GATK classes accessing package protected htsjdk classes changed to new package names.
POMs updated to support merging of sam/tribble/variant -> htsjdk and changes to picard artifact.
RodSystemValidation outputs changed due to variant codec packages changes, requiring test md5 updates.
Second of four commits for picard/htsjdk package rename.
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.
Khalid Shakir
David Roazen