This bug still exists, and can be reproduced with the one liner:

touch index.php start.php; php -dauto_prepend_file=start.php -dxdebug.profiler_output_name=^Cachegrind.out.%s -dxdebug.profiler_enable=1 index.php

However, I don't see how I can figure our which script is the "auto prepend" script, or the normal script in PHP itself.

I couldn't reproduce this now (3 years after so might have been fixed):

--TEST--

Test for bug 0000407: Profilerdumpfile name is always auto_prepend_file name

--INI--

auto_prepend_file = C:\dev\git\php-7.3.3\ext\xdebug\tests\bug00407.prepend.php

xdebug.profiler_enable = 1

xdebug.profiler_output_dir = C:\dev\git\php-7.3.3\ext\xdebug\tests

xdebug.profiler_output_name = bug00407.cachegrind.%s.out

--FILE--

<?php

echo "\$prepended = $prepended\n";
--EXPECTF--

$prepended = yes

Gets 2 files:
bug00407.cachegrind.C__dev_git_php-7.3.3_ext_xdebug_tests_bug00407_php.out =

version: 1

creator: xdebug 2.7.3-dev (PHP 7.3.3)

cmd: C:\dev\git\php-7.3.3\ext\xdebug\tests\bug00407.php

part: 1

positions: line

events: Time Memory
fl=(2) C:\dev\git\php-7.3.3\ext\xdebug\tests\bug00407.php

fn=(1)
summary: 26 32
1 26 32

bug00407.cachegrind.C__dev_git_php-7.3.3_ext_xdebug_tests_bug00407.prepend_php.out =

version: 1

creator: xdebug 2.7.3-dev (PHP 7.3.3)

cmd: C:\dev\git\php-7.3.3\ext\xdebug\tests\bug00407.prepend.php

part: 1

positions: line

events: Time Memory
fl=(1) C:\dev\git\php-7.3.3\ext\xdebug\tests\bug00407.prepend.php

fn=(1) {main}
summary: 16 0
1 16 0

So, should this issue be closed? Do I need to commit the phpt? If so, I would like to know how to remove the two absolute paths I have in the phpt file (otherwise, it's gonna fail on everyone else's computer!)

Check whether this is now fixed.

This is still a problem, now with the reproducible new case:

touch /tmp/prepend.inc && touch /tmp/test.php && php -n -dzend_extension=xdebug -dxdebug.mode=profile -dauto_prepend_file=/tmp/prepend.inc -dxdebug.profiler_output_name=bug00407.cachegrind.%s.out /tmp/test.php