Convert to use the java-library plugin #1934
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* this more clearly defines the necessary dependencies needed downstream to use picard * reorganized the libraries a bit to make things clearer
* replace the dependency with a version constraint so we don't import a buggy version
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Use the 'java-library' plugin instead of the 'java' one. This should improve our dependency resolution for downstream projects.
As part of this change, remove picard dependency on log4j and replace it with a version constraint so that transitive dependencies don't import a vulnerable version.
I don't have any automatic tooling to distinguish api from implementation dependencies so this is a best effort. We should be ready to change any if we are exposing some that we don't expect.
Addresses the issue brought up in #1919, however we've made the deliberate decision to include the minimum required dependencies instead of marking them all as api.