extract package set loading and updating into a separate class

This commit extracts the loading/updating of package sets into
a separate Ops::Configuration class. The end goal is to move
all operations in this clearer area, in order to refactor the
CLI to use thor.

During this refactoring, the complexity of loading package sets
"minimally" or "completely", which is horribly fragile has been
removed. The package set load/update code properly loads package
set information when available and required, and does with minimal
information until then.

Moreover, the package set updating code has been updated to properly
update *before* resolving the imports, as well as loading init.rb
before the imports get resolved as well.
fix enumerator returned by Manifest#each_autobuild_file and Manifest#each_osdeps_file
bail earlier in CmdLine.initialize if the current root is not our root
minor fixes