This change should allow us to test that the GATK jar has been
correctly packaged at release time, by ensuring that only the
packaged jar + a few test-related dependencies are on the classpath
when tests are run.
Note that we still need to actually test that this works as intended
before we can make this live in the Bamboo release plan.
New properties to disable regenerating example resources artifact when each parallel test runs under packagetest.
Moved collection of packagetest parameters from shell scripts into maven profiles.
Fixed necessity of test-utils jar by removing incorrect dependenciesToScan element during packagetests.
When building picard libraries, run clean first.
Fixed tools jar dependency in picard pom.
Integration tests properly use the ant-bridge.sh test.debug.port variable, like unit tests.
Added pom.xml workarounds for duplicate classpath error, due to gatk-framework dependency containing required BaseTest, and jarred *UnitTest/*IntegrationTest classes that also exist as files under target/test-classes.
Khalid Shakir
David Roazen