Why can't I find my uploaded file on disk?
You're just missing the third parameter for file_save_upload():


  $destination: A string containing the URI $source should be copied to. This must be a stream wrapper URI. If this value is omitted, Drupal's temporary files scheme will be used ("temporary://").


The uri in your table is temporary://download.jpg which seems to support that.

To save your file in the public file system you just need to pass that parameter in:

$destination = 'public://some/folder/';
$file = file_save_upload('myFile', $validators, $destination);