>found by PHP and then you need to pass the full path to it (gettable in
>your terminal using `which php_beautifier`).

via terminal, this string give me the usual error messages but it works (it creates the test2.php file):

php -d error_reporting='E_ALL & ~(E_STRICT|E_DEPRECATED|E_NOTICE)' /usr/bin/php_beautifier -s4 -f /home/user/public_html/test.php -o /home/user/public_html/test2.php -l "ArrayNested() NewLines(before=if:switch:while:for:foreach:function:T_CLASS:return:break,after=T_COMMENT) IndentStyles(style=k&r)"


those two strings in Geany do not work and return the usual error messages:
/usr/bin/php_beautifier -s4 -l "ArrayNested() NewLines(before=if:switch:while:for:foreach:function:T_CLASS:return:break,after=T_COMMENT) IndentStyles(style=k&r)"
nor
php -d error_reporting='E_ALL & ~(E_STRICT|E_DEPRECATED|E_NOTICE)' /usr/bin/php_beautifier -s4 -l "ArrayNested() NewLines(before=if:switch:while:for:foreach:function:T_CLASS:return:break,after=T_COMMENT) IndentStyles(style=k&r)"