Fix "pending" state on files created by metadata plugin

Conflicts:

	seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/plugins/Metadata.java
Remove creating files without workflow runs

Add creating workflow runs with files
Add creating workflows
Added test to enforce processsing status on imported files

Conflicts:

	seqware-pipeline/src/main/java/io/seqware/cli/Main.java
	seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/plugins/Metadata.java
	seqware-webservice/src/test/java/net/sourceforge/seqware/pipeline/plugins/MetadataTest.java
Fix documentation for BasicDecider tutorial and user getting started

Also some code changes to support

Conflicts:

	seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/plugins/GenericMetadataSaverET.java
	seqware-pipeline/src/main/java/io/seqware/cli/Main.java
	seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/deciders/BasicDecider.java
	seqware-webservice/src/test/java/net/sourceforge/seqware/pipeline/plugins/ExtendedPluginTest.java
Fix extra 'seqware' in test
Merge