Merge from nonclausal-simplification-v2 branch:

Merge from nonclausal-simplification-v2 branch:

* Preprocessing-time, non-clausal, Boolean simplification round to
  support "quasi-non-linear rewrites" as discussed at last few meetings.

* --simplification=none is the default for now, but we'll probably
  change that to --simplification=incremental.  --simplification=batch
  is also a possibility.  See --simplification=help for details.

* RecursionBreaker<T> now uses a hash set for the seen trail.
* Fixes to TLS stuff to support that.
* Fixes to theory and SmtEngine documentation.
* Fixes to stream indentation.
* Other miscellaneous stuff.