Add documentation on linking to local dependencies
Update document source
Try to fix Jenkins
Merge branch 'hotfix/0.13.6.8' of github.com:SeqWare/seqware into hotfix/0.13.6.8
Just updated the docs to mention that 1.0.x are available
Update database scripts with supporting indices for SymLinkFileReporter, SequencerRunReporter, and BasicDecider
Iterate version numbers
Fix typo
Iterate version numbers
Enable code coverage for local Sonar install
Convert pipeline tests to JUnit for simplicity and sonar compatibility.
Add a few tests for SymLinkFileReporter and working integration and unit tests code coverage (with mapping) for sonar.
Finish removing jetty. New procedure for sonar code coverage.

mvn clean install -DskipITs=false
mvn sonar:sonar -Pcoverage-per-test
Switch extended integration tests to tomcat as well.
Merge branch 'hotfix/0.13.6.8' into develop

Conflicts:
	seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/plugins/MarkdownPlugin.java
Use mvn versions:display-plugin-updates to make sure our build is stable

Also, update all plugins to most recent versions
Adding some dummy files and and updated Vagrant file. Still have more SeqWare setup tasks to do in the startup script.
Just fixed a bug in the param validation