file_put_contents() strips the last line ending
If you really want an extra line ending at the end of a file when writing with file_put_contents(), you must append an extra PHP_EOL to the end of the line as follows.
<?php
$a_str = array("these","are","new","lines");
$contents = implode(PHP_EOL, $a_str);
$contents .= PHP_EOL . PHP_EOL;
file_put_contents("newfile.txt", $contents);
print("|$contents|");
?>
You can see that when you print $contents you get two extra line endings, but if you view the file newfile.txt, you only get one.
