The test was not consistent, since first time it would use the svn file, which renames it... and on next run it would be missing!
I added the '.' to the unlik() step so it properly cleans up. Opened bug 29512 for the strange UploadStash behavior.
However, although it passes now most of the times, it sometimes fails with the strange exception:
Only variables should be passed by reference
phase3/includes/upload/UploadStash.php:143
phase3/tests/phpunit/includes/upload/UploadStashTest.php:22
phase3/tests/phpunit/MediaWikiTestCase.php:64
phase3/tests/phpunit/MediaWikiPHPUnitCommand.php:20
phase3/tests/phpunit/phpunit.php:60
Fixed this by relaxing the stash key regex. For some files MediaWiki is simply not able to guess an extension. If the wiki has been configured to allow them, we should just let them pass in the stash as well.