WorkflowRunTest command PATH now will be set to the bundledBinPath system property (if set in the workflow)
- Workflows specify the the bundledBinPath in their pom.xml's <systemPropertyVariables> section
- If bundledBinPath is set, the PATH will be set to "/usr/bin:/bin:/usr/sbin:/sbin" + the bundledBinPath + all subdirectories (non recursively) in bundledBinPath.
- If bundledBinPath is not set, the PATH will remain as "/usr/bin:/bin:/usr/sbin:/sbin"
Ran into SEQWARE-1845 where spaces are poorly treated by ProvisionFiles, so taking steps to remove the problem.
A fix taht ensures that deciders only use input from completed workflow runs. See SEQWARE-1809, PDE-474
Merge branch 'master' into develop

Conflicts:
	common-utilities/src/test/java/ca/on/oicr/pde/common/utilities/CommandRunnerTest.java
	workflows/pom.xml
	workflows/src/test/java/ca/on/oicr/pde/common/WorkflowRunTest.java
	workflows/src/test/java/ca/on/oicr/pde/common/tests/CommandRunnerTest.java
	workflows/src/test/java/ca/on/oicr/pde/utilities/workflows/CommandRunnerTest.java