SEQWARE-1928 - rename force run all to ignore previous runs and fix
doFinalCheck behaviour plus tests

Conflicts:

	seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/deciders/BasicDecider.java
	seqware-pipeline/src/test/java/net/sourceforge/seqware/pipeline/deciders/BasicDeciderConditionsTest.java
	seqware-webservice/src/test/java/net/sourceforge/seqware/pipeline/deciders/BasicDeciderTest.java
Fix formatting, formatting conflict
Merge pull request #241 from SeqWare/feature/fix_merge

Fix merge conflict