Changed tests and scripts to use gatkdir full path instead of relative testdata/qscripts symbolic links.
Although symlinks not created, left the symlink deletion script execution with a comment about future removal.
Re-enabled example UG pipeline queue test.
Replaced all hardcoded strings of {public,private}/testdata with BaseTest variables.
Refactored temp list creation method from ListFileUtilsUnitTest to BaseTest.createTempListFile.
Removed list files with hardcoded paths, now using createTempListFile instead with private test dir variable.
To reduce merge conflicts, this commit modifies contents of files, while file renamings are in previous commit.
See previous commit message for list of changes.
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.
Khalid Shakir
Geraldine Van der Auwera
David Roazen