Try to fix Jenkins
Fix up markdown plugin
Update database scripts with supporting indices for SymLinkFileReporter, SequencerRunReporter, and BasicDecider
Iterate version numbers

Conflicts:
	pom.xml
	seqware-archetypes/seqware-archetype-decider/pom.xml
	seqware-archetypes/seqware-archetype-decider/src/main/resources/archetype-resources/pom.xml
	seqware-archetypes/seqware-archetype-java-workflow/pom.xml
	seqware-archetypes/seqware-archetype-java-workflow/src/main/resources/archetype-resources/pom.xml
	seqware-archetypes/seqware-archetype-legacy-ftl-workflow/pom.xml
	seqware-archetypes/seqware-archetype-legacy-ftl-workflow/src/main/resources/archetype-resources/pom.xml
	seqware-archetypes/seqware-archetype-module/pom.xml
	seqware-archetypes/seqware-archetype-module/src/main/resources/archetype-resources/pom.xml
	seqware-archetypes/seqware-archetype-simple-legacy-ftl-workflow/pom.xml
	seqware-archetypes/seqware-archetype-simple-legacy-ftl-workflow/src/main/resources/archetype-resources/pom.xml
	seqware-archetypes/seqware-archetype-simplified-ftl-workflow/pom.xml
	seqware-archetypes/seqware-archetype-simplified-ftl-workflow/src/main/resources/archetype-resources/pom.xml
	seqware-common/pom.xml
	seqware-distribution/pom.xml
	seqware-ext-testing/pom.xml
	seqware-meta-db/pom.xml
	seqware-pipeline/pom.xml
	seqware-portal/pom.xml
	seqware-queryengine-legacy/pom.xml
	seqware-queryengine/pom.xml
	seqware-webservice-dto/pom.xml
	seqware-webservice/pom.xml
Propagate study report options to the webservice as query params.
SEQWARE-1646 and associated test
Tests and fix SEQWARE-1632, SEQWARE-1516
AttributeAnnotator unit tests
Allow some extended tests that do not require Pegasus/Globus/Condor to execute normally.
Forgot to install Maven
Revert "Propagate study report options to the webservice as query params."

This reverts commit 79666db80d3013b9f7bb4077a43670fd0e3236b6.
Tests that identify current flaws with attribute annotator.

Refactored database creation and querying.
reports init pass
Test-ready impl of new study report
move non-java files into resources
Fix JNDI name for db
Expose new study report via new plugin
Add all-studies report to ws and client.
Use default study report output file name instead of writing to stdout.
Better help doc.