Added AMI
Changed web.xml for SeqWare Portal to correctly fit the new schema for Tomcat 7.
Update documentation
Integrate sanity check tool into seqware script
Expose skip-if-missing in Java API
Merge pull request #218 from SeqWare/feature/seqware-1886-check-cli-integration

Feature/seqware 1886 check cli integration
Add documentation
Merge pull request #219 from SeqWare/feature/seqware-1884-expose_skip_if_missing_java_api

Expose skip-if-missing in Java API
SEQWARE-1909

Allow workflow launcher to intepret null parameters as empty string. It
looks like we have other behaviour that relies upon null parameter
values, so this cannot be a change at install-time (at schedule time,
the parameter is not necessarily specified)
SEQWARE-1901

Allow launching with only an override (or really, without a bundle ini
even)
Merge pull request #220 from SeqWare/feature/ini_file_changes

Feature/ini file changes
Fix the workflow classloader to ignore private classes
Allow our generated bash scripts to error out
Merge pull request #222 from SeqWare/feature/seqware-1897_mid_bash_fails

Allow our generated bash scripts to error out
Merge pull request #221 from SeqWare/feature/seqware-1904_private_classes

Fix the workflow classloader to ignore private classes