Bundle support for FeatureInputs, references; add CreateBundle tool.

[cmnbroad]

Draft until a release of htsjdk with https://github.com/samtools/htsjdk/pull/1702, https://github.com/samtools/htsjdk/pull/1703, and https://github.com/samtools/htsjdk/pull/1713 is available.

[gatk-bot]

Github actions tests reported job failures from actions build 15116986367 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	17.0.6+10	15116986367.10	logs
integration	17.0.6+10	15116986367.11	logs
integration	17.0.6+10	15116986367.0	logs

[gatk-bot]

Github actions tests reported job failures from actions build 15276672036 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	17.0.6+10	15276672036.11	logs
integration	17.0.6+10	15276672036.0	logs

[gatk-bot]

Github actions tests reported job failures from actions build 15278279141 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	17.0.6+10	15278279141.11	logs
integration	17.0.6+10	15278279141.0	logs

[gatk-bot]

Github actions tests reported job failures from actions build 15279368938 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	17.0.6+10	15279368938.11	logs
integration	17.0.6+10	15279368938.0	logs

[gatk-bot]

Github actions tests reported job failures from actions build 15280418616 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	17.0.6+10	15280418616.11	logs
integration	17.0.6+10	15280418616.0	logs

[gatk-bot]

Github actions tests reported job failures from actions build 15282306387 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	17.0.6+10	15282306387.11	logs
integration	17.0.6+10	15282306387.0	logs

[gatk-bot]

Github actions tests reported job failures from actions build 15394324790 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	17.0.6+10	15394324790.11	logs
integration	17.0.6+10	15394324790.0	logs