Add better tests and re-evaluate Pileup-Caller support for Mutect2

[jamesemery]

As part of #8083 we are drastically rewriting the entire Pileup-Caller infrastructure for DRAGEN-GATK. In doing so we have largely neglected its original functionality in Mutect2 and some of the changes (namely the re-factoring of that code to now happen after trimming like in with the GGA code) are going to impact the overall results for pileupcalling. It seems that we never added a real test of this functionality and its unclear to me currently what the meterics are that we want to assure ourselves that its working as intended.

In #8083 I have checked that the code is hooked up manually, but its not clear to me what a proper test looks like for mutect without re-hashing the test samples that were being used in the bacterial project. I'm a little skeptical about adding a test that just asserts "these results were different somehow" and yet thats essentially the sort of test i would like and that would have saved me here. I would really like to have something better in place, especially if we are going to keep sharing the pileup-calling code between HC and M2 going forward.