refs #9826. Stitch as part of process.

If stitch is checked, then the stitched output workspace will be generated as part of the processing. If it is done after, then it is completed as part of the plot process
refs #9826. Sort upon transfer.

This is max's prefered method of transfer
refs #9826. Refl workspace filter on save.
Merge branch 'feature/9826_refl_beta_fixes' into develop