Fixer incorrectly handles filepaths with repeated dir names

[orx0r]

Fixer incorrectly handles filepath, e.g.:

For example, if filePath is /app/path/app/file.php and cwd is /app/, expected filepath should be path/app/file.php
But in fact, filepath became wrong - pathfile.php

Because str_replace replaces all occurrences in target filepath:
https://github.com/squizlabs/PHP_CodeSniffer/blob/master/CodeSniffer/Fixer.php#L246

$cwd      = getcwd().DIRECTORY_SEPARATOR;
$filename = str_replace($cwd, '', $filePath);

[orx0r]

PR: #1269