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.
Revert "Propagate study report options to the webservice as query params."

This reverts commit 79666db80d3013b9f7bb4077a43670fd0e3236b6.
Reformatting, no code change.
Function to emit runner exec.
Function to emit the metadata args of runner.
Function to emit the arguments to gcr.
Functions to create the sge script contents and sge action xml node.
Reformatting, no code change.
Clean up arg creation for ooze jobs.
Functionality to emit sge scripts.
Reformatting no code change.
Eliminate silliness.
Reformatting, no code change.
Exposing SGE-selection params.
Tweak docs and naming.
Added function for obtaining the scripts subdir.