This option *IS* settable within your PHP scripts.

Example:

<?php
  ini_set('auto_detect_line_endings', true);
  $contents = file('unknowntype.txt');

  ini_set('auto_detect_line_endings', false);
  $content2 = file('unixfile.txt');
?>

Note, with PHP 4.3 anytime Mac files are read using fgets or file you'll need to auto_detect_line_endings since \n is otherwise assumed.  However, with PHP 5.0, stream_get_line() will allow you to specify what line ending character to read up to.

\\ Read a line from a MAC file
stream_get_line($fp, 4096, "\r"); 

\\ Read a line from a UNIX file
stream_get_line($fp, 4096, "\n"); 

\\ Read a line from a DOS file
stream_get_line($fp, 4096, "\r\n"); 

\\ Read a line up to any filesystem line ending
ini_set('auto_detect_line_endings', true); fgets($fp); 

\\ You can also make up your own line ending characters:
\\ Read up to the first instance of ":"
stream_get_line($fp, 4096, ":"); 

Thanks - so maybe the docs should be updated to show that 
a) the settings are settable, the implication is that they can only be set in php.ini 
b) the stream_get_line alternative to fgets 

Oops - since this is OpenSource documentation, maybe I should do it ...... done

The documentation already shows it as being PHP_INI_ALL so why did you feel it implies otherwise?

http://www.php.net/manual/en/ref.filesystem.php

How is one supposed to deduce that PHP_INI_ALL means you can change it with "ini_set", if one doesn't know that function exists. There is nothing on the ref.filesystem page, nor any link from PHP_INI_ALL to something that explains what it means. (not intending to be critical, but as someone whose done a lot of PHP programming, and was explicitly looking for a programatic way to set this variable, I couldn't find it).

It is worth noting that:
ini_set('auto_detect_line_endings', true);
is only inspected and used by the stream when it reads the *first* line (via fgets).  Subsequent reads use the value it detect then.
This is only an issue if (for some strange reason!) you have a mixture of different line ending conventions in a file.

In other words, the ini setting is only inspected at the time the stream is opened via fopen() or fsockopen().