Call to flake8 when using (mini)conda breaks the --format option #9481

Environment data

• VS Code version: 1.41.1
• Extension version (available under the Extensions sidebar): 2020.1.57204
• OS and version: Windows 10
• Python version (& distribution if applicable, e.g. Anaconda): 3.7.6 Anaconda
• Type of virtual environment used (N/A | venv | virtualenv | conda | ...): miniconda (conda 4.8.1)
• Relevant/affected Python packages and their versions: flake8 3.7.9
• Jedi or Language Server? (i.e. what is "python.jediEnabled" set to; more info How to update the language server to the latest stable version #3977): jedi

Expected behaviour

The flake8 output is formatted correctly using the supplied --format argument

Actual behaviour

The flake8 output is garbage (part of the format string and the path to the file to link). This happens any time I run flake8 with conda.exe run -n smsl even outside of VSCode. The --format argument gets messed up when calling it via conda run.

This is definitely a bug regarding conda and/or flake8 too. But....
The syntax of this call has changed apparently, IIRC it used to be calling the python executable for a given environment directly in previous versions of the extension.

Since the conda run --help doc says it's experimental, maybe it should not be used for this extension.

Steps to reproduce:

1. create a new conda environment with python 3.7.6
2. pip install flake8
3. choose this env as the python executable in VSCode
4. enable flake8 linting
5. lint a file that contains an error
6. observe the result in the output tab

Logs

Output for Python in the Output panel (View→Output, change the drop-down the upper-right of the Output panel to Python)

> ~\AppData\Local\Continuum\miniconda3\Scripts\conda.exe run -n smsl python -m flake8 --max-line-length=120 --exclude=__init__.py --format=%(row)d,%(col)d,%(code).1s,%(code)s:%(text)s c:\Users\...\Documents\folder\file.py
...
##########Linting Output - flake8##########
(col)d,(code)s:\Users\...\Documents\folder\file.py

As you can see, flake8 is invoked with conda run instead of just calling the python executable of the environment directly. For some reason this messes up the parsing of the --format by flake8.

After some investigating, I noticed this is the temporary .bat script that is generated by conda when running the command is:

@ECHO OFF
@SET PYTHONIOENCODING=utf-8
@SET PYTHONUTF8=1
@FOR /F "tokens=2 delims=:." %%A in ('chcp') do for %%B in (%%A) do set "_CONDA_OLD_CHCP=%%B"
@chcp 65001 > NUL
@CALL "C:\Users\...\AppData\Local\Continuum\miniconda3\condabin\conda.bat" activate "C:\Users\...\AppData\Local\Continuum\miniconda3\envs\smsl"
@IF %ERRORLEVEL% NEQ 0 EXIT /b %ERRORLEVEL%
@python -m flake8 --max-line-length=120 --exclude=__init__.py --format=%(row)d,%(col)d,%(code).1s,%(code)s:%(text)s C:\Users\...\Documents\folder\file.py
@IF %ERRORLEVEL% NEQ 0 EXIT /b %ERRORLEVEL%
@chcp %_CONDA_OLD_CHCP%>NUL

Since this is a batch script, the % character needs to be escaped (as %%).. Can the VSCode Python extension fix that by escaping this character while we wait that conda fixes it?