Improve tempfile hadling

[luxaritas]

A couple aspects of this:

1. It would be better to use python's builtin tempfile handling for temporary files and directories - this makes it less likely for there to be conflicts, will put it in a location on the system intended for tempfiles, and ensure tempfiles are cleaned up automatically
2. By setting the cwd of a subprocess to a tempdir it can avoid some packages creating temporary files in the current working directory that are never cleaned up (or could cause race conditions when running in parallel, like vienna's rna.ps)