Add shading to the build system; removed hidden intelliJ stuff. Updated the ADAM parquet formats.

Crusher is now parameterized by the kind of record a tool takes. Projection is enabled and tools can define the fields they will look at
(see CountReads and ErrorRateByCycle).

Crusher now removes the void keys, so tools need only operate on RDD[RecordType]

DiagnoseTargets beautified.

ErrorRateByCycle tool added to compute mismatch error rates per cycle.

Known issues:
 - DiagnoseTargets does not stratify by sample
 - ErrorRateByCycle does not look at the CIGAR string - insertions will throw off the cycle accounting