Remove use of PreservesAll, cleanup dependencies (#1558)

Remove usages of the deprecated trait PreservesAll and use an explicit
false invalidates. Additionally, all phases are converted to be more
canonical in there specification of dependencies by:

  1. Overriding all default dependency implementations
  2. Using def instead of val

Signed-off-by: Schuyler Eldridge <schuyler.eldridge@ibm.com>