.coala taking priority over command-line arguments

[Seanny123]

I have created a repo to demonstrate this error:
https://github.com/Seanny123/coala-fail

Expected Behaviour

coala -f=cfail/check.py would only run bears on the file check.py.

Actual Behaviour

In .coala, the rule files=**.py takes priority over the command line argument -f=cfail/check.py. Thus, both check.py and ignore.py are checked.

Work-Around

Anytime I want to verify an individual file, I have to delete the files= line from .coala. This is a bit inconvenient and goes against my expectations.

In this intended behaviour or a bug?

[codehobbyist06]

Yes, I have reproduced this issue and it persists. What actually happens is coala first runs the settings given in the coafile and then the settings given by cli(I have checked this by running coala in debug mode). According to the coala documentation this is a bug because it says that,

Settings given in the project-wide coafile override all settings given by other files and can only be overridden by settings given via the command line interface

Can someone from coala maintainers pls tell how this issue can be resolved?
According to me, I first need to check the flow of programs to find the file that is responsible for this behaviour. Can someone help with this?