Different order in files passed from the command line produces different (and incorrect) output

[andreaTP]

Steps to reproduce

I prepared a minimal repro here:
https://github.com/andreaTP/pylint_order_bug

Current behavior

Cloning the example project and running:

python3 -m pylint test2/test3/test.py test2/test4/test.py test/__init__.py

R0801 (similarity) is reported on an incorrect file:

test/__init__.py:1:0: R0801: Similar lines in 2 files

Expected behavior

Cloning the example project and running:

python3 -m pylint test2/test3/test.py test2/test4/test.py test/__init__.py

produces the same result as:

python3 -m pylint test/__init__.py test2/test3/test.py test2/test4/test.py

Such as R0801 is reported on the correct file:

test2/test4/test.py:1:0: R0801: Similar lines in 2 files

pylint --version output

pylint 2.5.2
astroid 2.4.1
Python 3.6.9 (default, Apr 18 2020, 01:56:04) 
[GCC 8.4.0]

[Pierre-Sassoulas]

Seems somewhat similar to #4053

[Pierre-Sassoulas]

I'm going to close as a duplicate of #4053, the fix will probably be the same.