Fix the difference between adding files or a single file to the filter
Fix the difference between adding files or a single file to the filter

 * Add the check flag to check the existence of each added file
 * Use the addFile* method to add the file to reference the realpath of the file

baloo/pkg-php-code-coverage,tarlabs/php-code-coverage-fix,dnalini/PHP-CODE-Coverage,kelunik/php-code-coverage,theseer/php-code-coverage,sebastianbergmann/php-code-coverage,Koc/php-code-coverage,iFixit/php-code-coverage,bwoebi/php-code-coverage,sebastianbergmann/php-code-coverage,theseer/php-code-coverage,sebastianbergmann/php-code-coverage,tarlabs/php-code-coverage-fix,theseer/php-code-coverage,baloo/pkg-php-code-coverage