Fix bad loader errors / messages for CommandFactory init and first plugin in build queue

[dankwart-de]

Required JRE/JDK: 1.8
Required Groovy: 2.4
/data/michael/.roddy/runtimeDevel/jdk1.8.0_121/bin/java
/data/michael/.roddy/runtimeDevel/groovy-2.4.8/bin/groovy
Roddy version 2.3.160
Loading feature toggle file /data/michael/.roddy/featureToggles.ini
Need to find a way to properly get the job state for a completed job. Neither tracejob, nor qstat -f are a good way. qstat -f only works for 'active' jobs. Lists with long active lists are not default.
Set logfile location, parameter file and job state log file on job creation (or override a method).
Allow enabling and disabling of options for resource arbitration for defective job managers.
parseToJob() is not implemented and will return null.
Ignore directory /data/michael/Projekte/RoddyInfra/plugins_2.3/IndelCallingWorkflow_1.0.167/resources/analysisTools/.HiddenAndBad; It is not a valid tools directory.
Ignore directory /data/michael/Projekte/RoddyInfra/plugins_2.3/IndelCallingWorkflow_1.0.167/resources/analysisTools/.HiddenAndyMaybeBad; It is not a valid tools directory.
Ignore directory /data/michael/Projekte/Roddy/dist/plugins/PluginBase/resources/analysisTools/.keep; It is not a valid tools directory.
Ignore directory /data/michael/Projekte/RoddyInfra/Roddy/dist/plugins/PluginBase/resources/analysisTools/.keep; It is not a valid tools directory.
The plugin SophiaWorkflow:current could not be found, are the plugin paths properly set?
Could not build the plugin queue for: 
SophiaWorkflow
The plugin :current could not be found, are the plugin paths properly set?
Could not build the plugin queue for: 

Unrecoverable errors, could not load plugins for analysis sophia
Could not load analysis coWorkflowsTestProject@sophia

[vinjana]

What exactly is missing? What should be changed?