Add JAVA_OPTS to run script.
Update handling of JAVA_OPTS in script so that it works with the bash array.
Add java opts to start.
Add opts to command flags docs.
Add function that makes sure arguments aren't appended twice when reading from filesystem config.
Add extra 0x20 to line 82 per code review.
Merge pull request #857 from BenWhitehead/add-java-opts

Add JAVA_OPTS to run script.