clean up concreteness detection

- Fixes bugs where concretization would fail due to an erroneously cached
  _concrete attribute.

- Ripped out a bunch of code in spec.py that isn't needed/valid anymore:
  - The various concrete() methods on different types of Specs would
    attempt to statically compute whether the Spec was concrete.
  - This dates back to when DAGs were simpler and there were no optional
    dependencies.  It's actually NOT possible to compute statically
    whether a Spec is concrete now.  The ONLY way you know is if it goes
    through concretization and is marked concrete once that completes.
  - This commit removes all simple concreteness checks and relies only on
    the _concrete attribute.  This should make thinking about
    concreteness simpler.

- Fixed a couple places where Specs need to be marked concrete explicitly.
  - Specs read from files and Specs that are destructively copied from
    concrete Specs now need to be marked concrete explicitly.
  - These spots may previously have "worked", but they were brittle and
    should be explcitly marked anyway.

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