refactor RDD loading; explicitly load alignments

There’s really not a case where we are loading a generic Parquet file of
SpecificRecords whose type we don’t have a strong requirement about;
on the other hand, there is a case where we know what type we want
(AlignmentRecord) but don’t know which code path to read it in via (sam,
bam, ifq, fq, parquet, …).

Here I’ve made the caller explicitly specify if it wants
AlignmentRecords (which it was previously doing by labeling the return
value), but wants to benefit from the smarts around file-extension
inference.

Parquet reads with a known type can still go through one place so that
we can continue to benefit from that code not needing to be duplicated,
by only relying on SpecificRecord.
Merge pull request #468 from ryan-williams/loading

refactor RDD loading; explicitly load alignments
Switched to SparkFunSuite from bdg-utils, as part of #475.
Removed parquet and flat genotype code.
Removing migrated instrumentation.
Removing metrics work that has migrated to bdg-utils.
[ADAM-475] Removed code that has migrated to bdg-utils.