SEQWARE-1710 - Hook the extended integration tests into the new CLI

Ensure script permissions and fix up inherited test
Account for default behaviour of new command line
Need to direct output to files and relax the output checks
Fix up format of new CLI output to match old filters
Merge branch 'feature/SEQWARE-1242_cli_testing_and_fixes' of https://github.com/SeqWare/seqware into feature/SEQWARE-1242_cli_testing_and_fixes

Conflicts:
	seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/cli_tutorial/CLIUserPhase6.java
	seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/plugins/PluginRunnerET.java