase):
     def tearDown(self):
         gc.collect()
diff --git a/test/test_repo.py b/test/test_repo.py
index e38da5bb6..2a92c2523 100644
--- a/test/test_repo.py
+++ b/test/test_repo.py
@@ -14,7 +14,8 @@
 import pickle
 import sys
 import tempfile
-from unittest import mock, skip
+from unittest import mock
+from pathlib import Path
 
 import pytest
 
@@ -36,11 +37,11 @@
     Submodule,
     Tree,
 )
-from git.exc import BadObject, UnsafeOptionError, UnsafeProtocolError
+from git.exc import BadObject
 from git.repo.fun import touch
 from git.util import bin_to_hex, cwd, cygpath, join_path_native, rmfile, rmtree
 
-from test.lib import TestBase, fixture, with_rw_directory, with_rw_repo
+from test.lib import TestBase, fixture, with_rw_directory, with_rw_repo, PathLikeMock
 
 
 def iter_flatten(lol):
@@ -105,6 +106,11 @@ def test_repo_creation_pathlib(self, rw_repo):
         r_from_gitdir = Repo(pathlib.Path(rw_repo.git_dir))
         self.assertEqual(r_from_gitdir.git_dir, rw_repo.git_dir)
 
+    @with_rw_repo("0.3.2.1")
+    def test_repo_creation_pathlike(self, rw_repo):
+        r_from_gitdir = Repo(PathLikeMock(rw_repo.git_dir))
+        self.assertEqual(r_from_gitdir.git_dir, rw_repo.git_dir)
+
     def test_description(self):
         txt = "Test repository"
         self.rorepo.description = txt
@@ -214,285 +220,6 @@ def test_date_format(self, rw_dir):
         # @-timestamp is the format used by git commit hooks.
         repo.index.commit("Commit messages", commit_date="@1400000000 +0000")
 
-    @with_rw_directory
-    def test_clone_from_pathlib(self, rw_dir):
-        original_repo = Repo.init(osp.join(rw_dir, "repo"))
-
-        Repo.clone_from(original_repo.git_dir, pathlib.Path(rw_dir) / "clone_pathlib")
-
-    @with_rw_directory
-    def test_clone_from_pathlib_withConfig(self, rw_dir):
-        original_repo = Repo.init(osp.join(rw_dir, "repo"))
-
-        cloned = Repo.clone_from(
-            original_repo.git_dir,
-            pathlib.Path(rw_dir) / "clone_pathlib_withConfig",
-            multi_options=[
-                "--recurse-submodules=repo",
-                "--config core.filemode=false",
-                "--config submodule.repo.update=checkout",
-                "--config filter.lfs.clean='git-lfs clean -- %f'",
-            ],
-            allow_unsafe_options=True,
-        )
-
-        self.assertEqual(cloned.config_reader().get_value("submodule", "active"), "repo")
-        self.assertEqual(cloned.config_reader().get_value("core", "filemode"), False)
-        self.assertEqual(cloned.config_reader().get_value('submodule "repo"', "update"), "checkout")
-        self.assertEqual(
-            cloned.config_reader().get_value('filter "lfs"', "clean"),
-            "git-lfs clean -- %f",
-        )
-
-    def test_clone_from_with_path_contains_unicode(self):
-        with tempfile.TemporaryDirectory() as tmpdir:
-            unicode_dir_name = "\u0394"
-            path_with_unicode = os.path.join(tmpdir, unicode_dir_name)
-            os.makedirs(path_with_unicode)
-
-            try:
-                Repo.clone_from(
-                    url=self._small_repo_url(),
-                    to_path=path_with_unicode,
-                )
-            except UnicodeEncodeError:
-                self.fail("Raised UnicodeEncodeError")
-
-    @with_rw_directory
-    @skip(
-        """The referenced repository was removed, and one needs to set up a new
-        password controlled repo under the org's control."""
-    )
-    def test_leaking_password_in_clone_logs(self, rw_dir):
-        password = "fakepassword1234"
-        try:
-            Repo.clone_from(
-                url="https://fakeuser:{}@fakerepo.example.com/testrepo".format(password),
-                to_path=rw_dir,
-            )
-        except GitCommandError as err:
-            assert password not in str(err), "The error message '%s' should not contain the password" % err
-        # Working example from a blank private project.
-        Repo.clone_from(
-            url="https://gitlab+deploy-token-392045:mLWhVus7bjLsy8xj8q2V@gitlab.com/mercierm/test_git_python",
-            to_path=rw_dir,
-        )
-
-    @with_rw_repo("HEAD")
-    def test_clone_unsafe_options(self, rw_repo):
-        with tempfile.TemporaryDirectory() as tdir:
-            tmp_dir = pathlib.Path(tdir)
-            tmp_file = tmp_dir / "pwn"
-            unsafe_options = [
-                f"--upload-pack='touch {tmp_file}'",
-                f"-u 'touch {tmp_file}'",
-                "--config=protocol.ext.allow=always",
-                "-c protocol.ext.allow=always",
-            ]
-            for unsafe_option in unsafe_options:
-                with self.assertRaises(UnsafeOptionError):
-                    rw_repo.clone(tmp_dir, multi_options=[unsafe_option])
-                assert not tmp_file.exists()
-
-            unsafe_options = [
-                {"upload-pack": f"touch {tmp_file}"},
-                {"u": f"touch {tmp_file}"},
-                {"config": "protocol.ext.allow=always"},
-                {"c": "protocol.ext.allow=always"},
-            ]
-            for unsafe_option in unsafe_options:
-                with self.assertRaises(UnsafeOptionError):
-                    rw_repo.clone(tmp_dir, **unsafe_option)
-                assert not tmp_file.exists()
-
-    @pytest.mark.xfail(
-        sys.platform == "win32",
-        reason=(
-            "File not created. A separate Windows command may be needed. This and the "
-            "currently passing test test_clone_unsafe_options must be adjusted in the "
-            "same way. Until then, test_clone_unsafe_options is unreliable on Windows."
-        ),
-        raises=AssertionError,
-    )
-    @with_rw_repo("HEAD")
-    def test_clone_unsafe_options_allowed(self, rw_repo):
-        with tempfile.TemporaryDirectory() as tdir:
-            tmp_dir = pathlib.Path(tdir)
-            tmp_file = tmp_dir / "pwn"
-            unsafe_options = [
-                f"--upload-pack='touch {tmp_file}'",
-                f"-u 'touch {tmp_file}'",
-            ]
-            for i, unsafe_option in enumerate(unsafe_options):
-                destination = tmp_dir / str(i)
-                assert not tmp_file.exists()
-                # The options will be allowed, but the command will fail.
-                with self.assertRaises(GitCommandError):
-                    rw_repo.clone(destination, multi_options=[unsafe_option], allow_unsafe_options=True)
-                assert tmp_file.exists()
-                tmp_file.unlink()
-
-            unsafe_options = [
-                "--config=protocol.ext.allow=always",
-                "-c protocol.ext.allow=always",
-            ]
-            for i, unsafe_option in enumerate(unsafe_options):
-                destination = tmp_dir / str(i)
-                assert not destination.exists()
-                rw_repo.clone(destination, multi_options=[unsafe_option], allow_unsafe_options=True)
-                assert destination.exists()
-
-    @with_rw_repo("HEAD")
-    def test_clone_safe_options(self, rw_repo):
-        with tempfile.TemporaryDirectory() as tdir:
-            tmp_dir = pathlib.Path(tdir)
-            options = [
-                "--depth=1",
-                "--single-branch",
-                "-q",
-            ]
-            for option in options:
-                destination = tmp_dir / option
-                assert not destination.exists()
-                rw_repo.clone(destination, multi_options=[option])
-                assert destination.exists()
-
-    @with_rw_repo("HEAD")
-    def test_clone_from_unsafe_options(self, rw_repo):
-        with tempfile.TemporaryDirectory() as tdir:
-            tmp_dir = pathlib.Path(tdir)
-            tmp_file = tmp_dir / "pwn"
-            unsafe_options = [
-                f"--upload-pack='touch {tmp_file}'",
-                f"-u 'touch {tmp_file}'",
-                "--config=protocol.ext.allow=always",
-                "-c protocol.ext.allow=always",
-            ]
-            for unsafe_option in unsafe_options:
-                with self.assertRaises(UnsafeOptionError):
-                    Repo.clone_from(rw_repo.working_dir, tmp_dir, multi_options=[unsafe_option])
-                assert not tmp_file.exists()
-
-            unsafe_options = [
-                {"upload-pack": f"touch {tmp_file}"},
-                {"u": f"touch {tmp_file}"},
-                {"config": "protocol.ext.allow=always"},
-                {"c": "protocol.ext.allow=always"},
-            ]
-            for unsafe_option in unsafe_options:
-                with self.assertRaises(UnsafeOptionError):
-                    Repo.clone_from(rw_repo.working_dir, tmp_dir, **unsafe_option)
-                assert not tmp_file.exists()
-
-    @pytest.mark.xfail(
-        sys.platform == "win32",
-        reason=(
-            "File not created. A separate Windows command may be needed. This and the "
-            "currently passing test test_clone_from_unsafe_options must be adjusted in the "
-            "same way. Until then, test_clone_from_unsafe_options is unreliable on Windows."
-        ),
-        raises=AssertionError,
-    )
-    @with_rw_repo("HEAD")
-    def test_clone_from_unsafe_options_allowed(self, rw_repo):
-        with tempfile.TemporaryDirectory() as tdir:
-            tmp_dir = pathlib.Path(tdir)
-            tmp_file = tmp_dir / "pwn"
-            unsafe_options = [
-                f"--upload-pack='touch {tmp_file}'",
-                f"-u 'touch {tmp_file}'",
-            ]
-            for i, unsafe_option in enumerate(unsafe_options):
-                destination = tmp_dir / str(i)
-                assert not tmp_file.exists()
-                # The options will be allowed, but the command will fail.
-                with self.assertRaises(GitCommandError):
-                    Repo.clone_from(
-                        rw_repo.working_dir, destination, multi_options=[unsafe_option], allow_unsafe_options=True
-                    )
-                assert tmp_file.exists()
-                tmp_file.unlink()
-
-            unsafe_options = [
-                "--config=protocol.ext.allow=always",
-                "-c protocol.ext.allow=always",
-            ]
-            for i, unsafe_option in enumerate(unsafe_options):
-                destination = tmp_dir / str(i)
-                assert not destination.exists()
-                Repo.clone_from(
-                    rw_repo.working_dir, destination, multi_options=[unsafe_option], allow_unsafe_options=True
-                )
-                assert destination.exists()
-
-    @with_rw_repo("HEAD")
-    def test_clone_from_safe_options(self, rw_repo):
-        with tempfile.TemporaryDirectory() as tdir:
-            tmp_dir = pathlib.Path(tdir)
-            options = [
-                "--depth=1",
-                "--single-branch",
-                "-q",
-            ]
-            for option in options:
-                destination = tmp_dir / option
-                assert not destination.exists()
-                Repo.clone_from(rw_repo.common_dir, destination, multi_options=[option])
-                assert destination.exists()
-
-    def test_clone_from_unsafe_protocol(self):
-        with tempfile.TemporaryDirectory() as tdir:
-            tmp_dir = pathlib.Path(tdir)
-            tmp_file = tmp_dir / "pwn"
-            urls = [
-                f"ext::sh -c touch% {tmp_file}",
-                "fd::17/foo",
-            ]
-            for url in urls:
-                with self.assertRaises(UnsafeProtocolError):
-                    Repo.clone_from(url, tmp_dir / "repo")
-                assert not tmp_file.exists()
-
-    def test_clone_from_unsafe_protocol_allowed(self):
-        with tempfile.TemporaryDirectory() as tdir:
-            tmp_dir = pathlib.Path(tdir)
-            tmp_file = tmp_dir / "pwn"
-            urls = [
-                f"ext::sh -c touch% {tmp_file}",
-                "fd::/foo",
-            ]
-            for url in urls:
-                # The URL will be allowed into the command, but the command will
-                # fail since we don't have that protocol enabled in the Git config file.
-                with self.assertRaises(GitCommandError):
-                    Repo.clone_from(url, tmp_dir / "repo", allow_unsafe_protocols=True)
-                assert not tmp_file.exists()
-
-    def test_clone_from_unsafe_protocol_allowed_and_enabled(self):
-        with tempfile.TemporaryDirectory() as tdir:
-            tmp_dir = pathlib.Path(tdir)
-            tmp_file = tmp_dir / "pwn"
-            urls = [
-                f"ext::sh -c touch% {tmp_file}",
-            ]
-            allow_ext = [
-                "--config=protocol.ext.allow=always",
-            ]
-            for url in urls:
-                # The URL will be allowed into the command, and the protocol is enabled,
-                # but the command will fail since it can't read from the remote repo.
-                assert not tmp_file.exists()
-                with self.assertRaises(GitCommandError):
-                    Repo.clone_from(
-                        url,
-                        tmp_dir / "repo",
-                        multi_options=allow_ext,
-                        allow_unsafe_protocols=True,
-                        allow_unsafe_options=True,
-                    )
-                assert tmp_file.exists()
-                tmp_file.unlink()
-
     @with_rw_repo("HEAD")
     def test_max_chunk_size(self, repo):
         class TestOutputStream(TestBase):
@@ -643,6 +370,15 @@ def test_is_dirty_with_path(self, rwrepo):
         assert rwrepo.is_dirty(path="doc") is False
         assert rwrepo.is_dirty(untracked_files=True, path="doc") is True
 
+    @with_rw_repo("HEAD")
+    def test_is_dirty_with_pathlib_and_pathlike(self, rwrepo):
+        with open(osp.join(rwrepo.working_dir, "git", "util.py"), "at") as f:
+            f.write("junk")
+        assert rwrepo.is_dirty(path=Path("git")) is True
+        assert rwrepo.is_dirty(path=PathLikeMock("git")) is True
+        assert rwrepo.is_dirty(path=Path("doc")) is False
+        assert rwrepo.is_dirty(path=PathLikeMock("doc")) is False
+
     def test_head(self):
         self.assertEqual(self.rorepo.head.reference.object, self.rorepo.active_branch.object)
 
@@ -1064,9 +800,9 @@ def test_rev_parse(self):
         # TODO: Dereference tag into a blob 0.1.7^{blob} - quite a special one.
         # Needs a tag which points to a blob.
 
-        # ref^0 returns commit being pointed to, same with ref~0, and ^{}
+        # ref^0 returns commit being pointed to, same with ref~0, ^{}, and ^{commit}
         tag = rev_parse("0.1.4")
-        for token in ("~0", "^0", "^{}"):
+        for token in ("~0", "^0", "^{}", "^{commit}"):
             self.assertEqual(tag.object, rev_parse("0.1.4%s" % token))
         # END handle multiple tokens
 
diff --git a/test/test_stats.py b/test/test_stats.py
index eec73c802..91d2cf6ae 100644
--- a/test/test_stats.py
+++ b/test/test_stats.py
@@ -14,13 +14,19 @@ def test_list_from_string(self):
         output = fixture("diff_numstat").decode(defenc)
         stats = Stats._list_from_string(self.rorepo, output)
 
-        self.assertEqual(2, stats.total["files"])
-        self.assertEqual(52, stats.total["lines"])
-        self.assertEqual(29, stats.total["insertions"])
+        self.assertEqual(3, stats.total["files"])
+        self.assertEqual(59, stats.total["lines"])
+        self.assertEqual(36, stats.total["insertions"])
         self.assertEqual(23, stats.total["deletions"])
 
         self.assertEqual(29, stats.files["a.txt"]["insertions"])
         self.assertEqual(18, stats.files["a.txt"]["deletions"])
+        self.assertEqual("M", stats.files["a.txt"]["change_type"])
 
         self.assertEqual(0, stats.files["b.txt"]["insertions"])
         self.assertEqual(5, stats.files["b.txt"]["deletions"])
+        self.assertEqual("M", stats.files["b.txt"]["change_type"])
+
+        self.assertEqual(7, stats.files["c.txt"]["insertions"])
+        self.assertEqual(0, stats.files["c.txt"]["deletions"])
+        self.assertEqual("A", stats.files["c.txt"]["change_type"])
diff --git a/test/test_submodule.py b/test/test_submodule.py
index d88f9dab0..2bf0940c9 100644
--- a/test/test_submodule.py
+++ b/test/test_submodule.py
@@ -28,7 +28,7 @@
 from git.repo.fun import find_submodule_git_dir, touch
 from git.util import HIDE_WINDOWS_KNOWN_ERRORS, join_path_native, to_native_path_linux
 
-from test.lib import TestBase, with_rw_directory, with_rw_repo
+from test.lib import TestBase, with_rw_directory, with_rw_repo, PathLikeMock
 
 
 @contextlib.contextmanager
@@ -58,6 +58,7 @@ def update(self, op, cur_count, max_count, message=""):
         print(op, cur_count, max_count, message)
 
 
+TestRootProgress.__test__ = False
 prog = TestRootProgress()
 
 
@@ -174,6 +175,10 @@ def _do_base_tests(self, rwrepo):
             sma = Submodule.add(rwrepo, sm.name, sm.path)
             assert sma.path == sm.path
 
+            # Adding existing as pathlike
+            sma = Submodule.add(rwrepo, sm.name, PathLikeMock(sm.path))
+            assert sma.path == sm.path
+
             # No url and no module at path fails.
             self.assertRaises(ValueError, Submodule.add, rwrepo, "newsubm", "pathtorepo", url=None)
 
@@ -753,6 +758,22 @@ def test_add_empty_repo(self, rwdir):
             )
         # END for each checkout mode
 
+    @with_rw_directory
+    @_patch_git_config("protocol.file.allow", "always")
+    def test_update_submodule_with_relative_path(self, rwdir):
+        repo_path = osp.join(rwdir, "parent")
+        repo = git.Repo.init(repo_path)
+        module_repo_path = osp.join(rwdir, "module")
+        module_repo = git.Repo.init(module_repo_path)
+        module_repo.git.commit(m="test", allow_empty=True)
+        repo.git.submodule("add", "../module", "module")
+        repo.index.commit("add submodule")
+
+        cloned_repo_path = osp.join(rwdir, "cloned_repo")
+        cloned_repo = git.Repo.clone_from(repo_path, cloned_repo_path)
+
+        cloned_repo.submodule_update(init=True, recursive=True)
+
     @with_rw_directory
     @_patch_git_config("protocol.file.allow", "always")
     def test_list_only_valid_submodules(self, rwdir):
@@ -916,7 +937,7 @@ def assert_exists(sm, value=True):
         csm.repo.index.commit("Have to commit submodule change for algorithm to pick it up")
         assert csm.url == "bar"
 
-        self.assertRaises(
+        self.assertRaises(  # noqa: B017
             Exception,
             rsm.update,
             recursive=True,
@@ -1334,3 +1355,23 @@ def test_submodule_update_unsafe_options_allowed(self, rw_repo):
             for unsafe_option in unsafe_options:
                 with self.assertRaises(GitCommandError):
                     submodule.update(clone_multi_options=[unsafe_option], allow_unsafe_options=True)
+
+    @with_rw_directory
+    @_patch_git_config("protocol.file.allow", "always")
+    def test_submodule_update_relative_url(self, rwdir):
+        parent_path = osp.join(rwdir, "parent")
+        parent_repo = git.Repo.init(parent_path)
+        submodule_path = osp.join(rwdir, "module")
+        submodule_repo = git.Repo.init(submodule_path)
+        submodule_repo.git.commit(m="initial commit", allow_empty=True)
+
+        parent_repo.git.submodule("add", "../module", "module")
+        parent_repo.index.commit("add submodule with relative URL")
+
+        cloned_path = osp.join(rwdir, "cloned_repo")
+        cloned_repo = git.Repo.clone_from(parent_path, cloned_path)
+
+        cloned_repo.submodule_update(init=True, recursive=True)
+
+        has_module = any(sm.name == "module" for sm in cloned_repo.submodules)
+        assert has_module, "Relative submodule was not updated properly"
diff --git a/test/test_tree.py b/test/test_tree.py
index 73158113d..7ba93bd36 100644
--- a/test/test_tree.py
+++ b/test/test_tree.py
@@ -126,12 +126,18 @@ def test_traverse(self):
         assert len(list(root)) == len(list(root.traverse(depth=1)))
 
         # Only choose trees.
-        trees_only = lambda i, d: i.type == "tree"
+
+        def trees_only(i, _d):
+            return i.type == "tree"
+
         trees = list(root.traverse(predicate=trees_only))
         assert len(trees) == len([i for i in root.traverse() if trees_only(i, 0)])
 
         # Test prune.
-        lib_folder = lambda t, d: t.path == "lib"
+
+        def lib_folder(t, _d):
+            return t.path == "lib"
+
         pruned_trees = list(root.traverse(predicate=trees_only, prune=lib_folder))
         assert len(pruned_trees) < len(trees)
 
diff --git a/test/test_util.py b/test/test_util.py
index dad2f3dcd..000830f41 100644
--- a/test/test_util.py
+++ b/test/test_util.py
@@ -34,6 +34,7 @@
     LockFile,
     cygpath,
     decygpath,
+    is_cygwin_git,
     get_user_id,
     remove_password_if_present,
     rmtree,
@@ -349,6 +350,24 @@ def test_decygpath(self, wpath, cpath):
         assert wcpath == wpath.replace("/", "\\"), cpath
 
 
+class TestIsCygwinGit:
+    """Tests for :func:`is_cygwin_git`"""
+
+    def test_on_path_executable(self):
+        # Currently we assume tests run on Cygwin use Cygwin git. See #533 and #1455 for background.
+        if sys.platform == "cygwin":
+            assert is_cygwin_git("git")
+        else:
+            assert not is_cygwin_git("git")
+
+    def test_none_executable(self):
+        assert not is_cygwin_git(None)
+
+    def test_with_missing_uname(self):
+        """Test for handling when `uname` isn't in the same directory as `git`"""
+        assert not is_cygwin_git("/bogus_path/git")
+
+
 class _Member:
     """A member of an IterableList."""