Package tests now hard coding just the gatk-framework tests jar, to include ONLY BaseTest, until the exclusions may be debugged.
Removing cofoja's annotation service from the package jars, to allow javac -cp <package>.jar.
-These tests are really integration tests for Queue rather than generalized
pipeline tests, so it makes sense to call them QueueTests.
-Rename test classes and maven build targets, and update shell scripts
to reflect new naming.
Updated path for output gatkdocs in nightly build script.
Removed patch in plugin manager that contained a workaround for gatkdocs running in the top level directory.
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.
David Roazen
Khalid Shakir