Fix some bugs in LeftAlignAndTrimVariants

[kachulis]

A few different bugs in LeftAlignAndTrimVariants.

First, only indels will have their alleles trimmed. This PR changes this so that alleles trimming will happen for MNPs if possible as well.

Additionally, when multiple variants occur at the same location (either due to splitting multiallelics before running LeftAlignAndTrimVariants, or running with --split-multi-allelics), the tool will not currently behave correctly. Only the first variant processed at a location will be correctly left aligned and trimmed, other variants can only currently be left aligned up to the base following the left aligned start of the first processed variant in the set.

This PR fixes both issues, so that:

1. MNPs will be trimmed when possible
2. variants at the same location can be left aligned to different locations, and resorted as necessary.

Also adds tests of these types of edge cases.

[gatk-bot]

Github actions tests reported job failures from actions build 20723309215
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
conda	17.0.6+10	20723309215.3	logs

[gatk-bot]

Github actions tests reported job failures from actions build 20723608771
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
conda	17.0.6+10	20723608771.3	logs

[gatk-bot]

Github actions tests reported job failures from actions build 20724995214
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
conda	17.0.6+10	20724995214.3	logs

[gatk-bot]

Github actions tests reported job failures from actions build 20784893281
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
conda	17.0.6+10	20784893281.3	logs