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This commit enables DRAT-optimization, which consists of two sub-processes:
1. removing unnecessary instructions from DRAT-proofs and
2. not proving clauses which are not needed by DRAT proofs.
These changes have the effect of dramatically shortening some some bit-vector proofs. Specifically, proofs using lemmas in the ER, DRAT, and LRAT formats, since proofs in any of these formats are derived from a (now optimized!) DRAT proof produced by CryptoMiniSat. What follows is a description of the main parts of this PR:
## DRAT Optimization
The DRAT-optimization is done by `drat-trim`, which is bundled with `drat2er`. The (new) function `ClausalBitVectorProof::optimizeDratProof` is our interface to the optimization machinery, and most of the new logic in this PR is in that function.
## CNF Representation
The ability to not prove unused clauses requires a slight architectural change as well. In particular, we need to be able to describe **which** subset of the original clause set actually needs to be proved. To facilitate this, when the clause set for CryptoMiniSat is first formed it is represented as a (a) map from clause indices to clauses and (b) a list of indices. Then, when the CNF is optimized, we temporarily store a new list of the clauses in the optimized formula. This change in representation requires a number of small tweaks throughout the code.
## Small Fixes to Signatures
When we decided to check and accept two different kinds of DRAT, some of our DRAT-checking broke. In particular, when supporting one kind of DRAT, it is okay to `fail` (crash) when a proof fails to check. If you're supporting two kinds of DRAT, crashing in response to the first checker rejecting the proof denies the second checker an opportunity to check the proof. This PR tweaks the signatures slightly (and soundly!) to do something else instead of `fail`ing.
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Creating LRAT proofs reuqires writing SAT problems in the DIMACS format.
Before this code was in the LRAT class.
However, since creating ER proofs will also require writing DIMACS, I
decided to extract it.
At the same time I realized that my prior representation of used clauses
was unnecessarily poor. I had chosen it to align with
`CnfProof::collectAtomsForClauses`, but the format is really bad (it
requires extra allocations & manual memory management), and I discovered
that the aforementioned method is super simple, so I'm moving to a
better format.
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