Change use_temporary_dir behavior with latexmk

Hi. 

Here's a proposed change to the `use_temporary_dir` behavior when using `latexmk`. The current framework fails when the tex file depends on other ones (via \input or \include). With the `-jobname` option in `latexmk` it works as expected. As a side effect, and since there is a dot in the default temp dir (`.latex-tmp`), a temporary `texmf.cnf` file is created to circunvent any `openout_any` problems.

Tested in OS X and Linux, should be OK for Windows, but I can't test that.