Symfony version(s) affected: 4.1.3

Description
I'm using PHP-CS-Fixer. It's using symfony/finder to create files list, that should be fixed. Some of my projects not using src/ directory for source files, so I need to write some exclude rules. For example:

<?php
$finder = \PhpCsFixer\Finder::create()
    ->in(__DIR__)
    ->exclude('data')
    ->exclude('docker')
    ->exclude('frontend')
    ->exclude('common/emails')
    ->exclude('common/templates')
    ->notPath('#.*/runtime#')
    ->notPath('#.*/views#')
    ->notPath('autocompletion.php')
    ->exclude('tests/codeception/_output')
    ->notPath('#tests/codeception/.*/_output#')
    ->notPath('#tests/codeception/.*/_support/_generated#')
    ->name('yii');

return \Ely\CS\Config::create()
    ->setFinder($finder);

Rule ->exclude('data') applies on any directory, so it excluding some nested folders:

api
├── config
│   ├── bootstrap.php
│   ├── config.php
│   └── params.php
├── controllers
│   ├── Controller.php
│   └── SiteController.php
├── data
│   └── test.php
├── models
├── runtime
├── views
└── web
    ├── assets
    ├── favicon.ico
    └── robots.txt
data
├── ...

In my case, the file api/data/test.php will not be fixed.

It's also strange, that ->exlude('autocompletion.php') not working, but ->notPath('autocompletion.php') works fine.

How to reproduce
Just create alternative folders structure and you will get it.

Possible Solution

1. Make ->exclude() filter applying relatively to root folder, defined by ->in() method.
2. Allow using absolute paths Finder exclude not working as expected with absolute paths #25945
3. Document this behavior and add some workaround.