Allow files to be ignored even if they are added to files to check.

[e42sh]

The ignore pattern is applied in the files to check loop, since it was
not possible to ignore a file that was already in the files to check
array.

For instance, I want all *.php files to be checked, except files with
*.ini.append.php extension.

This does not work, but it should:

phpcs -s --standard PEAR ./test.ini.append.php --ignore '.(ini.append.php)$'

Here is my config

PHPCS_IGNORE=".(ini.append.php)$"
PHPCS_FILE_PATTERN=".(php|phtml)$"