autoflake仅检测到未使用的导入/变量却不执行删除，且安装时触发externally-managed-environment错误的求助

我正在用autoflake工具清理Python文件里未使用的导入和变量，它明明检测到了这些内容，但就是不实际修改文件。

我执行的命令是：

autoflake --in-place --remove-unused-variables portal/reports.py

命令输出如下：

portal/reports.py: Unused imports/variables detected

尽管有这个明确的提示，目标文件却完全没有变化。我已经手动确认过，文件里确实存在应该被清理的未使用导入和变量。

环境版本信息 #

• Django: 5.0.7
• autoflake: 2.3.1
• Python: 3.11
• Ubuntu: 24.04

另外我还遇到一个安装相关的问题：当我在Django项目目录外关闭.venv虚拟环境，或者直接在系统全局环境下尝试安装autoflake时，会触发下面的错误：

error: externally-managed-environment

× This environment is externally managed
╰─> To install Python packages system-wide, try apt install
    python3-xyz, where xyz is the package you are trying to
    install.
    
    If you wish to install a non-Debian-packaged Python package,
    create a virtual environment using python3 -m venv path/to/venv.
    Then use path/to/venv/bin/python and path/to/venv/bin/pip. Make
    sure you have python3-full installed.
    
    If you wish to install a non-Debian packaged Python application,
    it may be easiest to use pipx install xyz, which will manage a
    virtual environment for you. Make sure you have pipx installed.
    
    See /usr/share/doc/python3.12/README.venv for more information.

note: If you believe this is a mistake, please contact your Python installation or OS distribution provider. You can override this, at the risk of breaking your Python installation or OS, by passing --break-system-packages.
hint: See PEP 668 for the detailed specification.

有没有人遇到过类似的问题？是什么原因导致的，我该怎么解决才能让autoflake正常清理文件，同时解决安装的报错？

备注：内容来源于stack exchange，提问作者Purushottam Nawale