Update gradle and build.gradle (#8998)

* Update gradle and build.gradle

* update gradle wrapper 8.2.1 ->  8.10.2
* remove 'versions' plugin because we don't use it
* update gradle plugins to new versions
  * shadow plugin changed maintainers and coordinates
	com.github.johnrengelman.shadow:8.1.1 -> com.gradleup.shadow:8.3.3
  * git-version 0.5.1 -> 3.1.0
  * sonatype scan 2.6.1 -> 2.8.3
  * download 5.4.0 -> 5.6.0
* use tasks.register() which is the newer style
* add gradle.properties to configure daemon memory

* update several vulnerable dependencies to safer versions
* update htsjdk and picard
* replace deprecated override of ThresholdStream.getStream() -> getOutputStream()