Remove unused classes following #5127.

[tomwhite]

• AddContextDataToReadSpark (and AddContextDataToReadSparkUnitTest) implemented the different JoinStrategy options for
  BQSR; has been replaced with the Spark Files mecahnism (see Use SparkFiles to localize reference and known sites #5127)
• BroadcastJoinReadsWithRefBases and JoinReadsWithRefBasesSparkUnitTest were only used by AddContextDataToReadSpark
• BroadcastJoinReadsWithVariants and JoinReadsWithVariantsSparkUnitTest were only used by AddContextDataToReadSpark
• ShuffleJoinReadsWithRefBases and ShuffleJoinReadsWithVariants were only used by AddContextDataToReadSpark
• JoinStrategy was only used for BQSR (HC always uses overlaps partitioner), but is no longer used since Use SparkFiles to localize reference and known sites #5127
• KnownSitesCache was replaced with Spark Files
• ReferenceMultiSourceAdapter in HaplotypeCallerSpark was replaced with the regular ReferenceDataSource
• BaseRecalibratorEngineSparkWrapper was only used by BaseRecalibratorSparkSharded, which was removed in Move/rename some stray Spark datasource classes, and delete BaseRecalibratorSparkSharded #5192

[codecov-io]

Codecov Report

Merging #5292 into master will decrease coverage by 0.04%.
The diff coverage is n/a.

@@             Coverage Diff              @@
##             master    #5292      +/-   ##
============================================
- Coverage     87.08%   87.04%   -0.05%     
+ Complexity    31522    31436      -86     
============================================
  Files          1930     1919      -11     
  Lines        145236   144942     -294     
  Branches      16096    16059      -37     
============================================
- Hits         126480   126163     -317     
- Misses        12903    12936      +33     
+ Partials       5853     5843      -10

Impacted Files	Coverage Δ	Complexity Δ
...der/tools/HaplotypeCallerSparkIntegrationTest.java	68.29% <ø> (ø)	16 <0> (ø)	⬇️
...stitute/hellbender/tools/HaplotypeCallerSpark.java	82.75% <ø> (ø)	20 <0> (ø)	⬇️
...spark/ReadsPreprocessingPipelineSparkTestData.java	0% <0%> (-94.03%)	0% <0%> (-11%)
...adinstitute/hellbender/engine/ReadContextData.java	0% <0%> (-70.38%)	0% <0%> (-6%)
...n/java/org/broadinstitute/hellbender/utils/KV.java	0% <0%> (-57.15%)	0% <0%> (-5%)
...ute/hellbender/utils/reference/ReferenceBases.java	38.46% <0%> (-19.24%)	4% <0%> (-2%)
...oadinstitute/hellbender/engine/ReferenceShard.java	62.5% <0%> (-18.75%)	6% <0%> (-1%)
...broadinstitute/hellbender/engine/VariantShard.java	63.63% <0%> (-13.64%)	7% <0%> (-1%)
...ne/spark/datasources/ReferenceWindowFunctions.java	12.5% <0%> (-12.5%)	1% <0%> (ø)
...oadinstitute/hellbender/utils/gcs/BucketUtils.java	79.87% <0%> (+1.21%)	42% <0%> (ø)	⬇️

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[jamesemery]

I'm not sure that we won't ever decide we want these classes in the future, which is why I was hesitant to approve this commit. However we will always be able to refer back to these PR closings if we need to resurrect this code in the future.