For now, use the workaround Colomban recommended by changing the command to (all on one line):
>php -d error_reporting='E_ALL & ~(E_STRICT|E_DEPRECATED|E_NOTICE)' php_beautifier -s4 -l "..."
Or change it to (untested):
>php_beautifier -s4 -l "..." 2>/dev/null
Tried but without success: with the first string the selection is not changed nor there are error messages; with the second string I obtain the same error messages posted by me but, more, a last message as this: "Nov 28 20:28:54 php_beautifier [error] Can't match any file"