Oh, I see it now. You've added code to  __workflow-name__Workflow.java that is conditionally triggered based on this ini parameter. I was looking for actual change in behaviour in SeqWare but this is all user-level. I would just rephrase it as 

"manual output is provided as an example of a workflow parameter that modifies output behaviour. If false, the workflow will create output files in a directory specified by output_prefix/output_dir/workflowname_version/RANDOM/ where RANDOM is an integer. If true, the workflow places the files at output_prefix/output_dir and may overwrite existing files."