General cleanup of regression tests

Added .gitgnore and cleanup of a confout.part0002.gro file

Made a list of directories over which we can iterate, so we can avoid
forgetting to iterate over some directories. This also fixes the
refclean functionality.

Made warnings files a first-class citizen; versioned by precision,
cleaned with refclean.

Commented out reference to inactive tools directory

Change-Id: Ib728f8cd47eda7760d246c662cf9302f657eacbc