Improve configuration for search paths  #6544

Parts of this question was already answered several times, so be patient when reading. :)
Our usual workspace structure is:

rootDir/:
    - project.vscode-workspace
    - sources/:
        - main.py
        - someSrcFile.py
        - ...
        - common/:
            - commFileOne.py
            - ...

Nothing unusual here.
Than, we have another folder with common python modules in remote location - this location is added by modules (inserting to sys.path). I will call this location remoteDir.

<some remote location>
remoteDir/:
    - remoteModule.py
    - ...

When running main.py from VS Code, we specify launch configuration with cwd changed to rootDir/sources. It runs OK, files from common and remoteDir are accessible (since sys.path is manually modified).

To implement autocomplete (either Intellisense Python Language Server or JEDI) and Pylint, this directories are not seen by default - .vscode-workspace file is not in sources folder. I am aware of PYTHONPATH variable in .env file - I added sources and remoteDir to PYTHONPATH variable and VS Code autocomplete and pylint works as expected.

The problem is that this PYTHONPATH variable affects the code and is bound to this IDE, which I don't like - one could easily develop code with VS Code (which has specified PYTHONPATH) and forget to handle sys.path, not knowing that the code now can't be executed without this IDE and it's .env settings.
Example: A newbie come to our department, take prepared VS Code workspace and create a new module in common folder, which must be executed also in standalone mode. In this module, he wants to use functions from remoteDir. Since PYTHONPATH is already set in .env, he doesn't know that he actually have to manually handle sys.path - autocomplete and pylint just works out of the box. Also, using VS Code, he can run main.py or his new script without problems. But, if he (or someone else) run this script from a command line: cd ./sources/common; python hisCommonFile.py, this will fail. Why - because nothing specify PYTHONPATH variable, and he doesn't have sys.path handled properly.

The question is: how to properly configure folder paths for autocomplete and pylint in VS Code, that wouldn't have any effect on how code is executed? I don't expect autocomplete and linter would interactively resolve modified sys.path - seems like there should be something similar to PYTHONPATH, but would be only applied to autocomplete/pylint VS Code tasks, not launch configurations.

Just for a clarification: I know this might be a silly example. Our case is a little more complex than described above, but the problem is somewhat simillar - I miss includeFolders=[] in both autocomplete and pylint settings section, or better, some common settings. autocomplete.extraPaths only solve problems for autocomplete (if it is working, last time I was checking It didn't work properly), not pylint - again, duplicated settings.