Initial prototype for the tool including a check that runs through the pre-CLI tutorial

We need to break the dependency on mvn archetype:generate as well as the use of /tmp which is not guaranteed to work across clusters
Run through the CLI, alllow tests to pick up CLI from ~/bin
Add check that database is consistent with web service
Suppress output from dependent code
Try to run from command-line
First pass at more basic checks, prioritization, and better descriptions
Script check
Documentation and executable jar
Merge branch 'feature/sanity_check' of github.com:SeqWare/seqware into feature/sanity_check
Fix jar execution to match IDE execution (tests rely upon manifest description of seqware version)
Allow for running sanity checking with an arbitrary provided bundle in the working directory
Update readme for bundle shortcut
Merge from develop
Some cleanup for Java version and sync seqware version
Revert "Some cleanup for Java version and sync seqware version"

This reverts commit cdb8ddd4fa161b8e0cd060ed66bd53e1ad651167.
Revert "Merge from develop"

This reverts commit 9182db365cd505950d3497c7716be3e42ed006e8.
Merge branch 'develop' into feature/sanity_check

Conflicts:
	seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/tutorial/UserPhase6.java
Some cleanup for Java version and sync seqware version
Added some boolean checks to the interface for the tests. Now only certain tests will be run depending on the type of environment seqware is in
Merge branch 'feature/sanity_check' of git://github.com/SeqWare/seqware into feature/sanity_check