Improvement to handle 'mismatching' ref alleles for indel comparison conditions.
If ref allele in truth does not match ref allele in call, then verify first that the shorter ref allele string is the prefix of the longer, and then
append the remainder of the longer ref allele (i.e. that which follows the prefix) onto the shorter's ref and genotype alleles.
Changed extension for summary and detail metrics file.  Replacing old test data metrics files with ones with new extensions
Results of review - consolidated if statements, commented further
Merge pull request #90 from broadinstitute/gg_handle_ref_allele_mismatch_right

Improvement to handle 'mismatching' ref alleles for indel comparison conditions.  Also changed default extension of metrics files produced by the tool