First pass of oozie-sge stdout/stderr writeback to metadb.
Merge branch 'develop' into feature/SEQWARE-1681_vagrant

Conflicts:
	seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/plugins/PluginRunnerET.java
	seqware-vagrant/templates/Vagrantfile
Just removing the FTL-based workflow extended tests. We're not going to support Pegasus/Condor/Globus in the 1.0.x series forward. The code will  still be there for the time being but we're only going to test Oozie-* engines.
Just added a note about the instance type
Just restoring this
Merge pull request #64 from SeqWare/feature/cli

Feature/cli
Merge branch 'develop' into feature/SEQWARE-1681_vagrant

Conflicts:
	seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/plugins/PluginRunnerET.java
Merge pull request #66 from SeqWare/feature/SEQWARE-1681_vagrant

Feature/seqware 1681 vagrant
Merge branch 'feature/SEQWARE-1693_decider_logic' into feature/SEQWARE-1693_decider_logic_mark_2

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/docs/site/content/docs/11-api.md
	seqware-distribution/docs/site/content/release-notes.md
	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
When scheduling a workflow run, set current_working_dir to null instead of the workflow bundle dir.
Store the current working directory of the workflow run.
Wrap-up stdout and stderr writeback
Merge pull request #67 from SeqWare/feature/oozie-sge-wb

Feature/oozie sge wb
Add specifying workflow-run accession to launch-scheduled and propagate-statuses.
Actually run the propagate-statuses.
Rename 'bundle launch' to ;bundle test'; remove 'bundle validate'
Correct some schedule params as required instead of optional.
Start implementation of input_files collection for workflow_run

Conflicts:
	seqware-common/src/main/java/net/sourceforge/seqware/common/model/WorkflowRun.java
	seqware-common/src/main/resources/net/sourceforge/seqware/common/model/Mappings.hbm.xml
	seqware-meta-db/1.0.1_to_1.0.2.sql
	seqware-webservice/src/test/java/net/sourceforge/seqware/common/metadata/MetadataWSTest.java
Correct sub-command for 'bundle test'
Change to use sw_accession, we can't constrain this in the DB

However, we don't want to expose file_id either

Conflicts:
	seqware-meta-db/src/main/resources/net/sourceforge/seqware/metadb/util/seqware_meta_db.sql