Ruff linter / fixer - Path to file in `--stdin-filename` not consistent

## Information

VIM - Vi IMproved 9.1 (2024 Jan 02, compiled Sep 25 2024 10:13:04)
Included patches: 1-16, 647, 678, 697

Operating System: Ubuntu 24.04

## What went wrong

I'm using `ruff` linter and fixer for python files.

I have a project where the linter detects errors and the fixer doesn't.

I suspect that the difference comes from the fact that the path to the file provided for `--stdin-filename` is different. It's an absolute path for the linter whereas it's a relative one for the fixer.

Here are the commands that ALE uses to run the linter and fixer (copied and simplified from ALEInfo and simplified):
``` shell
$ #linter
$ cd '/path/to/project/lib' && '/path/to/project/.venv/bin/ruff' check -q --no-fix --output-format json-lines --stdin-filename '/path/to/project/lib/file.py' - < '/tmp/vsQmWbc/15/file.py'
$ #fixer
$ cd '/path/to/project/lib' && '/path/to/project/.venv/bin/ruff' check --stdin-filename 'lib/file.py' --fix - < '/tmp/vsQmWbc/12/file.py'
```

Additional note : in our project, the structure of files may be a bit specific. We have 2 packages, each with its own `pyproject.toml` file. The configuration file for ruff is at the root of the project.

```
project
└─ruff.toml
└─lib
│ └─pyproject.toml
│ └─file.py
└─cli
└─pyproject.toml
└─file.py
```

It seems like given the path of the file (ie. relative), ruff doesn't use its configuration file. Also, I think the path is wrong: after the `cd` the path should actually be `file.py`, not `lib/file.py`.

### :ALEInfo

Expand
Current Filetype: python
Available Linters: ['bandit', 'cspell', 'flake8', 'flakehell', 'jedils', 'mypy', 'prospector', 'pycln', 'pycodestyle', 'pydocstyle', 'pyflakes', 'pylama', 'pylint', 'pylsp', 'pyre', 'pyright', 'refurb', 'ruff', 'unimport', 'vulture']
Linter Aliases:
'jedils' -> ['jedi_language_server']
Enabled Linters: ['mypy', 'ruff']
Ignored Linters: []
Suggested Fixers:
'add_blank_lines_for_python_control_statements' - Add blank lines before control statements.
'autoflake' - Fix flake issues with autoflake.
'autoimport' - Fix import issues with autoimport.
'autopep8' - Fix PEP8 issues with autopep8.
'black' - Fix PEP8 issues with black.
'isort' - Sort Python imports with isort.
'pycln' - remove unused python import statements
'pyflyby' - Tidy Python imports with pyflyby.
'remove_trailing_lines' - Remove all blank lines at the end of a file.
'reorder-python-imports' - Sort Python imports with reorder-python-imports.
'ruff' - A python linter/fixer for Python written in Rust
'ruff_format' - Fix python files with the ruff formatter.
'trim_whitespace' - Remove all trailing whitespace characters at the end of every line.
'yapf' - Fix Python files with yapf.

Linter Variables:
" Press Space to read :help for a setting
let g:ale_python_auto_pipenv = 0
let g:ale_python_auto_poetry = 0
let g:ale_python_auto_uv = 0
let g:ale_python_auto_virtualenv = 0
let g:ale_python_mypy_auto_pipenv = 0
let g:ale_python_mypy_auto_poetry = 0
let g:ale_python_mypy_auto_uv = 0
let g:ale_python_mypy_executable = 'mypy'
let g:ale_python_mypy_ignore_invalid_syntax = 0
let g:ale_python_mypy_options = ''
let b:ale_python_mypy_options = '--strict --ignore-missing-imports'
let g:ale_python_mypy_show_notes = 1
let g:ale_python_mypy_use_global = 0
let g:ale_python_ruff_auto_pipenv = 0
let g:ale_python_ruff_auto_poetry = 0
let g:ale_python_ruff_auto_uv = 0
let g:ale_python_ruff_change_directory = 1
let g:ale_python_ruff_executable = 'ruff'
let g:ale_python_ruff_format_auto_pipenv = 0
let g:ale_python_ruff_format_auto_poetry = 0
let g:ale_python_ruff_format_auto_uv = 0
let g:ale_python_ruff_format_change_directory = 1
let g:ale_python_ruff_format_executable = 'ruff'
let g:ale_python_ruff_format_options = ''
let g:ale_python_ruff_format_use_global = 0
let g:ale_python_ruff_options = ''
let g:ale_python_ruff_use_global = 0

Global Variables:
" Press Space to read :help for a setting
let g:ale_cache_executable_check_failures = v:null
let g:ale_change_sign_column_color = 0
let g:ale_command_wrapper = ''
let g:ale_completion_delay = v:null
let g:ale_completion_enabled = 0
let g:ale_completion_max_suggestions = v:null
let g:ale_disable_lsp = 'auto'
let g:ale_echo_cursor = 1
let g:ale_echo_msg_error_str = 'Error'
let g:ale_echo_msg_format = '%code: %%s'
let g:ale_echo_msg_info_str = 'Info'
let g:ale_echo_msg_warning_str = 'Warning'
let g:ale_enabled = 1
let g:ale_fix_on_save = 1
let g:ale_fixers = {'vue': ['prettier'], 'javascript': ['prettier']}
let b:ale_fixers = ['ruff', 'ruff_format']
let g:ale_history_enabled = 1
let g:ale_info_default_mode = 'preview'
let g:ale_history_log_output = 1
let g:ale_keep_list_window_open = 0
let g:ale_lint_delay = 200
let g:ale_lint_on_enter = 1
let g:ale_lint_on_filetype_changed = 1
let g:ale_lint_on_insert_leave = 1
let g:ale_lint_on_save = 1
let g:ale_lint_on_text_changed = 'normal'
let g:ale_linter_aliases = {}
let g:ale_linters = {}
let b:ale_linters = ['mypy', 'ruff']
let g:ale_linters_explicit = 0
let g:ale_linters_ignore = {}
let g:ale_list_vertical = 0
let g:ale_list_window_size = 10
let g:ale_loclist_msg_format = '%code: %%s'
let g:ale_max_buffer_history_size = 20
let g:ale_max_signs = -1
let g:ale_maximum_file_size = v:null
let g:ale_open_list = 0
let g:ale_pattern_options = v:null
let g:ale_pattern_options_enabled = v:null
let g:ale_root = {}
let g:ale_set_balloons = 0
let g:ale_set_highlights = 1
let g:ale_set_loclist = 1
let g:ale_set_quickfix = 0
let g:ale_set_signs = 1
let g:ale_sign_column_always = 0
let g:ale_sign_error = 'E'
let g:ale_sign_info = 'I'
let g:ale_sign_offset = 1000000
let g:ale_sign_style_error = 'E'
let g:ale_sign_style_warning = 'W'
let g:ale_sign_warning = 'W'
let g:ale_sign_highlight_linenrs = 0
let g:ale_type_map = {}
let g:ale_use_neovim_diagnostics_api = 0
let g:ale_use_global_executables = v:null
let g:ale_virtualtext_cursor = 'all'
let g:ale_warn_about_trailing_blank_lines = 1
let g:ale_warn_about_trailing_whitespace = 1

Command History:

(executable check - success) /home/pierre/work/pglift/.venv/bin/mypy
(finished - exit code 0) ['/bin/sh', '-c', 'cd ''/home/pierre/work/pglift'' && ''/home/pierre/work/pglift/.venv/bin/mypy'' --strict --ignore-missing-imports --show-column-numbers --shadow-file ''/home/pierre/work/pglift/cli/src/pglift_cli/__init__.py'' ''/tmp/v8TjPzN/2/__init__.py'' ''/home/pierre/work/pglift/cli/src/pglift_cli/__init__.py''']

<<>>
Success: no issues found in 1 source file
<<>>

(executable check - success) /home/pierre/work/pglift/.venv/bin/ruff
(finished - exit code 0) ['/bin/sh', '-c', 'cd ''/home/pierre/work/pglift/cli'' && ''/home/pierre/work/pglift/.venv/bin/ruff'' --version']

<<>>
ruff 0.7.1
<<>>

(finished - exit code 0) ['/bin/sh', '-c', 'cd ''/home/pierre/work/pglift/cli'' && ''/home/pierre/work/pglift/.venv/bin/ruff'' check -q --no-fix --output-format json-lines --stdin-filename ''/home/pierre/work/pglift/cli/src/pglift_cli/__init__.py'' - < ''/tmp/v8TjPzN/3/__init__.py''']

<<>>

(finished - exit code 0) ['/bin/sh', '-c', 'cd ''/home/pierre/work/pglift'' && ''/home/pierre/work/pglift/.venv/bin/mypy'' --strict --ignore-missing-imports --show-column-numbers --shadow-file ''/home/pierre/work/pglift/cli/src/pglift_cli/__init__.py'' ''/tmp/v8TjPzN/10/__init__.py'' ''/home/pierre/work/pglift/cli/src/pglift_cli/__init__.py''']

<<>>
Success: no issues found in 1 source file
<<>>

(finished - exit code 1) ['/bin/sh', '-c', 'cd ''/home/pierre/work/pglift/cli'' && ''/home/pierre/work/pglift/.venv/bin/ruff'' check -q --no-fix --output-format json-lines --stdin-filename ''/home/pierre/work/pglift/cli/src/pglift_cli/__init__.py'' - < ''/tmp/v8TjPzN/11/__init__.py''']

<<>>
{"cell":null,"code":"I001","end_location":{"column":1,"row":10},"filename":"/home/pierre/work/pglift/cli/src/pglift_cli/__init__.py","fix":{"applicability":"safe","edits":[{"content":"import logging\nimport os\n\nimport pluggy\n\n","end_location":{"column":1,"row":10},"location":{"column":1,"row":5}}],"message":"Organize imports"},"location":{"column":1,"row":5},"message":"Import block is un-sorted or un-formatted","noqa_row":5,"url":"https://docs.astral.sh/ruff/rules/unsorted-imports"}
<<>>

(finished - exit code 0) ['/bin/sh', '-c', 'cd ''/home/pierre/work/pglift/cli'' && ''/home/pierre/work/pglift/.venv/bin/ruff'' check --stdin-filename ''cli/src/pglift_cli/__init__.py'' --fix - < ''/tmp/v8TjPzN/12/__init__.py''']
(finished - exit code 0) ['/bin/sh', '-c', 'cd ''/home/pierre/work/pglift/cli'' && ''/home/pierre/work/pglift/.venv/bin/ruff'' format --stdin-filename ''cli/src/pglift_cli/__init__.py'' - < ''/tmp/v8TjPzN/13/__init__.py''']
(finished - exit code 0) ['/bin/sh', '-c', 'cd ''/home/pierre/work/pglift'' && ''/home/pierre/work/pglift/.venv/bin/mypy'' --strict --ignore-missing-imports --show-column-numbers --shadow-file ''/home/pierre/work/pglift/cli/src/pglift_cli/__init__.py'' ''/tmp/v8TjPzN/14/__init__.py'' ''/home/pierre/work/pglift/cli/src/pglift_cli/__init__.py''']

<<>>
Success: no issues found in 1 source file
<<>>

(finished - exit code 1) ['/bin/sh', '-c', 'cd ''/home/pierre/work/pglift/cli'' && ''/home/pierre/work/pglift/.venv/bin/ruff'' check -q --no-fix --output-format json-lines --stdin-filename ''/home/pierre/work/pglift/cli/src/pglift_cli/__init__.py'' - < ''/tmp/v8TjPzN/15/__init__.py''']

<<>>
{"cell":null,"code":"I001","end_location":{"column":1,"row":10},"filename":"/home/pierre/work/pglift/cli/src/pglift_cli/__init__.py","fix":{"applicability":"safe","edits":[{"content":"import logging\nimport os\n\nimport pluggy\n\n","end_location":{"column":1,"row":10},"location":{"column":1,"row":5}}],"message":"Organize imports"},"location":{"column":1,"row":5},"message":"Import block is un-sorted or un-formatted","noqa_row":5,"url":"https://docs.astral.sh/ruff/rules/unsorted-imports"}
<<>>