Move code into a scheduler class, part II

Moved all major functionalities, like adding audit/repair scripts,
the watchdog handler, etc to the engine class. There is still some
cleanup to do, like getting rid of some references to the globals
variables, which will come in part III, in progress.

Realized that we need full names to at least the audit.cfg and
repair.cfg files, removing all the cfg files from git, because
it makes the repo look ugly with usernames in them. Will add in
sample cfg files, even though they shouldn't really be created
manually.

Verified that the code is now in the same state as before we used
a scheduler class, ie no difference in expected behavior

Change-Id: If9eeb9201ac6dd30705c3246c304b304054dc577