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
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
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
Initial tracking for input files
Saving work in progress on fix for multiple files attached to processing event
Fix cyclic graph error, extended tests for web resource
Redirect BasicDecider to new web resource exposing input files
Working on population script

Initial population script
Implementation of workflow-run-files script, update of DB creation scripts, and matching modifications to tests.

Also some additional re-pointing of BasicDecider at the new web resource.
Empty file test
Only output when running/scheduling.

Also, squashed duplicates for output.

Conflicts:
	seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/deciders/BasicDecider.java
Also report launches for non-test mode
Fix migration of input files through hibernate and jaxb layers
Only output when running/scheduling.

Also, squashed duplicates for output.

Conflicts:
	seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/deciders/BasicDecider.java
Also report launches for non-test mode
Allow multiple overlapping runs to schedule/launch

This is possible since we properly track input files now as early as schedule time
Fix up conditions for test
Merge branch 'develop' 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/pom.xml
	seqware-ext-testing/pom.xml
	seqware-meta-db/pom.xml
	seqware-pipeline/pom.xml
	seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/deciders/BasicDecider.java
	seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/plugin/WorkflowPlugin.java
	seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/plugins/WorkflowStatusChecker.java
	seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/workflow/BasicWorkflow.java
	seqware-portal/pom.xml
	seqware-queryengine-legacy/pom.xml
	seqware-queryengine/pom.xml
	seqware-webservice-dto/pom.xml
	seqware-webservice/pom.xml
Refactor a few names for clarity
Constrained file_id in workflow_run_input_files with associated Hibernate, DB, and web service changes